Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In eukaryotic cells, DNA with genomic information is first stored in nucleosomes as the fundamental units, and then highly folded into chromatin.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
145
2,800
0
false
In eukaryotic cells, DNA with genomic information is first stored in nucleosomes as the fundamental units, and then highly folded into chromatin.
[]
In eukaryotic cells, DNA with genomic information is first stored in nucleosomes as the fundamental units, and then highly folded into chromatin.
true
true
true
true
true
476
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In the process of differentiation, to switch ‘ON’ the cell type-specific genes that have not been transcribed so far, it is first necessary to convert the chromatin of a gene and its flanking region from an inactive state to an active state.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
241
2,801
0
false
In the process of differentiation, to switch ‘ON’ the cell type-specific genes that have not been transcribed so far, it is first necessary to convert the chromatin of a gene and its flanking region from an inactive state to an active state.
[]
In the process of differentiation, to switch ‘ON’ the cell type-specific genes that have not been transcribed so far, it is first necessary to convert the chromatin of a gene and its flanking region from an inactive state to an active state.
true
true
true
true
true
476
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In vertebrate cells, chromatin of the committed or active gene and its flanking region shows the following features: (i) sensitivity to DNase I (2); (ii) cell type-specific DNase I hypersensitive sites (DHSs) (3,4); (iii) core histone modifications such as acetylation and methylation specific for the active chromatin s...
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
422
2,802
1
false
In vertebrate cells, chromatin of the committed or active gene and its flanking region shows the following features: (i) sensitivity to DNase I ; (ii) cell type-specific DNase I hypersensitive sites (DHSs) ; (iii) core histone modifications such as acetylation and methylation specific for the active chromatin state, la...
[ "2", "3,4", "5", "6" ]
In vertebrate cells, chromatin of the committed or active gene and its flanking region shows the following features: (i) sensitivity to DNase I ; (ii) cell type-specific DNase I hypersensitive sites (DHSs) ; (iii) core histone modifications such as acetylation and methylation specific for the active chromatin state, la...
true
true
true
true
true
476
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In addition, hypomethylation at the cytosine (C) residues of the cytosine–guanine (CG) dinucleotides is shown in the active promoter (7,8).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
139
2,803
0
false
In addition, hypomethylation at the cytosine (C) residues of the cytosine–guanine (CG) dinucleotides is shown in the active promoter.
[ "7,8" ]
In addition, hypomethylation at the cytosine (C) residues of the cytosine–guanine (CG) dinucleotides is shown in the active promoter.
true
true
true
true
true
476
1
INTRODUCTION
1
3
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Cell type-specific DHSs not only correspond to promoters and enhancers but also are likely to be the regulatory regions participating in the change and maintenance of the chromatin structure from an inactive state to an active state (3,4).
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
239
2,804
0
false
Cell type-specific DHSs not only correspond to promoters and enhancers but also are likely to be the regulatory regions participating in the change and maintenance of the chromatin structure from an inactive state to an active state.
[ "3,4" ]
Cell type-specific DHSs not only correspond to promoters and enhancers but also are likely to be the regulatory regions participating in the change and maintenance of the chromatin structure from an inactive state to an active state.
true
true
true
true
true
477
1
INTRODUCTION
1
3
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
In addition to their presence in and close to committed or active genes, cell type-specific DHSs are reported to reside inside the flanking genes (9,10) or between the flanking genes (10–13).
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
191
2,805
0
false
In addition to their presence in and close to committed or active genes, cell type-specific DHSs are reported to reside inside the flanking genes or between the flanking genes.
[ "9,10", "10–13" ]
In addition to their presence in and close to committed or active genes, cell type-specific DHSs are reported to reside inside the flanking genes or between the flanking genes.
true
true
true
true
true
477
1
INTRODUCTION
1
3
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Several investigations have been carried out to determine the regions necessary for chromatin changes in the scattered regulatory regions (10,14–18).
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
149
2,806
0
false
Several investigations have been carried out to determine the regions necessary for chromatin changes in the scattered regulatory regions.
[ "10,14–18" ]
Several investigations have been carried out to determine the regions necessary for chromatin changes in the scattered regulatory regions.
true
true
true
true
true
477
1
INTRODUCTION
1
3
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Deletion of DHS1-6 in the mouse β-globin locus control region (LCR) results in an extraordinary low level of β-globin transcription.
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
132
2,807
0
false
Deletion of DHS1-6 in the mouse β-globin locus control region (LCR) results in an extraordinary low level of β-globin transcription.
[]
Deletion of DHS1-6 in the mouse β-globin locus control region (LCR) results in an extraordinary low level of β-globin transcription.
true
true
true
true
true
477
1
INTRODUCTION
1
14
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
However, the acetylation of H3 and H4 histones at the β-globin promoter is the same as in the undeleted control (16) and no change in DNase I sensitivity in the β-globin locus has also been observed (14).
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
204
2,808
1
false
However, the acetylation of H3 and H4 histones at the β-globin promoter is the same as in the undeleted control and no change in DNase I sensitivity in the β-globin locus has also been observed.
[ "16", "14" ]
However, the acetylation of H3 and H4 histones at the β-globin promoter is the same as in the undeleted control and no change in DNase I sensitivity in the β-globin locus has also been observed.
true
true
true
true
true
477
1
INTRODUCTION
1
10
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Transgenic mice with 0.1 kb deletion of the DHS I region, which constitutes the LCR in the human GH locus, show loss of H3 and H4 acetylation starting from 32 kb upstream of the transcriptional starting site of the GH gene to the GH gene (10).
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
243
2,809
1
false
Transgenic mice with 0.1 kb deletion of the DHS I region, which constitutes the LCR in the human GH locus, show loss of H3 and H4 acetylation starting from 32 kb upstream of the transcriptional starting site of the GH gene to the GH gene.
[ "10" ]
Transgenic mice with 0.1 kb deletion of the DHS I region, which constitutes the LCR in the human GH locus, show loss of H3 and H4 acetylation starting from 32 kb upstream of the transcriptional starting site of the GH gene to the GH gene.
true
true
true
true
true
477
1
INTRODUCTION
1
3
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Accordingly, the deleted sequence is essential for the establishment and maintenance of histone acetylation in the GH locus.
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
124
2,810
0
false
Accordingly, the deleted sequence is essential for the establishment and maintenance of histone acetylation in the GH locus.
[]
Accordingly, the deleted sequence is essential for the establishment and maintenance of histone acetylation in the GH locus.
true
true
true
true
true
477
1
INTRODUCTION
1
3
[ "b3", "b4", "b9", "b10", "b10", "b13", "b10", "b14", "b18", "b16", "b14", "b10" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
However, no example has been reported that demonstrates the change in chromatin structure from sensitive to resistant to DNase I by deleting DHS.
[ "3", "4", "9", "10", "10", "13", "10", "14", "18", "16", "14", "10" ]
145
2,811
0
false
However, no example has been reported that demonstrates the change in chromatin structure from sensitive to resistant to DNase I by deleting DHS.
[]
However, no example has been reported that demonstrates the change in chromatin structure from sensitive to resistant to DNase I by deleting DHS.
true
true
true
true
true
477
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
To determine the in vivo role of the scattered DHSs, genetic studies such as gene targeting are effective.
[ "19", "20", "21", "18", "22", "18" ]
106
2,812
0
false
To determine the in vivo role of the scattered DHSs, genetic studies such as gene targeting are effective.
[]
To determine the in vivo role of the scattered DHSs, genetic studies such as gene targeting are effective.
true
true
true
true
true
478
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Chicken B-lymphocyte-derived DT40 cells are particularly useful for gene targeting because of the high rate of homologous recombination (19,20).
[ "19", "20", "21", "18", "22", "18" ]
144
2,813
0
false
Chicken B-lymphocyte-derived DT40 cells are particularly useful for gene targeting because of the high rate of homologous recombination.
[ "19,20" ]
Chicken B-lymphocyte-derived DT40 cells are particularly useful for gene targeting because of the high rate of homologous recombination.
true
true
true
true
true
478
2
INTRODUCTION
1
21
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Along with membrane immunoglobulin and Ig-α/mb1, Ig-β is a component of the antigen receptor complex (21).
[ "19", "20", "21", "18", "22", "18" ]
106
2,814
1
false
Along with membrane immunoglobulin and Ig-α/mb1, Ig-β is a component of the antigen receptor complex.
[ "21" ]
Along with membrane immunoglobulin and Ig-α/mb1, Ig-β is a component of the antigen receptor complex.
true
true
true
true
true
478
2
INTRODUCTION
1
18
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Chicken Ig-β gene is specifically expressed in B lymphocytes such as DT40 cells (18) and a project has been planned to elucidate the in vivo role of DT40-specific DHSs in B-cell-specific transcription of the Ig-β gene by deleting the DHSs.
[ "19", "20", "21", "18", "22", "18" ]
239
2,815
1
false
Chicken Ig-β gene is specifically expressed in B lymphocytes such as DT40 cells and a project has been planned to elucidate the in vivo role of DT40-specific DHSs in B-cell-specific transcription of the Ig-β gene by deleting the DHSs.
[ "18" ]
Chicken Ig-β gene is specifically expressed in B lymphocytes such as DT40 cells and a project has been planned to elucidate the in vivo role of DT40-specific DHSs in B-cell-specific transcription of the Ig-β gene by deleting the DHSs.
true
true
true
true
true
478
2
INTRODUCTION
1
22
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
A total of 13 DT40-specific DHSs were mapped in the 40 kb region spanning from 19 kb upstream to 21 kb downstream from the transcriptional starting site of Ig-β gene (Figure 1) (22).
[ "19", "20", "21", "18", "22", "18" ]
182
2,816
1
false
A total of 13 DT40-specific DHSs were mapped in the 40 kb region spanning from 19 kb upstream to 21 kb downstream from the transcriptional starting site of Ig-β gene (Figure 1).
[ "22" ]
A total of 13 DT40-specific DHSs were mapped in the 40 kb region spanning from 19 kb upstream to 21 kb downstream from the transcriptional starting site of Ig-β gene (Figure 1).
true
true
true
true
true
478
2
INTRODUCTION
1
18
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Based on these results, 11 DT40-specific DHSs found in the Ig-β locus were divided into four regions and deleted (18).
[ "19", "20", "21", "18", "22", "18" ]
118
2,817
1
false
Based on these results, 11 DT40-specific DHSs found in the Ig-β locus were divided into four regions and deleted.
[ "18" ]
Based on these results, 11 DT40-specific DHSs found in the Ig-β locus were divided into four regions and deleted.
true
true
true
true
true
478
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
The deletion of a single region demonstrated no prominent effect on the Ig-β mRNA level.
[ "19", "20", "21", "18", "22", "18" ]
88
2,818
0
false
The deletion of a single region demonstrated no prominent effect on the Ig-β mRNA level.
[]
The deletion of a single region demonstrated no prominent effect on the Ig-β mRNA level.
true
true
true
true
true
478
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
In this study, combinations of deletions of the four DHS regions were carried out.
[ "19", "20", "21", "18", "22", "18" ]
82
2,819
0
false
In this study, combinations of deletions of the four DHS regions were carried out.
[]
In this study, combinations of deletions of the four DHS regions were carried out.
true
true
true
true
true
478
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
A marked decrease in the level of Ig-β mRNA was observed in cells with deletion of all four regions (All Del cells).
[ "19", "20", "21", "18", "22", "18" ]
116
2,820
0
false
A marked decrease in the level of Ig-β mRNA was observed in cells with deletion of all four regions (All Del cells).
[]
A marked decrease in the level of Ig-β mRNA was observed in cells with deletion of all four regions (All Del cells).
true
true
true
true
true
478
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Thus, it has been demonstrated that the collaboration of scattered regulatory regions causes a effect on the expression of the Ig-β gene.
[ "19", "20", "21", "18", "22", "18" ]
137
2,821
0
false
Thus, it has been demonstrated that the collaboration of scattered regulatory regions causes a effect on the expression of the Ig-β gene.
[]
Thus, it has been demonstrated that the collaboration of scattered regulatory regions causes a effect on the expression of the Ig-β gene.
true
true
true
true
true
478
2
INTRODUCTION
1
19
[ "b19", "b20", "b21", "b18", "b22", "b18" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Examination of Ig-β chromatin in All Del cells showed that the collaboration of the four regions is capable of converting the Ig-β chromatin from a condensed state to a relaxed state and enhancing H3 and H4 acetylation in the Ig-β gene.
[ "19", "20", "21", "18", "22", "18" ]
236
2,822
0
false
Examination of Ig-β chromatin in All Del cells showed that the collaboration of the four regions is capable of converting the Ig-β chromatin from a condensed state to a relaxed state and enhancing H3 and H4 acetylation in the Ig-β gene.
[]
Examination of Ig-β chromatin in All Del cells showed that the collaboration of the four regions is capable of converting the Ig-β chromatin from a condensed state to a relaxed state and enhancing H3 and H4 acetylation in the Ig-β gene.
true
true
true
true
true
478
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
On the roles of the scattered DHSs in the cell type-specific transcription of vertebrate genes, many questions remain unsolved.
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
127
2,823
0
false
On the roles of the scattered DHSs in the cell type-specific transcription of vertebrate genes, many questions remain unsolved.
[]
On the roles of the scattered DHSs in the cell type-specific transcription of vertebrate genes, many questions remain unsolved.
true
true
true
true
true
479
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
To solve these, the deletion effect of the cell type-specific DHSs was investigated in mouse and human β-globin loci and the human GH locus (10,14–17).
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
151
2,824
0
false
To solve these, the deletion effect of the cell type-specific DHSs was investigated in mouse and human β-globin loci and the human GH locus.
[ "10,14–17" ]
To solve these, the deletion effect of the cell type-specific DHSs was investigated in mouse and human β-globin loci and the human GH locus.
true
true
true
true
true
479
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In any deletion, the change of DNase I general sensitivity had not been obtained so far.
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
88
2,825
0
false
In any deletion, the change of DNase I general sensitivity had not been obtained so far.
[]
In any deletion, the change of DNase I general sensitivity had not been obtained so far.
true
true
true
true
true
479
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In this study, however, combinations of deletions of the scattered DHS regions were shown to convert the chromatin from sensitive to resistant to DNase I digestion.
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
164
2,826
0
false
In this study, however, combinations of deletions of the scattered DHS regions were shown to convert the chromatin from sensitive to resistant to DNase I digestion.
[]
In this study, however, combinations of deletions of the scattered DHS regions were shown to convert the chromatin from sensitive to resistant to DNase I digestion.
true
true
true
true
true
479
0
DISCUSSION
1
12
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
In transgenic mice carrying the 185 kb human β-globin locus, a combination of deletions of HS3 and the β-globin promoter causes changes in chromatin structure not only into a DNase I-resistant state but also into H3 hypoacetylation in the locus (12).
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
250
2,827
1
false
In transgenic mice carrying the 185 kb human β-globin locus, a combination of deletions of HS3 and the β-globin promoter causes changes in chromatin structure not only into a DNase I-resistant state but also into H3 hypoacetylation in the locus.
[ "12" ]
In transgenic mice carrying the 185 kb human β-globin locus, a combination of deletions of HS3 and the β-globin promoter causes changes in chromatin structure not only into a DNase I-resistant state but also into H3 hypoacetylation in the locus.
true
true
true
true
true
479
0
DISCUSSION
1
1
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
However, to convert the chromatin into a DNase I-resistant state with the DHS at the promoter intact, it would be necessary to perform combinations of deletions of the scattered DHSs in human and mouse β-globin loci and in the human GH locus (1).
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
246
2,828
1
false
However, to convert the chromatin into a DNase I-resistant state with the DHS at the promoter intact, it would be necessary to perform combinations of deletions of the scattered DHSs in human and mouse β-globin loci and in the human GH locus.
[ "1" ]
However, to convert the chromatin into a DNase I-resistant state with the DHS at the promoter intact, it would be necessary to perform combinations of deletions of the scattered DHSs in human and mouse β-globin loci and in the human GH locus.
true
true
true
true
true
479
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
As was observed in this study, collaboration of cell type-specific DHSs that are found not only in and around a particular gene but also in the regions situated far upstream or downstream of the gene may participate in cell type-specific transcription in vertebrates through changes in chromatin structure including DNas...
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
344
2,829
0
false
As was observed in this study, collaboration of cell type-specific DHSs that are found not only in and around a particular gene but also in the regions situated far upstream or downstream of the gene may participate in cell type-specific transcription in vertebrates through changes in chromatin structure including DNas...
[]
As was observed in this study, collaboration of cell type-specific DHSs that are found not only in and around a particular gene but also in the regions situated far upstream or downstream of the gene may participate in cell type-specific transcription in vertebrates through changes in chromatin structure including DNas...
true
true
true
true
true
479
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
It is unclear how to convert the chromatin by the collaboration of many DHSs.
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
77
2,830
0
false
It is unclear how to convert the chromatin by the collaboration of many DHSs.
[]
It is unclear how to convert the chromatin by the collaboration of many DHSs.
true
true
true
true
true
479
0
DISCUSSION
1
12
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
It is reported that scattered DHSs located in more than the 100 kb region assemble to form the active chromatin hub in the transcription of the β-globin gene family in mouse (13) and human (12) β-globin loci.
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
208
2,831
1
false
It is reported that scattered DHSs located in more than the 100 kb region assemble to form the active chromatin hub in the transcription of the β-globin gene family in mouse and human β-globin loci.
[ "13", "12" ]
It is reported that scattered DHSs located in more than the 100 kb region assemble to form the active chromatin hub in the transcription of the β-globin gene family in mouse and human β-globin loci.
true
true
true
true
true
479
0
DISCUSSION
1
10
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
Perhaps the same situation is true in the chicken Ig-β locus.
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
61
2,832
0
false
Perhaps the same situation is true in the chicken Ig-β locus.
[]
Perhaps the same situation is true in the chicken Ig-β locus.
true
true
true
true
true
479
0
DISCUSSION
1
16
[ "b10", "b14", "b17", "b12", "b1", "b13", "b12", "b16" ]
16,916,790
pmid-12971721|pmid-948749|pmid-3052270|pmid-3198625|pmid-15797199|pmid-15688000|pmid-15780602|pmid-15797202|pmid-11864603|pmid-10882079|pmid-12672691|pmid-15198986|pmid-12971721|pmid-12504019|pmid-15198986|pmid-11553791
To gain further insight into how the different deleted regions might contribute to Ig-β gene activation, it would be useful to determine whether the lower level of Ig-β mRNA in the deletion mutant such as region IV result from a generalized decrease in all cells, or complete shutdown in some (16).
[ "10", "14", "17", "12", "1", "13", "12", "16" ]
298
2,833
1
false
To gain further insight into how the different deleted regions might contribute to Ig-β gene activation, it would be useful to determine whether the lower level of Ig-β mRNA in the deletion mutant such as region IV result from a generalized decrease in all cells, or complete shutdown in some.
[ "16" ]
To gain further insight into how the different deleted regions might contribute to Ig-β gene activation, it would be useful to determine whether the lower level of Ig-β mRNA in the deletion mutant such as region IV result from a generalized decrease in all cells, or complete shutdown in some.
true
true
true
true
true
479
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Among several parameters that determine the active chromatin state, such as (i) DNase I general sensitivity, (ii) active-type histone modifications, (iii) formation of cell type-specific DHSs, (iv) replacement of histone variant and (v) CG hypomethylation, which comes first for chromatin activation?
[ "10", "31", "32", "33", "34" ]
300
2,834
0
false
Among several parameters that determine the active chromatin state, such as (i) DNase I general sensitivity, (ii) active-type histone modifications, (iii) formation of cell type-specific DHSs, (iv) replacement of histone variant and (v) CG hypomethylation, which comes first for chromatin activation?
[]
Among several parameters that determine the active chromatin state, such as (i) DNase I general sensitivity, (ii) active-type histone modifications, (iii) formation of cell type-specific DHSs, (iv) replacement of histone variant and (v) CG hypomethylation, which comes first for chromatin activation?
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
In All Del cells, Ig-β chromatin turned out to be DNase I-resistant and a decrease in H3 and H4 acetylation at the Ig-β promoter and exon 3 was observed, whereas three parameters (H3K4 di-methylation, CG hypomethylation state in the region situated upstream the transcriptional start site, and cell type-specific DHSs in...
[ "10", "31", "32", "33", "34" ]
387
2,835
0
false
In All Del cells, Ig-β chromatin turned out to be DNase I-resistant and a decrease in H3 and H4 acetylation at the Ig-β promoter and exon 3 was observed, whereas three parameters (H3K4 di-methylation, CG hypomethylation state in the region situated upstream the transcriptional start site, and cell type-specific DHSs in...
[]
In All Del cells, Ig-β chromatin turned out to be DNase I-resistant and a decrease in H3 and H4 acetylation at the Ig-β promoter and exon 3 was observed, whereas three parameters (H3K4 di-methylation, CG hypomethylation state in the region situated upstream the transcriptional start site, and cell type-specific DHSs in...
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
In the case of the DHS deletion that causes hypoacetylation of H3 and H4 histones in the wide range of the human GH locus (10), chromatin of the locus still seems to remain sensitive to DNase I, and thus the change in chromatin structure to a DNase I general sensitive state may come earlier than the hyperacetylation of...
[ "10", "31", "32", "33", "34" ]
335
2,836
1
false
In the case of the DHS deletion that causes hypoacetylation of H3 and H4 histones in the wide range of the human GH locus, chromatin of the locus still seems to remain sensitive to DNase I, and thus the change in chromatin structure to a DNase I general sensitive state may come earlier than the hyperacetylation of core...
[ "10" ]
In the case of the DHS deletion that causes hypoacetylation of H3 and H4 histones in the wide range of the human GH locus, chromatin of the locus still seems to remain sensitive to DNase I, and thus the change in chromatin structure to a DNase I general sensitive state may come earlier than the hyperacetylation of core...
true
true
true
true
true
480
1
DISCUSSION
1
31
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Di- and tri-methylation of H3K4 is shown to be linked with active transcription in vertebrate genes (31).
[ "10", "31", "32", "33", "34" ]
105
2,837
1
false
Di- and tri-methylation of H3K4 is shown to be linked with active transcription in vertebrate genes.
[ "31" ]
Di- and tri-methylation of H3K4 is shown to be linked with active transcription in vertebrate genes.
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
In this study, a different effect of the DHS deletion on the acetylation and methylation of core histones has been demonstrated.
[ "10", "31", "32", "33", "34" ]
128
2,838
0
false
In this study, a different effect of the DHS deletion on the acetylation and methylation of core histones has been demonstrated.
[]
In this study, a different effect of the DHS deletion on the acetylation and methylation of core histones has been demonstrated.
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
In contrast to the decrease to <8% in H3 and H4 acetylation in All Del cells, H3K4 hypermethylation remained in the Ig-β gene.
[ "10", "31", "32", "33", "34" ]
126
2,839
0
false
In contrast to the decrease to <8% in H3 and H4 acetylation in All Del cells, H3K4 hypermethylation remained in the Ig-β gene.
[]
In contrast to the decrease to <8% in H3 and H4 acetylation in All Del cells, H3K4 hypermethylation remained in the Ig-β gene.
true
true
true
true
true
480
1
DISCUSSION
1
32
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
In murine β-globin (32) and GATA-2 (33) loci, the same situations have been described in which histone acetylation is reduced without a concomitant reduction in H3K4 di-methylation.
[ "10", "31", "32", "33", "34" ]
181
2,840
1
false
In murine β-globin and GATA-2 loci, the same situations have been described in which histone acetylation is reduced without a concomitant reduction in H3K4 di-methylation.
[ "32", "33" ]
In murine β-globin and GATA-2 loci, the same situations have been described in which histone acetylation is reduced without a concomitant reduction in H3K4 di-methylation.
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
The hypomethylation state in the Ig-β promoter is virtually unchanged in All Del cells except for significant methylation at +12 and +14.
[ "10", "31", "32", "33", "34" ]
137
2,841
0
false
The hypomethylation state in the Ig-β promoter is virtually unchanged in All Del cells except for significant methylation at +12 and +14.
[]
The hypomethylation state in the Ig-β promoter is virtually unchanged in All Del cells except for significant methylation at +12 and +14.
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Preventing methylation of these sites might be crucial for proper transcription of the Ig-β gene, or transcription may be necessary to prevent methylation.
[ "10", "31", "32", "33", "34" ]
155
2,842
0
false
Preventing methylation of these sites might be crucial for proper transcription of the Ig-β gene, or transcription may be necessary to prevent methylation.
[]
Preventing methylation of these sites might be crucial for proper transcription of the Ig-β gene, or transcription may be necessary to prevent methylation.
true
true
true
true
true
480
1
DISCUSSION
1
34
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Intragenic DNA methylation has been reported to repress gene expression and to alter chromatin structure in murine erythroleukemia cells (34), and then it would be interesting to determine the intragenic CG methylation of the Ig-β gene in All Del cells.
[ "10", "31", "32", "33", "34" ]
253
2,843
1
false
Intragenic DNA methylation has been reported to repress gene expression and to alter chromatin structure in murine erythroleukemia cells, and then it would be interesting to determine the intragenic CG methylation of the Ig-β gene in All Del cells.
[ "34" ]
Intragenic DNA methylation has been reported to repress gene expression and to alter chromatin structure in murine erythroleukemia cells, and then it would be interesting to determine the intragenic CG methylation of the Ig-β gene in All Del cells.
true
true
true
true
true
480
1
DISCUSSION
1
10
[ "b10", "b31", "b32", "b33", "b34" ]
16,916,790
pmid-3052270|pmid-3198625|pmid-11593024|pmid-11864603|pmid-11864603|pmid-12504019|pmid-11864603|pmid-10882079|pmid-15654880|pmid-11553791|pmid-10882079|pmid-11864603|pmid-11864603|pmid-14661024|pmid-12379744|pmid-12857954|pmid-15467727
Based on the data obtained in this study, it is still difficult to determine the changing order of chromatin parameters.
[ "10", "31", "32", "33", "34" ]
120
2,844
0
false
Based on the data obtained in this study, it is still difficult to determine the changing order of chromatin parameters.
[]
Based on the data obtained in this study, it is still difficult to determine the changing order of chromatin parameters.
true
true
true
true
true
480
2
DISCUSSION
1
33
[ "b33" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
At the Ig-β promoter in III–IV Del cells, H3 and H4 acetylation decreased to 20 and 40%, respectively, whereas H3K4 di-methylation showed a 2.2-fold increase (Figure 6).
[ "33" ]
169
2,845
0
false
At the Ig-β promoter in III–IV Del cells, H3 and H4 acetylation decreased to 20 and 40%, respectively, whereas H3K4 di-methylation showed a 2.2-fold increase (Figure 6).
[]
At the Ig-β promoter in III–IV Del cells, H3 and H4 acetylation decreased to 20 and 40%, respectively, whereas H3K4 di-methylation showed a 2.2-fold increase (Figure 6).
true
true
true
true
true
481
2
DISCUSSION
1
33
[ "b33" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
In place of the GATA-2 protein, the induced GATA-1 protein is reported to bind to the regulatory region present upstream of the GATA-2 gene, which is known to be one of the targets of the GATA-1 transcription factor in mouse proerythroblast-like G1E cells; binding of GATA-1 then blocks the transcription of the GATA-2 g...
[ "33" ]
367
2,846
1
false
In place of the GATA-2 protein, the induced GATA-1 protein is reported to bind to the regulatory region present upstream of the GATA-2 gene, which is known to be one of the targets of the GATA-1 transcription factor in mouse proerythroblast-like G1E cells; binding of GATA-1 then blocks the transcription of the GATA-2 g...
[ "33" ]
In place of the GATA-2 protein, the induced GATA-1 protein is reported to bind to the regulatory region present upstream of the GATA-2 gene, which is known to be one of the targets of the GATA-1 transcription factor in mouse proerythroblast-like G1E cells; binding of GATA-1 then blocks the transcription of the GATA-2 g...
true
true
true
true
true
481
2
DISCUSSION
1
33
[ "b33" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
In this case, the decrease in H3 and H4 acetylation and the increase in H3K4 methylation are demonstrated at the 1G promoter of the GATA-2 gene.
[ "33" ]
144
2,847
0
false
In this case, the decrease in H3 and H4 acetylation and the increase in H3K4 methylation are demonstrated at the 1G promoter of the GATA-2 gene.
[]
In this case, the decrease in H3 and H4 acetylation and the increase in H3K4 methylation are demonstrated at the 1G promoter of the GATA-2 gene.
true
true
true
true
true
481
2
DISCUSSION
1
33
[ "b33" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
To explain this finding, we propose that an unidentified factor(s) increases H3 and H4 acetylation but represses H3K4 methylation at the Ig-β promoter through binding in the III–IV regions, consistent with the decrease in H3 and H4 acetylation and the increase in H3K4 methylation observed in III–IV Del cells.
[ "33" ]
310
2,848
0
false
To explain this finding, we propose that an unidentified factor(s) increases H3 and H4 acetylation but represses H3K4 methylation at the Ig-β promoter through binding in the III–IV regions, consistent with the decrease in H3 and H4 acetylation and the increase in H3K4 methylation observed in III–IV Del cells.
[]
To explain this finding, we propose that an unidentified factor(s) increases H3 and H4 acetylation but represses H3K4 methylation at the Ig-β promoter through binding in the III–IV regions, consistent with the decrease in H3 and H4 acetylation and the increase in H3K4 methylation observed in III–IV Del cells.
true
true
true
true
true
481
2
DISCUSSION
1
33
[ "b33" ]
16,916,790
pmid-1913816|pmid-11226459|pmid-10533310|pmid-15654880|pmid-15276208|pmid-15654880|pmid-12857954
Detailed investigations of the proteins capable of binding to III–IV regions should clarify whether other factor(s) are involved and may facilitate their identification.
[ "33" ]
169
2,849
0
false
Detailed investigations of the proteins capable of binding to III–IV regions should clarify whether other factor(s) are involved and may facilitate their identification.
[]
Detailed investigations of the proteins capable of binding to III–IV regions should clarify whether other factor(s) are involved and may facilitate their identification.
true
true
true
true
true
481
3
DISCUSSION
1
35
[ "b35", "b37" ]
16,916,790
pmid-11864602|pmid-15930108
For the maintenance of DT40-specific DHSs at −13.6 and +12.7 kb, neither the DNase I-sensitive state in the Ig-β chromatin nor hyperacetylation of H3 and H4 histones is required.
[ "35", "37" ]
178
2,850
0
false
For the maintenance of DT40-specific DHSs at −13.6 and +12.7 kb, neither the DNase I-sensitive state in the Ig-β chromatin nor hyperacetylation of H3 and H4 histones is required.
[]
For the maintenance of DT40-specific DHSs at −13.6 and +12.7 kb, neither the DNase I-sensitive state in the Ig-β chromatin nor hyperacetylation of H3 and H4 histones is required.
true
true
true
true
true
482
3
DISCUSSION
1
35
[ "b35", "b37" ]
16,916,790
pmid-11864602|pmid-15930108
The presence of the so-called ‘pioneer transcription factors’ such as HNF3, GATA-4 and MyoD capable of binding to compact chromatin and opening chromatin locally has been reported previously (35–37).
[ "35", "37" ]
199
2,851
0
false
The presence of the so-called ‘pioneer transcription factors’ such as HNF3, GATA-4 and MyoD capable of binding to compact chromatin and opening chromatin locally has been reported previously.
[ "35–37" ]
The presence of the so-called ‘pioneer transcription factors’ such as HNF3, GATA-4 and MyoD capable of binding to compact chromatin and opening chromatin locally has been reported previously.
true
true
true
true
true
482
3
DISCUSSION
1
35
[ "b35", "b37" ]
16,916,790
pmid-11864602|pmid-15930108
Thus, in the first step, the binding of pioneer transcription factors may cause some DHS formation in the inactive chromatin and then active-type change in chromatin structure occurs.
[ "35", "37" ]
183
2,852
0
false
Thus, in the first step, the binding of pioneer transcription factors may cause some DHS formation in the inactive chromatin and then active-type change in chromatin structure occurs.
[]
Thus, in the first step, the binding of pioneer transcription factors may cause some DHS formation in the inactive chromatin and then active-type change in chromatin structure occurs.
true
true
true
true
true
482
3
DISCUSSION
1
35
[ "b35", "b37" ]
16,916,790
pmid-11864602|pmid-15930108
The regions required for the maintenance of H3K4 methylation and CG hypomethylation have not been determined in this study; combinations of deletions between the −13.6 and +12.7 kb regions and All Del regions may have an effect on these two parameters, although a single deletion of these upstream and downstream regions...
[ "35", "37" ]
371
2,853
0
false
The regions required for the maintenance of H3K4 methylation and CG hypomethylation have not been determined in this study; combinations of deletions between the −13.6 and +12.7 kb regions and All Del regions may have an effect on these two parameters, although a single deletion of these upstream and downstream regions...
[]
The regions required for the maintenance of H3K4 methylation and CG hypomethylation have not been determined in this study; combinations of deletions between the −13.6 and +12.7 kb regions and All Del regions may have an effect on these two parameters, although a single deletion of these upstream and downstream regions...
true
true
true
true
true
482
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b1", "b5", "b7", "b10" ]
16,893,950
pmid-9774669|pmid-1606614|pmid-8177735|pmid-11445535|pmid-16354688|pmid-9774669|pmid-11445535|pmid-9663395|pmid-12665582
Proteins that have been demonstrated to bind specifically to methylated DNA belong to two characterized families.
[ "1", "3", "4", "5", "6", "1", "5", "7", "10" ]
113
2,854
0
false
Proteins that have been demonstrated to bind specifically to methylated DNA belong to two characterized families.
[]
Proteins that have been demonstrated to bind specifically to methylated DNA belong to two characterized families.
true
true
true
true
true
483
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b1", "b5", "b7", "b10" ]
16,893,950
pmid-9774669|pmid-1606614|pmid-8177735|pmid-11445535|pmid-16354688|pmid-9774669|pmid-11445535|pmid-9663395|pmid-12665582
The methyl-CpG-binding domain (MBD) family comprises five polypeptides in mammals, four of which MBD1, MBD2, MBD4 and MeCP2 have been shown to preferentially bind a symmetrically methylated CpG motif (1–3).
[ "1", "3", "4", "5", "6", "1", "5", "7", "10" ]
206
2,855
0
false
The methyl-CpG-binding domain (MBD) family comprises five polypeptides in mammals, four of which MBD1, MBD2, MBD4 and MeCP2 have been shown to preferentially bind a symmetrically methylated CpG motif.
[ "1–3" ]
The methyl-CpG-binding domain (MBD) family comprises five polypeptides in mammals, four of which MBD1, MBD2, MBD4 and MeCP2 have been shown to preferentially bind a symmetrically methylated CpG motif.
true
true
true
true
true
483
0
INTRODUCTION
1
4
[ "b1", "b3", "b4", "b5", "b6", "b1", "b5", "b7", "b10" ]
16,893,950
pmid-9774669|pmid-1606614|pmid-8177735|pmid-11445535|pmid-16354688|pmid-9774669|pmid-11445535|pmid-9663395|pmid-12665582
These proteins share the MBD which confers specific DNA binding (4).
[ "1", "3", "4", "5", "6", "1", "5", "7", "10" ]
68
2,856
1
false
These proteins share the MBD which confers specific DNA binding.
[ "4" ]
These proteins share the MBD which confers specific DNA binding.
true
true
true
true
true
483
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b1", "b5", "b7", "b10" ]
16,893,950
pmid-9774669|pmid-1606614|pmid-8177735|pmid-11445535|pmid-16354688|pmid-9774669|pmid-11445535|pmid-9663395|pmid-12665582
The unrelated Kaiso protein family binds to DNA sequences containing methyl-CpGs via a distinctive zinc finger motif (5,6).
[ "1", "3", "4", "5", "6", "1", "5", "7", "10" ]
123
2,857
0
false
The unrelated Kaiso protein family binds to DNA sequences containing methyl-CpGs via a distinctive zinc finger motif.
[ "5,6" ]
The unrelated Kaiso protein family binds to DNA sequences containing methyl-CpGs via a distinctive zinc finger motif.
true
true
true
true
true
483
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b1", "b5", "b7", "b10" ]
16,893,950
pmid-9774669|pmid-1606614|pmid-8177735|pmid-11445535|pmid-16354688|pmid-9774669|pmid-11445535|pmid-9663395|pmid-12665582
In keeping with evidence that DNA methylation is a signal for transcriptional repression, MeCP2, MBD1, MBD2 and Kaiso all repress transcription in vitro and associate with co-repressors (1,5,7–10).
[ "1", "3", "4", "5", "6", "1", "5", "7", "10" ]
197
2,858
0
false
In keeping with evidence that DNA methylation is a signal for transcriptional repression, MeCP2, MBD1, MBD2 and Kaiso all repress transcription in vitro and associate with co-repressors.
[ "1,5,7–10" ]
In keeping with evidence that DNA methylation is a signal for transcriptional repression, MeCP2, MBD1, MBD2 and Kaiso all repress transcription in vitro and associate with co-repressors.
true
true
true
true
true
483
1
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b15", "b16", "b4" ]
16,893,950
pmid-464298|pmid-11951658|pmid-8323540|pmid-11951652|pmid-4609195|pmid-7989044|pmid-8177735
The aim of the present study was to harness the affinity of the MBD to create a superior reagent for the detection of methyl-CpG in vitro and in vivo.
[ "11", "12", "13", "14", "15", "16", "4" ]
150
2,859
0
false
The aim of the present study was to harness the affinity of the MBD to create a superior reagent for the detection of methyl-CpG in vitro and in vivo.
[]
The aim of the present study was to harness the affinity of the MBD to create a superior reagent for the detection of methyl-CpG in vitro and in vivo.
true
true
true
true
true
484
1
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b15", "b16", "b4" ]
16,893,950
pmid-464298|pmid-11951658|pmid-8323540|pmid-11951652|pmid-4609195|pmid-7989044|pmid-8177735
Assessment of global levels of DNA methylation currently relies on mass spectrometry (11), ‘nearest neighbour’ methods (12), enzymatic methyl-group acceptance assays (13) or HPLC analysis (14).
[ "11", "12", "13", "14", "15", "16", "4" ]
193
2,860
1
false
Assessment of global levels of DNA methylation currently relies on mass spectrometry, ‘nearest neighbour’ methods, enzymatic methyl-group acceptance assays or HPLC analysis.
[ "11", "12", "13", "14" ]
Assessment of global levels of DNA methylation currently relies on mass spectrometry, ‘nearest neighbour’ methods, enzymatic methyl-group acceptance assays or HPLC analysis.
true
true
true
true
true
484
1
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b15", "b16", "b4" ]
16,893,950
pmid-464298|pmid-11951658|pmid-8323540|pmid-11951652|pmid-4609195|pmid-7989044|pmid-8177735
These quantitative measures are complemented by the use of antibodies against 5-methylcytosine (m5C), which in addition to quantification permit visualization of m5C distribution within DNA or chromosomes (15,16).
[ "11", "12", "13", "14", "15", "16", "4" ]
213
2,861
0
false
These quantitative measures are complemented by the use of antibodies against 5-methylcytosine (m5C), which in addition to quantification permit visualization of m5C distribution within DNA or chromosomes.
[ "15,16" ]
These quantitative measures are complemented by the use of antibodies against 5-methylcytosine (m5C), which in addition to quantification permit visualization of m5C distribution within DNA or chromosomes.
true
true
true
true
true
484
1
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b15", "b16", "b4" ]
16,893,950
pmid-464298|pmid-11951658|pmid-8323540|pmid-11951652|pmid-4609195|pmid-7989044|pmid-8177735
A disadvantage of anti-m5C antibodies is that the epitope is best exposed when DNA is single-stranded and DNA must therefore normally be denatured before detection.
[ "11", "12", "13", "14", "15", "16", "4" ]
164
2,862
0
false
A disadvantage of anti-m5C antibodies is that the epitope is best exposed when DNA is single-stranded and DNA must therefore normally be denatured before detection.
[]
A disadvantage of anti-m5C antibodies is that the epitope is best exposed when DNA is single-stranded and DNA must therefore normally be denatured before detection.
true
true
true
true
true
484
1
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b15", "b16", "b4" ]
16,893,950
pmid-464298|pmid-11951658|pmid-8323540|pmid-11951652|pmid-4609195|pmid-7989044|pmid-8177735
The MBD, on the other hand, is specific for native double-stranded DNA.
[ "11", "12", "13", "14", "15", "16", "4" ]
71
2,863
0
false
The MBD, on the other hand, is specific for native double-stranded DNA.
[]
The MBD, on the other hand, is specific for native double-stranded DNA.
true
true
true
true
true
484
1
INTRODUCTION
1
4
[ "b11", "b12", "b13", "b14", "b15", "b16", "b4" ]
16,893,950
pmid-464298|pmid-11951658|pmid-8323540|pmid-11951652|pmid-4609195|pmid-7989044|pmid-8177735
Another potential benefit of the MBD reagent would be its specificity for m5C in the context of a symmetrically methylated CpG sequence (4).
[ "11", "12", "13", "14", "15", "16", "4" ]
140
2,864
1
false
Another potential benefit of the MBD reagent would be its specificity for m5C in the context of a symmetrically methylated CpG sequence.
[ "4" ]
Another potential benefit of the MBD reagent would be its specificity for m5C in the context of a symmetrically methylated CpG sequence.
true
true
true
true
true
484
2
INTRODUCTION
0
null
null
16,893,950
null
To test the MBD reagent, we designed a series of artificial methyl-CpG-binding proteins based on multimerization of the MBD of Mbd1.
null
132
2,865
0
false
null
null
To test the MBD reagent, we designed a series of artificial methyl-CpG-binding proteins based on multimerization of the MBD of Mbd1.
true
true
true
true
true
485
2
INTRODUCTION
0
null
null
16,893,950
null
The resulting polypeptides bound strongly to methylated DNA with high specificity and could compete with other methyl-CpG-binding proteins for DNA binding in vitro.
null
164
2,866
0
false
null
null
The resulting polypeptides bound strongly to methylated DNA with high specificity and could compete with other methyl-CpG-binding proteins for DNA binding in vitro.
true
true
true
true
true
485
2
INTRODUCTION
0
null
null
16,893,950
null
When expressed in vivo, the poly-MBD protein localized to the methyl-CpG-rich heterochromatic foci of mouse cells and could recruit a functional domain specifically to methylated DNA sequences.
null
193
2,867
0
false
null
null
When expressed in vivo, the poly-MBD protein localized to the methyl-CpG-rich heterochromatic foci of mouse cells and could recruit a functional domain specifically to methylated DNA sequences.
true
true
true
true
true
485
2
INTRODUCTION
0
null
null
16,893,950
null
Poly-MBD proteins proved to be sensitive and specific reagents for the detection of methyl-CpGs in immobilized DNA and cytological preparations.
null
144
2,868
0
false
null
null
Poly-MBD proteins proved to be sensitive and specific reagents for the detection of methyl-CpGs in immobilized DNA and cytological preparations.
true
true
true
true
true
485
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
Over the past years, the systematic analyses of structural data have given important insights into protein evolution.
[ "1" ]
117
2,869
0
false
Over the past years, the systematic analyses of structural data have given important insights into protein evolution.
[]
Over the past years, the systematic analyses of structural data have given important insights into protein evolution.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
Proteins, which have descended from a common ancestor generally share a common fold but also retain characteristic structural and functional features.
[ "1" ]
150
2,870
0
false
Proteins, which have descended from a common ancestor generally share a common fold but also retain characteristic structural and functional features.
[]
Proteins, which have descended from a common ancestor generally share a common fold but also retain characteristic structural and functional features.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
This empirical observation was used as a basis for protein classification.
[ "1" ]
74
2,871
0
false
This empirical observation was used as a basis for protein classification.
[]
This empirical observation was used as a basis for protein classification.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
Created over a decade ago, structural classification of proteins (SCOP) is a database of known structural and probable evolutionary relationships amongst proteins of known structure (1).
[ "1" ]
186
2,872
1
false
Created over a decade ago, structural classification of proteins (SCOP) is a database of known structural and probable evolutionary relationships amongst proteins of known structure.
[ "1" ]
Created over a decade ago, structural classification of proteins (SCOP) is a database of known structural and probable evolutionary relationships amongst proteins of known structure.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
These relationships are projected on a hierarchical tree which evolves with the increasing amount of structural data.
[ "1" ]
117
2,873
0
false
These relationships are projected on a hierarchical tree which evolves with the increasing amount of structural data.
[]
These relationships are projected on a hierarchical tree which evolves with the increasing amount of structural data.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
The basic unit of classification is the protein domain.
[ "1" ]
55
2,874
0
false
The basic unit of classification is the protein domain.
[]
The basic unit of classification is the protein domain.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
In the classification scheme, protein domains are initially linked on different hierarchical levels corresponding to their homology.
[ "1" ]
132
2,875
0
false
In the classification scheme, protein domains are initially linked on different hierarchical levels corresponding to their homology.
[]
In the classification scheme, protein domains are initially linked on different hierarchical levels corresponding to their homology.
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
Ranging from near to far, the relationships comprise the following levels: protein Species, representing a distinct protein sequence and its naturally occurring or artificially created variants; Protein, grouping together similar sequences of essentially the same functions that either originate from different biologica...
[ "1" ]
534
2,876
0
false
Ranging from near to far, the relationships comprise the following levels: protein Species, representing a distinct protein sequence and its naturally occurring or artificially created variants; Protein, grouping together similar sequences of essentially the same functions that either originate from different biologica...
[]
Ranging from near to far, the relationships comprise the following levels: protein Species, representing a distinct protein sequence and its naturally occurring or artificially created variants; Protein, grouping together similar sequences of essentially the same functions that either originate from different biologica...
true
true
true
true
true
486
0
INTRODUCTION
1
1
[ "b1" ]
17,068,077
pmid-7723011
Near the root, the basis of classification is purely structural: structurally similar Superfamilies with different characteristic features are grouped into Folds, which are further arranged into Classes based mainly on their secondary structure content and organization.
[ "1" ]
270
2,877
0
false
Near the root, the basis of classification is purely structural: structurally similar Superfamilies with different characteristic features are grouped into Folds, which are further arranged into Classes based mainly on their secondary structure content and organization.
[]
Near the root, the basis of classification is purely structural: structurally similar Superfamilies with different characteristic features are grouped into Folds, which are further arranged into Classes based mainly on their secondary structure content and organization.
true
true
true
true
true
486
1
INTRODUCTION
0
null
null
17,068,077
null
This tree-like classification was based on several assumptions for the nature of sequence-structure relationships that were generally accepted at the time of its creation.
null
171
2,878
0
false
null
null
This tree-like classification was based on several assumptions for the nature of sequence-structure relationships that were generally accepted at the time of its creation.
true
true
true
true
true
487
1
INTRODUCTION
0
null
null
17,068,077
null
It was assumed that: (i) sequences of proteins performing the same molecular function diverged with speciation of the organisms; (ii) a protein sequence can adopt only one native structure; (iii) homologous proteins fold into similar structures; (iv) protein structures are evolutionarily more conserved thansequences; (...
null
386
2,879
0
false
null
null
It was assumed that: (i) sequences of proteins performing the same molecular function diverged with speciation of the organisms; (ii) a protein sequence can adopt only one native structure; (iii) homologous proteins fold into similar structures; (iv) protein structures are evolutionarily more conserved thansequences; (...
true
true
true
true
true
487
1
INTRODUCTION
0
null
null
17,068,077
null
In summary, it was thought that protein fold is physically and biologically invariant, and that the number of protein folds in Nature is very limited.
null
150
2,880
0
false
null
null
In summary, it was thought that protein fold is physically and biologically invariant, and that the number of protein folds in Nature is very limited.
true
true
true
true
true
487
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
Since the creation of SCOP, the amount of structural data in the Protein Data Bank (PDB) (2) has increased 20-fold.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
115
2,881
1
false
Since the creation of SCOP, the amount of structural data in the Protein Data Bank (PDB) has increased 20-fold.
[ "2" ]
Since the creation of SCOP, the amount of structural data in the Protein Data Bank (PDB) has increased 20-fold.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
The recent advances in molecular biology and bioinformatics have made possible the detection of many unexpected evolutionary relationships.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
139
2,882
0
false
The recent advances in molecular biology and bioinformatics have made possible the detection of many unexpected evolutionary relationships.
[]
The recent advances in molecular biology and bioinformatics have made possible the detection of many unexpected evolutionary relationships.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
Classification of new structures has revealed numerous exceptions to the original assumptions, providing new insights into evolution of protein structure and shifting the paradigm of the protein fold (3–6).
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
206
2,883
0
false
Classification of new structures has revealed numerous exceptions to the original assumptions, providing new insights into evolution of protein structure and shifting the paradigm of the protein fold.
[ "3–6" ]
Classification of new structures has revealed numerous exceptions to the original assumptions, providing new insights into evolution of protein structure and shifting the paradigm of the protein fold.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
The evolvability of protein folds was further supported by the results of several recent experimental studies applying multiple gene rearrangement and non-homologous recombination approaches (7,8).
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
197
2,884
0
false
The evolvability of protein folds was further supported by the results of several recent experimental studies applying multiple gene rearrangement and non-homologous recombination approaches.
[ "7,8" ]
The evolvability of protein folds was further supported by the results of several recent experimental studies applying multiple gene rearrangement and non-homologous recombination approaches.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
The possible mechanisms of fold changes include circular permutations, segment-swapping, presence of chameleon sequences that can adopt alternative conformations etc.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
166
2,885
0
false
The possible mechanisms of fold changes include circular permutations, segment-swapping, presence of chameleon sequences that can adopt alternative conformations etc.
[]
The possible mechanisms of fold changes include circular permutations, segment-swapping, presence of chameleon sequences that can adopt alternative conformations etc.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
They create non-trivial structural relationships at any ‘evolutionary’ level of SCOP and increase the structural diversity within Families and Superfamilies.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
157
2,886
0
false
They create non-trivial structural relationships at any ‘evolutionary’ level of SCOP and increase the structural diversity within Families and Superfamilies.
[]
They create non-trivial structural relationships at any ‘evolutionary’ level of SCOP and increase the structural diversity within Families and Superfamilies.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
Thus homologous levels within the classification may contain proteins with technically different folds.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
103
2,887
0
false
Thus homologous levels within the classification may contain proteins with technically different folds.
[]
Thus homologous levels within the classification may contain proteins with technically different folds.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
These non-trivial cases of protein evolution add extra complexity and create practical difficulties for their presentation on the tree-like hierarchical classification scheme.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
175
2,888
0
false
These non-trivial cases of protein evolution add extra complexity and create practical difficulties for their presentation on the tree-like hierarchical classification scheme.
[]
These non-trivial cases of protein evolution add extra complexity and create practical difficulties for their presentation on the tree-like hierarchical classification scheme.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
In addition to the structural changes observed amongst related protein structures, the active sites of many functionally similar proteins were found to share common structural motifs embedded in otherwise different folds.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
221
2,889
0
false
In addition to the structural changes observed amongst related protein structures, the active sites of many functionally similar proteins were found to share common structural motifs embedded in otherwise different folds.
[]
In addition to the structural changes observed amongst related protein structures, the active sites of many functionally similar proteins were found to share common structural motifs embedded in otherwise different folds.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
These structural motifs can have a substantial sequence similarity which often results in significant sequence hits between members of different SCOP Superfamilies.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
164
2,890
0
false
These structural motifs can have a substantial sequence similarity which often results in significant sequence hits between members of different SCOP Superfamilies.
[]
These structural motifs can have a substantial sequence similarity which often results in significant sequence hits between members of different SCOP Superfamilies.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
The origin of these motifs is unclear and can be attributed to either divergent or convergent evolution (12–14).
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
112
2,891
0
false
The origin of these motifs is unclear and can be attributed to either divergent or convergent evolution.
[ "12–14" ]
The origin of these motifs is unclear and can be attributed to either divergent or convergent evolution.
true
true
true
true
true
488
2
INTRODUCTION
1
2
[ "b2", "b3", "b6", "b7", "b8", "b9", "b11", "b12", "b14" ]
17,068,077
pmid-10592235|pmid-9666335|pmid-12878003|pmid-15671167|pmid-16415885|pmid-9204286|pmid-16939206|pmid-9642096|pmid-12938173
These additional non-trivial structural relationships create cross-links between different branches of the hierarchical classification tree.
[ "2", "3", "6", "7", "8", "9", "11", "12", "14" ]
140
2,892
0
false
These additional non-trivial structural relationships create cross-links between different branches of the hierarchical classification tree.
[]
These additional non-trivial structural relationships create cross-links between different branches of the hierarchical classification tree.
true
true
true
true
true
488
3
INTRODUCTION
0
null
null
17,068,077
null
Most of the aforementioned relationships are readily identified during the expert analysis used in our SCOP database but their automatic identification using the existing computational tools still remains difficult or impossible.
null
229
2,893
0
false
null
null
Most of the aforementioned relationships are readily identified during the expert analysis used in our SCOP database but their automatic identification using the existing computational tools still remains difficult or impossible.
true
true
true
true
true
489
3
INTRODUCTION
0
null
null
17,068,077
null
Such relationships are also known to pose a problem to multiple alignment algorithms and to impede comparative modeling studies.
null
128
2,894
0
false
null
null
Such relationships are also known to pose a problem to multiple alignment algorithms and to impede comparative modeling studies.
true
true
true
true
true
489
3
INTRODUCTION
0
null
null
17,068,077
null
To facilitate the understanding and to provide a comprehensive annotation of proteins with such non-trivial structural relationships we have created SISYPHUS, a compendium to the SCOP database.
null
193
2,895
0
false
null
null
To facilitate the understanding and to provide a comprehensive annotation of proteins with such non-trivial structural relationships we have created SISYPHUS, a compendium to the SCOP database.
true
true
true
true
true
489
3
INTRODUCTION
0
null
null
17,068,077
null
The design of the database and its content are described in detail below.
null
73
2,896
0
false
null
null
The design of the database and its content are described in detail below.
true
true
true
true
true
489
0
INTRODUCTION
1
1
[ "b1", "b7", "b5", "b8" ]
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
Adenoviral vectors are a versatile tool in the investigations of gene expression and regulation as well as gene therapy.
[ "1", "7", "5", "8" ]
120
2,897
0
false
Adenoviral vectors are a versatile tool in the investigations of gene expression and regulation as well as gene therapy.
[]
Adenoviral vectors are a versatile tool in the investigations of gene expression and regulation as well as gene therapy.
true
true
true
true
true
490
0
INTRODUCTION
1
1
[ "b1", "b7", "b5", "b8" ]
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
Several advantages of the use of the adenovirus have been demonstrated.
[ "1", "7", "5", "8" ]
71
2,898
0
false
Several advantages of the use of the adenovirus have been demonstrated.
[]
Several advantages of the use of the adenovirus have been demonstrated.
true
true
true
true
true
490
0
INTRODUCTION
1
1
[ "b1", "b7", "b5", "b8" ]
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
These include the inability of the adenovirus to integrate into the genome of the target cells, its broad spectrum of applications in various cell types, its high expression of the gene of interest, the ability to produce high titers of recombinant viruses, and the ability to have gene transferred independent of active...
[ "1", "7", "5", "8" ]
341
2,899
0
false
These include the inability of the adenovirus to integrate into the genome of the target cells, its broad spectrum of applications in various cell types, its high expression of the gene of interest, the ability to produce high titers of recombinant viruses, and the ability to have gene transferred independent of active...
[ "1–7" ]
These include the inability of the adenovirus to integrate into the genome of the target cells, its broad spectrum of applications in various cell types, its high expression of the gene of interest, the ability to produce high titers of recombinant viruses, and the ability to have gene transferred independent of active...
true
true
true
true
true
490