Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
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citeids
list
pmid
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string
sentences
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3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
hVigilin: human vigilin; cVigilin: chicken vigilin; mVigilin: mouse vigilin; Ddp1p: D. melanogaster multi-KH-domain protein; Scp160p: yeast multi-KH-domain protein.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
164
10,300
0
false
hVigilin: human vigilin; cVigilin: chicken vigilin; mVigilin: mouse vigilin; Ddp1p: D. melanogaster multi-KH-domain protein; Scp160p: yeast multi-KH-domain protein.
[]
hVigilin: human vigilin; cVigilin: chicken vigilin; mVigilin: mouse vigilin; Ddp1p: D. melanogaster multi-KH-domain protein; Scp160p: yeast multi-KH-domain protein.
false
true
true
true
false
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Solid line represents N-terminal and C-terminal protein sequence not predicted to contain KH domain sequences.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
110
10,301
0
false
Solid line represents N-terminal and C-terminal protein sequence not predicted to contain KH domain sequences.
[]
Solid line represents N-terminal and C-terminal protein sequence not predicted to contain KH domain sequences.
true
true
true
true
true
1,640
4
DISCUSSION
0
null
null
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Domain structures of multi-KH-domain-containing proteins.
null
57
10,302
0
false
null
null
Domain structures of multi-KH-domain-containing proteins.
true
true
true
true
true
1,641
4
DISCUSSION
0
null
null
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Domain portions of the proteins are not drawn to scale.
null
55
10,303
0
false
null
null
Domain portions of the proteins are not drawn to scale.
true
true
true
true
true
1,641
4
DISCUSSION
0
null
null
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Numbered, filled boxes represent conserved KH domains; numbered, open boxes represent diverged KH domains.
null
106
10,304
0
false
null
null
Numbered, filled boxes represent conserved KH domains; numbered, open boxes represent diverged KH domains.
true
true
true
true
true
1,641
4
DISCUSSION
0
null
null
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
hVigilin: human vigilin; cVigilin: chicken vigilin; mVigilin: mouse vigilin; Ddp1p: D. melanogaster multi-KH-domain protein; Scp160p: yeast multi-KH-domain protein.
null
164
10,305
0
false
null
null
hVigilin: human vigilin; cVigilin: chicken vigilin; mVigilin: mouse vigilin; Ddp1p: D. melanogaster multi-KH-domain protein; Scp160p: yeast multi-KH-domain protein.
false
true
true
true
false
1,641
4
DISCUSSION
0
null
null
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Solid line represents N-terminal and C-terminal protein sequence not predicted to contain KH domain sequences.
null
110
10,306
0
false
null
null
Solid line represents N-terminal and C-terminal protein sequence not predicted to contain KH domain sequences.
true
true
true
true
true
1,641
5
DISCUSSION
1
34
[ "B34", "B35" ]
17,264,125
pmid-16381856|pmid-9600884
The KH domain models of two commonly used protein domain databases, SMART and Pfam (34,35), were capable of recognizing all the conserved KH domains in Scp160p, but only a subset of the diverged KH domains, which were not confidently predicted because the scores fell below the allowed significance threshold.
[ "34", "35" ]
309
10,307
0
false
The KH domain models of two commonly used protein domain databases, SMART and Pfam, were capable of recognizing all the conserved KH domains in Scp160p, but only a subset of the diverged KH domains, which were not confidently predicted because the scores fell below the allowed significance threshold.
[ "34,35" ]
The KH domain models of two commonly used protein domain databases, SMART and Pfam, were capable of recognizing all the conserved KH domains in Scp160p, but only a subset of the diverged KH domains, which were not confidently predicted because the scores fell below the allowed significance threshold.
true
true
true
true
true
1,642
5
DISCUSSION
1
34
[ "B34", "B35" ]
17,264,125
pmid-16381856|pmid-9600884
Nevertheless, these in silico systems were capable of recognizing all the diverged KH domains of most vigilins.
[ "34", "35" ]
111
10,308
0
false
Nevertheless, these in silico systems were capable of recognizing all the diverged KH domains of most vigilins.
[]
Nevertheless, these in silico systems were capable of recognizing all the diverged KH domains of most vigilins.
true
true
true
true
true
1,642
5
DISCUSSION
1
34
[ "B34", "B35" ]
17,264,125
pmid-16381856|pmid-9600884
It is interesting to note that, while Scp160p KH6 was not recognized by either program, this domain was still able to restore some biochemical function to the FLAG.Scp160Δ13p variant protein.
[ "34", "35" ]
191
10,309
0
false
It is interesting to note that, while Scp160p KH6 was not recognized by either program, this domain was still able to restore some biochemical function to the FLAG.Scp160Δ13p variant protein.
[]
It is interesting to note that, while Scp160p KH6 was not recognized by either program, this domain was still able to restore some biochemical function to the FLAG.Scp160Δ13p variant protein.
true
true
true
true
true
1,642
6
DISCUSSION
0
null
null
17,264,125
null
By calling into question a disparity between sequence and function among KH domains, our results raise the possibility that there may be more functional KH domains in the proteome than previously appreciated.
null
208
10,310
0
false
null
null
By calling into question a disparity between sequence and function among KH domains, our results raise the possibility that there may be more functional KH domains in the proteome than previously appreciated.
true
true
true
true
true
1,643
6
DISCUSSION
0
null
null
17,264,125
null
By extension, these results would suggest that more RNA-binding proteins may exist, as well.
null
92
10,311
0
false
null
null
By extension, these results would suggest that more RNA-binding proteins may exist, as well.
true
true
true
true
true
1,643
6
DISCUSSION
0
null
null
17,264,125
null
Finally, these data clearly imply the need for in vivo validation of other sequence motifs defined by in silico methods.
null
120
10,312
0
false
null
null
Finally, these data clearly imply the need for in vivo validation of other sequence motifs defined by in silico methods.
true
true
true
true
true
1,643
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b8", "b9", "b10", "b11", "b3", "b12", "b13", "b14" ]
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
Methylation of cytosine residues at CG dinucleotide sites in DNA is an important epigenetic modification (1–4) that, in general, leads to gene silencing (5–8).
[ "1", "4", "5", "8", "9", "10", "11", "3", "12", "13", "14" ]
159
10,313
0
false
Methylation of cytosine residues at CG dinucleotide sites in DNA is an important epigenetic modification that, in general, leads to gene silencing.
[ "1–4", "5–8" ]
Methylation of cytosine residues at CG dinucleotide sites in DNA is an important epigenetic modification that, in general, leads to gene silencing.
true
true
true
true
true
1,644
0
INTRODUCTION
1
11
[ "b1", "b4", "b5", "b8", "b9", "b10", "b11", "b3", "b12", "b13", "b14" ]
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
Aberrant changes in DNA methylation often contribute to tumorigenesis (9,10) and etiology of other diseases (11).
[ "1", "4", "5", "8", "9", "10", "11", "3", "12", "13", "14" ]
113
10,314
1
false
Aberrant changes in DNA methylation often contribute to tumorigenesis and etiology of other diseases.
[ "9,10", "11" ]
Aberrant changes in DNA methylation often contribute to tumorigenesis and etiology of other diseases.
true
true
true
true
true
1,644
0
INTRODUCTION
1
3
[ "b1", "b4", "b5", "b8", "b9", "b10", "b11", "b3", "b12", "b13", "b14" ]
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
Gene repression by DNA methylation is mediated by methyl-cytosine binding proteins assembled on methylated CGs (3).
[ "1", "4", "5", "8", "9", "10", "11", "3", "12", "13", "14" ]
115
10,315
1
false
Gene repression by DNA methylation is mediated by methyl-cytosine binding proteins assembled on methylated CGs.
[ "3" ]
Gene repression by DNA methylation is mediated by methyl-cytosine binding proteins assembled on methylated CGs.
true
true
true
true
true
1,644
0
INTRODUCTION
1
12
[ "b1", "b4", "b5", "b8", "b9", "b10", "b11", "b3", "b12", "b13", "b14" ]
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
These proteins recruit corepressors like mSin3 or Mi2-NuRD and histone deacetylase and trigger the formation of condensed, repressive chromatin, which leads to stable inactivation of gene expression (12).
[ "1", "4", "5", "8", "9", "10", "11", "3", "12", "13", "14" ]
204
10,316
1
false
These proteins recruit corepressors like mSin3 or Mi2-NuRD and histone deacetylase and trigger the formation of condensed, repressive chromatin, which leads to stable inactivation of gene expression.
[ "12" ]
These proteins recruit corepressors like mSin3 or Mi2-NuRD and histone deacetylase and trigger the formation of condensed, repressive chromatin, which leads to stable inactivation of gene expression.
true
true
true
true
true
1,644
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b8", "b9", "b10", "b11", "b3", "b12", "b13", "b14" ]
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
Another repressive mechanism of DNA methylation is to interfere with the DNA binding of transcription factors (13,14).
[ "1", "4", "5", "8", "9", "10", "11", "3", "12", "13", "14" ]
118
10,317
0
false
Another repressive mechanism of DNA methylation is to interfere with the DNA binding of transcription factors.
[ "13,14" ]
Another repressive mechanism of DNA methylation is to interfere with the DNA binding of transcription factors.
true
true
true
true
true
1,644
1
INTRODUCTION
1
2
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
DNA methylation is established by de novo DNA methyltransferases (MTases), Dnmt3a and Dnmt3b, during early embryogenesis and later maintained by Dnmt1 (2,6,15).
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
160
10,318
0
false
DNA methylation is established by de novo DNA methyltransferases (MTases), Dnmt3a and Dnmt3b, during early embryogenesis and later maintained by Dnmt1.
[ "2,6,15" ]
DNA methylation is established by de novo DNA methyltransferases (MTases), Dnmt3a and Dnmt3b, during early embryogenesis and later maintained by Dnmt1.
true
true
true
true
true
1,645
1
INTRODUCTION
1
2
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
The C-terminal catalytic domains (CDs) of Dnmt3a and 3b are active in the absence of their N-terminal part (16,17).
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
115
10,319
0
false
The C-terminal catalytic domains (CDs) of Dnmt3a and 3b are active in the absence of their N-terminal part.
[ "16,17" ]
The C-terminal catalytic domains (CDs) of Dnmt3a and 3b are active in the absence of their N-terminal part.
true
true
true
true
true
1,645
1
INTRODUCTION
1
2
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
They can be fused to a heterologous DNA binding domain (DBD) in order to target methylation activity to a predetermined DNA sequence (18–20).
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
141
10,320
0
false
They can be fused to a heterologous DNA binding domain (DBD) in order to target methylation activity to a predetermined DNA sequence.
[ "18–20" ]
They can be fused to a heterologous DNA binding domain (DBD) in order to target methylation activity to a predetermined DNA sequence.
true
true
true
true
true
1,645
1
INTRODUCTION
1
18
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
Targeted DNA methylation was observed in vitro using a fusion protein consisting of the DBD of Zif268 and the prokaryotic CG methytransferase M.SssI (18).
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
154
10,321
1
false
Targeted DNA methylation was observed in vitro using a fusion protein consisting of the DBD of Zif268 and the prokaryotic CG methytransferase M.SssI.
[ "18" ]
Targeted DNA methylation was observed in vitro using a fusion protein consisting of the DBD of Zif268 and the prokaryotic CG methytransferase M.SssI.
true
true
true
true
true
1,645
1
INTRODUCTION
1
2
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
In addition, in yeast cells, Carvin et al.
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
42
10,322
0
false
In addition, in yeast cells, Carvin et al.
[]
In addition, in yeast cells, Carvin et al.
true
true
true
true
true
1,645
1
INTRODUCTION
1
2
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
demonstrated targeted methylation, after fusing the transcriptional factor PHO5 to the viral M.CviPI MTase as well as fusing the DBDs of zinc-finger proteins based on Zif268 with M.CviPI and M.SssI (19,21).
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
206
10,323
0
false
demonstrated targeted methylation, after fusing the transcriptional factor PHO5 to the viral M.CviPI MTase as well as fusing the DBDs of zinc-finger proteins based on Zif268 with M.CviPI and M.SssI.
[ "19,21" ]
demonstrated targeted methylation, after fusing the transcriptional factor PHO5 to the viral M.CviPI MTase as well as fusing the DBDs of zinc-finger proteins based on Zif268 with M.CviPI and M.SssI.
false
true
true
true
false
1,645
1
INTRODUCTION
1
20
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
Targeted methylation also has been observed using the bacterial Dam adenine-N6 MTase and it has been applied to map the DNA binding sites of transcription factors (20).
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
168
10,324
1
false
Targeted methylation also has been observed using the bacterial Dam adenine-N6 MTase and it has been applied to map the DNA binding sites of transcription factors.
[ "20" ]
Targeted methylation also has been observed using the bacterial Dam adenine-N6 MTase and it has been applied to map the DNA binding sites of transcription factors.
true
true
true
true
true
1,645
1
INTRODUCTION
1
2
[ "b2", "b6", "b15", "b16", "b17", "b18", "b20", "b18", "b19", "b21", "b20" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
However, so far gene silencing by targeted methylation has not been demonstrated.
[ "2", "6", "15", "16", "17", "18", "20", "18", "19", "21", "20" ]
81
10,325
0
false
However, so far gene silencing by targeted methylation has not been demonstrated.
[]
However, so far gene silencing by targeted methylation has not been demonstrated.
true
true
true
true
true
1,645
2
INTRODUCTION
0
null
null
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
In this study, we fused DBDs of transcription factors or engineered zinc-finger proteins to the CDs of either the Dnmt3a or Dnmt3b DNA MTases in order to achieve targeted DNA methylation and selective silencing of gene expression.
null
230
10,326
0
false
null
null
In this study, we fused DBDs of transcription factors or engineered zinc-finger proteins to the CDs of either the Dnmt3a or Dnmt3b DNA MTases in order to achieve targeted DNA methylation and selective silencing of gene expression.
true
true
true
true
true
1,646
2
INTRODUCTION
0
null
null
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
These fusion proteins were directed to the specific target sites by the DBDs, such that DNA methylation only occurs in the vicinity of these target sites.
null
154
10,327
0
false
null
null
These fusion proteins were directed to the specific target sites by the DBDs, such that DNA methylation only occurs in the vicinity of these target sites.
true
true
true
true
true
1,646
2
INTRODUCTION
0
null
null
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
We here report targeted DNA methylation as well as efficient gene silencing in three different reporter systems with presumably very different natural gene regulatory elements.
null
176
10,328
0
false
null
null
We here report targeted DNA methylation as well as efficient gene silencing in three different reporter systems with presumably very different natural gene regulatory elements.
true
true
true
true
true
1,646
2
INTRODUCTION
0
null
null
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
This includes the TK (Human herpesvirus 1 thymidylate kinase) promoter with added binding sequence for GAL4 (UAS), the human c-Ha-ras gene promoter with added UAS and the immediate early IE175k promoter of the Herpes Simplex Virus type 1 (HSV-1).
null
246
10,329
0
false
null
null
This includes the TK (Human herpesvirus 1 thymidylate kinase) promoter with added binding sequence for GAL4 (UAS), the human c-Ha-ras gene promoter with added UAS and the immediate early IE175k promoter of the Herpes Simplex Virus type 1 (HSV-1).
true
true
true
true
true
1,646
2
INTRODUCTION
0
null
null
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
We also show that methylation-mediated gene silencing is effective in repressing infection with a wild type HSV-1.
null
114
10,330
0
false
null
null
We also show that methylation-mediated gene silencing is effective in repressing infection with a wild type HSV-1.
true
true
true
true
true
1,646
2
INTRODUCTION
0
null
null
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
This opens possibilities of using this strategy as an anti-viral treatment against other, more serious human pathogens.
null
119
10,331
0
false
null
null
This opens possibilities of using this strategy as an anti-viral treatment against other, more serious human pathogens.
true
true
true
true
true
1,646
0
DISCUSSION
0
null
null
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
In this study we have demonstrated that DNA methylation can be targeted to predetermined promoter regions and efficiently repress reporter gene expression.
null
155
10,332
0
false
null
null
In this study we have demonstrated that DNA methylation can be targeted to predetermined promoter regions and efficiently repress reporter gene expression.
true
true
true
true
true
1,647
0
DISCUSSION
0
null
null
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
Targeted DNA methylation was achieved by fusing natural or engineered DBDs to the CD of mouse de novo DNA MTase Dnmt3a or 3b.
null
125
10,333
0
false
null
null
Targeted DNA methylation was achieved by fusing natural or engineered DBDs to the CD of mouse de novo DNA MTase Dnmt3a or 3b.
true
true
true
true
true
1,647
0
DISCUSSION
0
null
null
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
DNA methylation and gene silencing were abolished when catalytically inactive DNA MTases were used, the DBD was mutated, or the target sequence in the promoter region was deleted.
null
179
10,334
0
false
null
null
DNA methylation and gene silencing were abolished when catalytically inactive DNA MTases were used, the DBD was mutated, or the target sequence in the promoter region was deleted.
true
true
true
true
true
1,647
0
DISCUSSION
0
null
null
17,151,075
pmid-11498579|pmid-12540921|pmid-14593183|pmid-10369268|pmid-14732866|pmid-12724226|pmid-15164071|pmid-11782440|pmid-9620804|pmid-3192075|pmid-2545524
Therefore, it provides the evidence that targeted gene methylation can be directly responsible for gene silencing.
null
114
10,335
0
false
null
null
Therefore, it provides the evidence that targeted gene methylation can be directly responsible for gene silencing.
true
true
true
true
true
1,647
1
DISCUSSION
1
46
[ "b46" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
The stable silencing of gene expression by DNA methylation observed here suggests that targeted DNA methylation could provide a powerful technology for specific gene silencing.
[ "46" ]
176
10,336
0
false
The stable silencing of gene expression by DNA methylation observed here suggests that targeted DNA methylation could provide a powerful technology for specific gene silencing.
[]
The stable silencing of gene expression by DNA methylation observed here suggests that targeted DNA methylation could provide a powerful technology for specific gene silencing.
true
true
true
true
true
1,648
1
DISCUSSION
1
46
[ "b46" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
Unregulated gene expression is often a central mechanism of disease.
[ "46" ]
68
10,337
0
false
Unregulated gene expression is often a central mechanism of disease.
[]
Unregulated gene expression is often a central mechanism of disease.
true
true
true
true
true
1,648
1
DISCUSSION
1
46
[ "b46" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
For example viral infections are characterized by the preferential expression of viral genes, and in cancer, up-regulated expression of oncogenes is frequently observed.
[ "46" ]
169
10,338
0
false
For example viral infections are characterized by the preferential expression of viral genes, and in cancer, up-regulated expression of oncogenes is frequently observed.
[]
For example viral infections are characterized by the preferential expression of viral genes, and in cancer, up-regulated expression of oncogenes is frequently observed.
true
true
true
true
true
1,648
1
DISCUSSION
1
46
[ "b46" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
Silencing of such genes by transcriptional inactivation could be an approach for therapy of these diseases.
[ "46" ]
107
10,339
0
false
Silencing of such genes by transcriptional inactivation could be an approach for therapy of these diseases.
[]
Silencing of such genes by transcriptional inactivation could be an approach for therapy of these diseases.
true
true
true
true
true
1,648
1
DISCUSSION
1
46
[ "b46" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
Furthermore, gene silencing by targeted methylation that is specific and stable could have applications in basic research and could be eventually used to directly correct some epigenetic defects as observed in many cancers (46).
[ "46" ]
228
10,340
1
false
Furthermore, gene silencing by targeted methylation that is specific and stable could have applications in basic research and could be eventually used to directly correct some epigenetic defects as observed in many cancers.
[ "46" ]
Furthermore, gene silencing by targeted methylation that is specific and stable could have applications in basic research and could be eventually used to directly correct some epigenetic defects as observed in many cancers.
true
true
true
true
true
1,648
1
DISCUSSION
1
46
[ "b46" ]
17,151,075
pmid-11498573|pmid-12209141|pmid-15526163|pmid-11919202|pmid-12787669|pmid-9398832|pmid-10748524|pmid-9398832|pmid-12808133|pmid-14602907|pmid-10748524|pmid-12637750
However, before a therapeutic application of the targeted methylation approach presented here could be considered, a genome wide scan for non-target methylation is required.
[ "46" ]
173
10,341
0
false
However, before a therapeutic application of the targeted methylation approach presented here could be considered, a genome wide scan for non-target methylation is required.
[]
However, before a therapeutic application of the targeted methylation approach presented here could be considered, a genome wide scan for non-target methylation is required.
true
true
true
true
true
1,648
2
DISCUSSION
1
23
[ "b23", "b47", "b49", "b23" ]
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
While we have shown that targeted methylation is a feasible approach to repress the propagation of viral infections in cell culture it ought to be compared with the previous approaches, which used engineered zinc finger DBDs fused to repressor domains (23,47–49).
[ "23", "47", "49", "23" ]
263
10,342
0
false
While we have shown that targeted methylation is a feasible approach to repress the propagation of viral infections in cell culture it ought to be compared with the previous approaches, which used engineered zinc finger DBDs fused to repressor domains.
[ "23,47–49" ]
While we have shown that targeted methylation is a feasible approach to repress the propagation of viral infections in cell culture it ought to be compared with the previous approaches, which used engineered zinc finger DBDs fused to repressor domains.
true
true
true
true
true
1,649
2
DISCUSSION
1
23
[ "b23", "b47", "b49", "b23" ]
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
The advantage of using targeted DNA methylation for gene silencing over the use of a gene repressor like the KRAB domain of KOX-1, is that the MTase has a direct enzymatic activity.
[ "23", "47", "49", "23" ]
181
10,343
0
false
The advantage of using targeted DNA methylation for gene silencing over the use of a gene repressor like the KRAB domain of KOX-1, is that the MTase has a direct enzymatic activity.
[]
The advantage of using targeted DNA methylation for gene silencing over the use of a gene repressor like the KRAB domain of KOX-1, is that the MTase has a direct enzymatic activity.
true
true
true
true
true
1,649
2
DISCUSSION
1
23
[ "b23", "b47", "b49", "b23" ]
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
Therefore, lower efficiency of targeting can lead to stable inhibition.
[ "23", "47", "49", "23" ]
71
10,344
0
false
Therefore, lower efficiency of targeting can lead to stable inhibition.
[]
Therefore, lower efficiency of targeting can lead to stable inhibition.
true
true
true
true
true
1,649
2
DISCUSSION
1
23
[ "b23", "b47", "b49", "b23" ]
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
Moreover, the DNA MTase introduces a permanent silencing imprint on DNA, which is propagated in vivo and remains stable even after dissociation of the modifying fusion protein.
[ "23", "47", "49", "23" ]
176
10,345
0
false
Moreover, the DNA MTase introduces a permanent silencing imprint on DNA, which is propagated in vivo and remains stable even after dissociation of the modifying fusion protein.
[]
Moreover, the DNA MTase introduces a permanent silencing imprint on DNA, which is propagated in vivo and remains stable even after dissociation of the modifying fusion protein.
true
true
true
true
true
1,649
2
DISCUSSION
1
23
[ "b23", "b47", "b49", "b23" ]
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
In agreement with this hypothesis we show here that 6F6-3a is significantly more efficient in gene silencing than 6F6-KOX (Figure 6B).
[ "23", "47", "49", "23" ]
134
10,346
0
false
In agreement with this hypothesis we show here that 6F6-3a is significantly more efficient in gene silencing than 6F6-KOX (Figure 6B).
[]
In agreement with this hypothesis we show here that 6F6-3a is significantly more efficient in gene silencing than 6F6-KOX (Figure 6B).
true
true
true
true
true
1,649
2
DISCUSSION
1
23
[ "b23", "b47", "b49", "b23" ]
17,151,075
pmid-12574501|pmid-12574502|pmid-15743774|pmid-12574501
In addition, B1-3a showed similar efficacy as 6F6-KOX in the present study, while B1-KOX was much less efficient than 6F6-KOX (23).
[ "23", "47", "49", "23" ]
131
10,347
1
false
In addition, B1-3a showed similar efficacy as 6F6-KOX in the present study, while B1-KOX was much less efficient than 6F6-KOX.
[ "23" ]
In addition, B1-3a showed similar efficacy as 6F6-KOX in the present study, while B1-KOX was much less efficient than 6F6-KOX.
true
true
true
true
true
1,649
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
Evidence from various studies suggests that in the biological context Dnmt3a and 3b are targeted to specific genomic sites by interaction with other proteins, which bind either DNA or chromatin, such as RP58, HP1, c-myc, PU.1, SETDB1, Mbd3, Hdac1, Brg1 or p53 (31,32,50–54).
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
274
10,348
0
false
Evidence from various studies suggests that in the biological context Dnmt3a and 3b are targeted to specific genomic sites by interaction with other proteins, which bind either DNA or chromatin, such as RP58, HP1, c-myc, PU.1, SETDB1, Mbd3, Hdac1, Brg1 or p53.
[ "31,32,50–54" ]
Evidence from various studies suggests that in the biological context Dnmt3a and 3b are targeted to specific genomic sites by interaction with other proteins, which bind either DNA or chromatin, such as RP58, HP1, c-myc, PU.1, SETDB1, Mbd3, Hdac1, Brg1 or p53.
true
true
true
true
true
1,650
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
We observed that targeted methylation induces dense methylation of DNA regions comprising up to 380 bp on both sides of the specific DNA binding site.
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
150
10,349
0
false
We observed that targeted methylation induces dense methylation of DNA regions comprising up to 380 bp on both sides of the specific DNA binding site.
[]
We observed that targeted methylation induces dense methylation of DNA regions comprising up to 380 bp on both sides of the specific DNA binding site.
true
true
true
true
true
1,650
3
DISCUSSION
1
18
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
In contrast, in their pioneering study conducted in vitro, Xu and Bestor have observed that a Zif268-M.SssI fusion protein methylates single CG sites 16–22 bp upstream of the Zif268 binding site (18).
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
200
10,350
1
false
In contrast, in their pioneering study conducted in vitro, Xu and Bestor have observed that a Zif268-M.SssI fusion protein methylates single CG sites 16–22 bp upstream of the Zif268 binding site.
[ "18" ]
In contrast, in their pioneering study conducted in vitro, Xu and Bestor have observed that a Zif268-M.SssI fusion protein methylates single CG sites 16–22 bp upstream of the Zif268 binding site.
true
true
true
true
true
1,650
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
This difference suggests that the initial methylation by Dnmt3a or 3b, targeted to the DNA by a heterologous DBD, might serve as a trigger for an epigenetic response.
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
166
10,351
0
false
This difference suggests that the initial methylation by Dnmt3a or 3b, targeted to the DNA by a heterologous DBD, might serve as a trigger for an epigenetic response.
[]
This difference suggests that the initial methylation by Dnmt3a or 3b, targeted to the DNA by a heterologous DBD, might serve as a trigger for an epigenetic response.
true
true
true
true
true
1,650
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
For example, the targeted methylation could induce histone 3 lysine 9 methylation and histone deacetylation (55–58).
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
116
10,352
0
false
For example, the targeted methylation could induce histone 3 lysine 9 methylation and histone deacetylation.
[ "55–58" ]
For example, the targeted methylation could induce histone 3 lysine 9 methylation and histone deacetylation.
true
true
true
true
true
1,650
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
In turn, these responses could trigger additional DNA methylation (59–62).
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
74
10,353
0
false
In turn, these responses could trigger additional DNA methylation.
[ "59–62" ]
In turn, these responses could trigger additional DNA methylation.
true
true
true
true
true
1,650
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
Alternatively, spreading of methylation could be mediated by Dnmt1, which could be recruited to DNA by Dnmt3a (63,64).
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
118
10,354
0
false
Alternatively, spreading of methylation could be mediated by Dnmt1, which could be recruited to DNA by Dnmt3a.
[ "63,64" ]
Alternatively, spreading of methylation could be mediated by Dnmt1, which could be recruited to DNA by Dnmt3a.
true
true
true
true
true
1,650
3
DISCUSSION
1
31
[ "b31", "b32", "b50", "b54", "b18", "b55", "b58", "b59", "b62", "b63", "b64" ]
17,151,075
pmid-16322236|pmid-16131836|pmid-11350943|pmid-16682412|pmid-9398832|pmid-15327775|pmid-12853574|pmid-11713521|pmid-12559178|pmid-12145218|pmid-11756544
Our data suggest that the CD of Dnmt3a and 3b are able to recruit endogenous gene silencing activities.
[ "31", "32", "50", "54", "18", "55", "58", "59", "62", "63", "64" ]
103
10,355
0
false
Our data suggest that the CD of Dnmt3a and 3b are able to recruit endogenous gene silencing activities.
[]
Our data suggest that the CD of Dnmt3a and 3b are able to recruit endogenous gene silencing activities.
true
true
true
true
true
1,650
4
DISCUSSION
0
null
null
17,151,075
null
In summary, our study demonstrates for the first time in transient co-transfection experiments that, targeted DNA methylation can be employed for gene silencing in human cells.
null
176
10,356
0
false
null
null
In summary, our study demonstrates for the first time in transient co-transfection experiments that, targeted DNA methylation can be employed for gene silencing in human cells.
true
true
true
true
true
1,651
4
DISCUSSION
0
null
null
17,151,075
null
Using this approach we silenced different promoters including the human Ha-ras oncogene promoter and the viral IE175k promoter by targeted methylation and demonstrated that, targeted DNA methylation antagonizes viral infection in the cell culture model.
null
253
10,357
0
false
null
null
Using this approach we silenced different promoters including the human Ha-ras oncogene promoter and the viral IE175k promoter by targeted methylation and demonstrated that, targeted DNA methylation antagonizes viral infection in the cell culture model.
true
true
true
true
true
1,651
4
DISCUSSION
0
null
null
17,151,075
null
Whether this approach is also applicable to endogenous genes in the context of natural chromatin needs further investigation.
null
125
10,358
0
false
null
null
Whether this approach is also applicable to endogenous genes in the context of natural chromatin needs further investigation.
true
true
true
true
true
1,651
4
DISCUSSION
0
null
null
17,151,075
null
For anti-viral applications, fusion to a more active DNA MTase domain might provide a stronger and less transient protective effect, that might justify proceeding to animal studies.
null
181
10,359
0
false
null
null
For anti-viral applications, fusion to a more active DNA MTase domain might provide a stronger and less transient protective effect, that might justify proceeding to animal studies.
true
true
true
true
true
1,651
4
DISCUSSION
0
null
null
17,151,075
null
Furthermore, for future application of this technique, the problem of MTase delivery to the target tissue has to be solved.
null
123
10,360
0
false
null
null
Furthermore, for future application of this technique, the problem of MTase delivery to the target tissue has to be solved.
true
true
true
true
true
1,651
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Comparative phylogenetics is a powerful tool, not just for establishing evolutionary relationships among taxa, but also for discerning biochemically significant aspects of a locus, versus those always present but variable.
[ "1", "2" ]
222
10,361
0
false
Comparative phylogenetics is a powerful tool, not just for establishing evolutionary relationships among taxa, but also for discerning biochemically significant aspects of a locus, versus those always present but variable.
[]
Comparative phylogenetics is a powerful tool, not just for establishing evolutionary relationships among taxa, but also for discerning biochemically significant aspects of a locus, versus those always present but variable.
true
true
true
true
true
1,652
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
The 3′ nuclear ribosomal transcribed spacer region [second internal transcribed spacer (ITS2)] sequence is much used for phylogenetic studies at the species and genus level.
[ "1", "2" ]
173
10,362
0
false
The 3′ nuclear ribosomal transcribed spacer region sequence is much used for phylogenetic studies at the species and genus level.
[ "second internal transcribed spacer (ITS2)" ]
The 3′ nuclear ribosomal transcribed spacer region sequence is much used for phylogenetic studies at the species and genus level.
true
true
true
true
true
1,652
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
More recently, additional phylogenetically useful information from these sequences has emerged as a consequence of the solution of their putative transcript secondary structure (1).
[ "1", "2" ]
181
10,363
1
false
More recently, additional phylogenetically useful information from these sequences has emerged as a consequence of the solution of their putative transcript secondary structure.
[ "1" ]
More recently, additional phylogenetically useful information from these sequences has emerged as a consequence of the solution of their putative transcript secondary structure.
true
true
true
true
true
1,652
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Initial analysis of potential folding homologies was presented by Wolf et al.
[ "1", "2" ]
77
10,364
0
false
Initial analysis of potential folding homologies was presented by Wolf et al.
[]
Initial analysis of potential folding homologies was presented by Wolf et al.
true
true
true
true
true
1,652
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
From folding of transcripts of many additional phyla, it now appears that conservation of secondary structure of ITS2 itself among essentially all eukaryotes is far more remarkable than had ever been anticipated.
[ "1", "2" ]
212
10,365
0
false
From folding of transcripts of many additional phyla, it now appears that conservation of secondary structure of ITS2 itself among essentially all eukaryotes is far more remarkable than had ever been anticipated.
[]
From folding of transcripts of many additional phyla, it now appears that conservation of secondary structure of ITS2 itself among essentially all eukaryotes is far more remarkable than had ever been anticipated.
true
true
true
true
true
1,652
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Although the highly conserved helix regions revealed are presumably essential for rRNA processing, the details of this complex activity are not yet fully understood.
[ "1", "2" ]
165
10,366
0
false
Although the highly conserved helix regions revealed are presumably essential for rRNA processing, the details of this complex activity are not yet fully understood.
[]
Although the highly conserved helix regions revealed are presumably essential for rRNA processing, the details of this complex activity are not yet fully understood.
true
true
true
true
true
1,652
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Here we point out homologies as they apply across animals, plants and protistan phyla to call attention to the breadth of information already available to both phylogenetic studies and to detailed analyses of ITS processing.
[ "1", "2" ]
224
10,367
0
false
Here we point out homologies as they apply across animals, plants and protistan phyla to call attention to the breadth of information already available to both phylogenetic studies and to detailed analyses of ITS processing.
[]
Here we point out homologies as they apply across animals, plants and protistan phyla to call attention to the breadth of information already available to both phylogenetic studies and to detailed analyses of ITS processing.
true
true
true
true
true
1,652
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
Phylogenetic studies have relied on a variety of DNA loci.
null
58
10,368
0
false
null
null
Phylogenetic studies have relied on a variety of DNA loci.
true
true
true
true
true
1,653
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
Protistans present probably the most difficult choice of locus to sequence, for the broad and ancient variety of cell types encompassed is greater than in fungi, animals or plants.
null
180
10,369
0
false
null
null
Protistans present probably the most difficult choice of locus to sequence, for the broad and ancient variety of cell types encompassed is greater than in fungi, animals or plants.
true
true
true
true
true
1,653
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
Among protistans, plastid rbcL has been sequenced for many algae and mitochondrial cox
null
86
10,370
0
false
null
null
Among protistans, plastid rbcL has been sequenced for many algae and mitochondrial cox
true
true
false
true
false
1,653
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
I for many non-photosynthetic protistans.
null
41
10,371
0
false
null
null
I for many non-photosynthetic protistans.
true
true
true
true
true
1,653
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
However, some protistans are photosynthetic and some not, even in the same class; and there are numerous examples of host cells with plastids transferred from a different eukaryote.
null
181
10,372
0
false
null
null
However, some protistans are photosynthetic and some not, even in the same class; and there are numerous examples of host cells with plastids transferred from a different eukaryote.
true
true
true
true
true
1,653
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
As for mitochondria, some protistans are even lacking standard mitochondrial genomes.
null
85
10,373
0
false
null
null
As for mitochondria, some protistans are even lacking standard mitochondrial genomes.
true
true
true
true
true
1,653
1
INTRODUCTION
0
null
null
17,459,886
pmid-8896380|pmid-9060392
These facts make organelle genes less appealing for broader comparisons.
null
72
10,374
0
false
null
null
These facts make organelle genes less appealing for broader comparisons.
true
true
true
true
true
1,653
2
INTRODUCTION
0
null
null
17,459,886
null
A single common nuclear locus would seem most useful, as long as it is appropriate for the task.
null
96
10,375
0
false
null
null
A single common nuclear locus would seem most useful, as long as it is appropriate for the task.
true
true
true
true
true
1,654
3
INTRODUCTION
1
3
[ "B3" ]
17,459,886
pmid-14615184
What should be its attributes?
[ "3" ]
30
10,376
0
false
What should be its attributes?
[]
What should be its attributes?
true
true
true
true
true
1,655
3
INTRODUCTION
1
3
[ "B3" ]
17,459,886
pmid-14615184
Such a locus should be present in all of the chosen taxa, and there should be no known case of horizontal transfer; and it should identify the organism to a unique species.
[ "3" ]
172
10,377
0
false
Such a locus should be present in all of the chosen taxa, and there should be no known case of horizontal transfer; and it should identify the organism to a unique species.
[]
Such a locus should be present in all of the chosen taxa, and there should be no known case of horizontal transfer; and it should identify the organism to a unique species.
true
true
true
true
true
1,655
3
INTRODUCTION
1
3
[ "B3" ]
17,459,886
pmid-14615184
One candidate is the single most frequently sequenced DNA region, with variability suitable to the species level, the ITS2 in the nuclear ribosomal gene cistron (3).
[ "3" ]
165
10,378
1
false
One candidate is the single most frequently sequenced DNA region, with variability suitable to the species level, the ITS2 in the nuclear ribosomal gene cistron.
[ "3" ]
One candidate is the single most frequently sequenced DNA region, with variability suitable to the species level, the ITS2 in the nuclear ribosomal gene cistron.
true
true
true
true
true
1,655
3
INTRODUCTION
1
3
[ "B3" ]
17,459,886
pmid-14615184
Here we review the ITS2 region across eukaryotes and find it is not just specific to species but also laden with surprisingly useful information concerning higher relationships, and clearly constrained in its evolution to maintain certain regions of transcript secondary structure universal among eukaryotes.
[ "3" ]
308
10,379
0
false
Here we review the ITS2 region across eukaryotes and find it is not just specific to species but also laden with surprisingly useful information concerning higher relationships, and clearly constrained in its evolution to maintain certain regions of transcript secondary structure universal among eukaryotes.
[]
Here we review the ITS2 region across eukaryotes and find it is not just specific to species but also laden with surprisingly useful information concerning higher relationships, and clearly constrained in its evolution to maintain certain regions of transcript secondary structure universal among eukaryotes.
true
true
true
true
true
1,655
3
INTRODUCTION
1
3
[ "B3" ]
17,459,886
pmid-14615184
Aspects of these conserved regions should be useful and very important to future studies of rRNA processing.
[ "3" ]
108
10,380
0
false
Aspects of these conserved regions should be useful and very important to future studies of rRNA processing.
[]
Aspects of these conserved regions should be useful and very important to future studies of rRNA processing.
true
true
true
true
true
1,655
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
The term ITS traditionally refers to the entire region between the nuclear genes for the ribosomal small subunit (SSU) and the ribosomal large subunit (LSU) RNAs; ITS1 is the first spacer, followed by the 5.8S RNA gene, and then the ITS2.
[ "9–12" ]
238
10,381
0
false
The term ITS traditionally refers to the entire region between the nuclear genes for the ribosomal small subunit (SSU) and the ribosomal large subunit (LSU) RNAs; ITS1 is the first spacer, followed by the 5.8S RNA gene, and then the ITS2.
[]
The term ITS traditionally refers to the entire region between the nuclear genes for the ribosomal small subunit (SSU) and the ribosomal large subunit (LSU) RNAs; ITS1 is the first spacer, followed by the 5.8S RNA gene, and then the ITS2.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Both the ITS1 and ITS2 regions of the long RNA transcript are removed, by ‘processing’ enzymes in the nucleolus, which produce the final SSU, 5.8S and LSU RNAs for ribosomes.
[ "9–12" ]
174
10,382
0
false
Both the ITS1 and ITS2 regions of the long RNA transcript are removed, by ‘processing’ enzymes in the nucleolus, which produce the final SSU, 5.8S and LSU RNAs for ribosomes.
[]
Both the ITS1 and ITS2 regions of the long RNA transcript are removed, by ‘processing’ enzymes in the nucleolus, which produce the final SSU, 5.8S and LSU RNAs for ribosomes.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
The ‘processing’ is not yet fully understood in biochemical terms, but it is clear that the folding pattern, the secondary structure, of the initial RNA transcript plays a role in guiding processing (9–12).
[ "9–12" ]
206
10,383
1
false
The ‘processing’ is not yet fully understood in biochemical terms, but it is clear that the folding pattern, the secondary structure, of the initial RNA transcript plays a role in guiding processing.
[ "9–12" ]
The ‘processing’ is not yet fully understood in biochemical terms, but it is clear that the folding pattern, the secondary structure, of the initial RNA transcript plays a role in guiding processing.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Hence, not only the sequence but also the transcript folding patterns of ITS1 and of ITS2 have been objects of study.
[ "9–12" ]
117
10,384
0
false
Hence, not only the sequence but also the transcript folding patterns of ITS1 and of ITS2 have been objects of study.
[]
Hence, not only the sequence but also the transcript folding patterns of ITS1 and of ITS2 have been objects of study.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
The second spacer, ITS2, has received vastly more attention, for plants, animals and protistans, than the ITS1.
[ "9–12" ]
111
10,385
0
false
The second spacer, ITS2, has received vastly more attention, for plants, animals and protistans, than the ITS1.
[]
The second spacer, ITS2, has received vastly more attention, for plants, animals and protistans, than the ITS1.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
More than 100 000 ITS2 sequences can be found in GenBank, and numerous studies have used this region for phylogenetic analyses.
[ "9–12" ]
127
10,386
0
false
More than 100 000 ITS2 sequences can be found in GenBank, and numerous studies have used this region for phylogenetic analyses.
[]
More than 100 000 ITS2 sequences can be found in GenBank, and numerous studies have used this region for phylogenetic analyses.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
When both ITS2 and another locus, plastid or mitochondrial, have been studied in parallel, the ITS2 has been found to contain at least as much information, and usually more (e.g.
[ "9–12" ]
178
10,387
0
false
When both ITS2 and another locus, plastid or mitochondrial, have been studied in parallel, the ITS2 has been found to contain at least as much information, and usually more (e.g.
[]
When both ITS2 and another locus, plastid or mitochondrial, have been studied in parallel, the ITS2 has been found to contain at least as much information, and usually more (e.g.
true
true
true
true
true
1,656
0
DISCUSSION
1
9–12
[ "B9 B10 B11 B12" ]
17,459,886
pmid-12850441|pmid-16244129|pmid-7312619|pmid-7602595|pmid-10961851|pmid-10556307
Its sequence is unique to a species, and usually to the subspecies level.
[ "9–12" ]
73
10,388
0
false
Its sequence is unique to a species, and usually to the subspecies level.
[]
Its sequence is unique to a species, and usually to the subspecies level.
true
true
true
true
true
1,656
1
DISCUSSION
1
18
[ "B18", "B5" ]
17,459,886
pmid-8896380|pmid-9060392
Basically, the reason for this is that ITS2 combines both remarkably conserved with relatively labile stretches of nucleotides, as shown in the alignment of Hershkovitz and Lewis (18).
[ "18", "5" ]
184
10,389
1
false
Basically, the reason for this is that ITS2 combines both remarkably conserved with relatively labile stretches of nucleotides, as shown in the alignment of Hershkovitz and Lewis.
[ "18" ]
Basically, the reason for this is that ITS2 combines both remarkably conserved with relatively labile stretches of nucleotides, as shown in the alignment of Hershkovitz and Lewis.
true
true
true
true
true
1,657
1
DISCUSSION
1
5
[ "B18", "B5" ]
17,459,886
pmid-8896380|pmid-9060392
The explanation for this apparent alternation of conserved with variable regions was presented by Mai and Coleman (5).
[ "18", "5" ]
118
10,390
1
false
The explanation for this apparent alternation of conserved with variable regions was presented by Mai and Coleman.
[ "5" ]
The explanation for this apparent alternation of conserved with variable regions was presented by Mai and Coleman.
true
true
true
true
true
1,657
1
DISCUSSION
1
18
[ "B18", "B5" ]
17,459,886
pmid-8896380|pmid-9060392
The regions of greatest sequence conservation contribute heavily to the pairings in the helices of the secondary structure that the initial RNA transcript takes on, as shown in the cartoon in Figure 1.
[ "18", "5" ]
201
10,391
0
false
The regions of greatest sequence conservation contribute heavily to the pairings in the helices of the secondary structure that the initial RNA transcript takes on, as shown in the cartoon in Figure 1.
[]
The regions of greatest sequence conservation contribute heavily to the pairings in the helices of the secondary structure that the initial RNA transcript takes on, as shown in the cartoon in Figure 1.
true
true
true
true
true
1,657
1
DISCUSSION
1
18
[ "B18", "B5" ]
17,459,886
pmid-8896380|pmid-9060392
This secondary structure, in turn, guides processing.
[ "18", "5" ]
53
10,392
0
false
This secondary structure, in turn, guides processing.
[]
This secondary structure, in turn, guides processing.
true
true
true
true
true
1,657
2
DISCUSSION
0
null
null
17,459,886
null
Contributing to the popularity of ITS2 for phylogenetic analyses is its ease of PCR and sequencing.
null
99
10,393
0
false
null
null
Contributing to the popularity of ITS2 for phylogenetic analyses is its ease of PCR and sequencing.
true
true
true
true
true
1,658
2
DISCUSSION
0
null
null
17,459,886
null
Because its primer regions are in the 5.8S and the 5′ region of the large subunit genes of the ribosomal DNA, both utterly essential genes, they are very highly conserved, yet offer the possibility of selecting phylum-specific primers.
null
235
10,394
0
false
null
null
Because its primer regions are in the 5.8S and the 5′ region of the large subunit genes of the ribosomal DNA, both utterly essential genes, they are very highly conserved, yet offer the possibility of selecting phylum-specific primers.
true
true
true
true
true
1,658
2
DISCUSSION
0
null
null
17,459,886
null
Also, ITS2 lengths are generally shorter than 350 nt, easily sequenced in one run.
null
82
10,395
0
false
null
null
Also, ITS2 lengths are generally shorter than 350 nt, easily sequenced in one run.
true
true
true
true
true
1,658
3
DISCUSSION
0
null
null
17,459,886
pmid-14615184
One hesitation affecting phylogenetic ITS2 studies has been the question of alignment of differing sequences, a question that arises because for proteins, with their triplet amino acid signature in the DNA sequence, the alignment is immediately obvious.
null
253
10,396
0
false
null
null
One hesitation affecting phylogenetic ITS2 studies has been the question of alignment of differing sequences, a question that arises because for proteins, with their triplet amino acid signature in the DNA sequence, the alignment is immediately obvious.
true
true
true
true
true
1,659
3
DISCUSSION
0
null
null
17,459,886
pmid-14615184
For DNA regions that do not code for protein products, alignment of subregions where sequence differs considerably presents difficult and often unjustifiable options, a facet that has sometimes led earlier workers to omit the more variable portions of ITS2 from an alignment.
null
275
10,397
0
false
null
null
For DNA regions that do not code for protein products, alignment of subregions where sequence differs considerably presents difficult and often unjustifiable options, a facet that has sometimes led earlier workers to omit the more variable portions of ITS2 from an alignment.
true
true
true
true
true
1,659
3
DISCUSSION
0
null
null
17,459,886
pmid-14615184
This problem has been largely overcome with the recognition of the role of transcript secondary structure, which dictates alignment of paired positions.
null
152
10,398
0
false
null
null
This problem has been largely overcome with the recognition of the role of transcript secondary structure, which dictates alignment of paired positions.
true
true
true
true
true
1,659
3
DISCUSSION
0
null
null
17,459,886
pmid-14615184
The alignment can be done either manually or by using computer programs (see below).
null
84
10,399
0
false
null
null
The alignment can be done either manually or by using computer programs (see below).
true
true
true
true
true
1,659