Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
1
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4
DISCUSSION
0
null
null
16,990,248
null
Therefore it is very reasonable to assume that the cost of L-DNA amidite synthesis can reach the range of normal DNA in a short time, once large-scale synthesis schemes are used.
null
178
3,100
0
false
null
null
Therefore it is very reasonable to assume that the cost of L-DNA amidite synthesis can reach the range of normal DNA in a short time, once large-scale synthesis schemes are used.
true
true
true
true
true
520
5
DISCUSSION
0
null
null
16,990,248
null
Because of its chiral difference, L-DNA can serve as a useful tool also on normal (D-DNA) microarray platforms and in other areas of molecular biology and biotechnology.
null
169
3,101
0
false
null
null
Because of its chiral difference, L-DNA can serve as a useful tool also on normal (D-DNA) microarray platforms and in other areas of molecular biology and biotechnology.
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
One important issue in microarray assays is still the aspect of quantifying the amount of bound analyte in absolute rather than only relative terms.
null
148
3,102
0
false
null
null
One important issue in microarray assays is still the aspect of quantifying the amount of bound analyte in absolute rather than only relative terms.
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
In order to do so, a control for both the amount of probe at the microarray surface as well as the efficiency of the hybridization process is required.
null
151
3,103
0
false
null
null
In order to do so, a control for both the amount of probe at the microarray surface as well as the efficiency of the hybridization process is required.
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
This could be achieved by mixing to each probe a small percentage of an L-DNA ICP and spiking the hybridization sample with a known amount of its labelled L-DNA complement (ICT).
null
178
3,104
0
false
null
null
This could be achieved by mixing to each probe a small percentage of an L-DNA ICP and spiking the hybridization sample with a known amount of its labelled L-DNA complement (ICT).
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
Neither the probe nor the target will interact with the other probes or the analyte at all, enabling a precise control of microarray quality and hybridization efficiency without any risk of affecting and thus jeopardising the binding of the actual D-formed analyte.
null
265
3,105
0
false
null
null
Neither the probe nor the target will interact with the other probes or the analyte at all, enabling a precise control of microarray quality and hybridization efficiency without any risk of affecting and thus jeopardising the binding of the actual D-formed analyte.
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
Its hybridization will permit the quantification across the entire microarray and between platforms.
null
100
3,106
0
false
null
null
Its hybridization will permit the quantification across the entire microarray and between platforms.
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
Even better would be the generation of chimeric probe molecules that consist of a common L-DNA portion for quantification with the ICT and the specific D-portion for binding the actual analyte.
null
193
3,107
0
false
null
null
Even better would be the generation of chimeric probe molecules that consist of a common L-DNA portion for quantification with the ICT and the specific D-portion for binding the actual analyte.
true
true
true
true
true
521
5
DISCUSSION
0
null
null
16,990,248
null
This kind of molecule could also be produced on in situ synthesized microarrays.
null
80
3,108
0
false
null
null
This kind of molecule could also be produced on in situ synthesized microarrays.
true
true
true
true
true
521
6
DISCUSSION
0
null
null
16,990,248
null
The apparent lack of enzymatic degradation, the absence of interaction with natural nucleic acids and the ability to produce by standard chemical processes chimeric molecules of L-DNA and D-DNA offer the potential for a number of applications of L-DNA in molecular biotechnology.
null
279
3,109
0
false
null
null
The apparent lack of enzymatic degradation, the absence of interaction with natural nucleic acids and the ability to produce by standard chemical processes chimeric molecules of L-DNA and D-DNA offer the potential for a number of applications of L-DNA in molecular biotechnology.
true
true
true
true
true
522
6
DISCUSSION
0
null
null
16,990,248
null
Especially the combination of the orthogonal hybridization system L-DNA and D-DNA with PNA—with their different structures and distinct patterns of interaction—could be put to good use.
null
185
3,110
0
false
null
null
Especially the combination of the orthogonal hybridization system L-DNA and D-DNA with PNA—with their different structures and distinct patterns of interaction—could be put to good use.
true
true
true
true
true
522
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
The organization of DNA into higher order chromatin structure is crucial for the correct temporal and spatial regulation of gene expression in most eukaryotic organisms.
[ "1", "2", "3" ]
169
3,111
0
false
The organization of DNA into higher order chromatin structure is crucial for the correct temporal and spatial regulation of gene expression in most eukaryotic organisms.
[]
The organization of DNA into higher order chromatin structure is crucial for the correct temporal and spatial regulation of gene expression in most eukaryotic organisms.
true
true
true
true
true
523
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
Chromatin is a dynamic DNA–protein structure that can exist as either transcriptionally permissive euchromatin or repressive heterochromatin.
[ "1", "2", "3" ]
141
3,112
0
false
Chromatin is a dynamic DNA–protein structure that can exist as either transcriptionally permissive euchromatin or repressive heterochromatin.
[]
Chromatin is a dynamic DNA–protein structure that can exist as either transcriptionally permissive euchromatin or repressive heterochromatin.
true
true
true
true
true
523
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
The difference between the two states is partly due to different combinations of covalent post-translational modifications of the histones, including phosphorylation, acetylation, ubiquitination, ADP ribosylation and methylation (1).
[ "1", "2", "3" ]
233
3,113
1
false
The difference between the two states is partly due to different combinations of covalent post-translational modifications of the histones, including phosphorylation, acetylation, ubiquitination, ADP ribosylation and methylation.
[ "1" ]
The difference between the two states is partly due to different combinations of covalent post-translational modifications of the histones, including phosphorylation, acetylation, ubiquitination, ADP ribosylation and methylation.
true
true
true
true
true
523
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
These modifications, constituting the so called histone code, may be interdependent, and create binding sites for chromatin-associated effector proteins (2,3) facilitating or restricting transcription.
[ "1", "2", "3" ]
201
3,114
0
false
These modifications, constituting the so called histone code, may be interdependent, and create binding sites for chromatin-associated effector proteins facilitating or restricting transcription.
[ "2,3" ]
These modifications, constituting the so called histone code, may be interdependent, and create binding sites for chromatin-associated effector proteins facilitating or restricting transcription.
true
true
true
true
true
523
1
INTRODUCTION
1
4
[ "b4", "b5", "b6", "b7" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
Two of the best studied protein families responsible for histone-tail modifications are the histone acetyltransferases (HATs) and the histone deacetylases (HDACs) that function in multiprotein complexes.
[ "4", "5", "6", "7" ]
203
3,115
0
false
Two of the best studied protein families responsible for histone-tail modifications are the histone acetyltransferases (HATs) and the histone deacetylases (HDACs) that function in multiprotein complexes.
[]
Two of the best studied protein families responsible for histone-tail modifications are the histone acetyltransferases (HATs) and the histone deacetylases (HDACs) that function in multiprotein complexes.
true
true
true
true
true
524
1
INTRODUCTION
1
4
[ "b4", "b5", "b6", "b7" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
The HATs promote gene activation by interaction with transcriptional activators and acetylation of the conserved lysine (K) residues on the histone tails (4), while the HDACs perform transcriptional repression by deacetylation at sites targeted by transcriptional repressors (5).
[ "4", "5", "6", "7" ]
279
3,116
1
false
The HATs promote gene activation by interaction with transcriptional activators and acetylation of the conserved lysine (K) residues on the histone tails, while the HDACs perform transcriptional repression by deacetylation at sites targeted by transcriptional repressors.
[ "4", "5" ]
The HATs promote gene activation by interaction with transcriptional activators and acetylation of the conserved lysine (K) residues on the histone tails, while the HDACs perform transcriptional repression by deacetylation at sites targeted by transcriptional repressors.
true
true
true
true
true
524
1
INTRODUCTION
1
6
[ "b4", "b5", "b6", "b7" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
Lysine residues may also be modified by methylation, which can stimulate or repress transcription depending on the position of the methylated residues (6).
[ "4", "5", "6", "7" ]
155
3,117
1
false
Lysine residues may also be modified by methylation, which can stimulate or repress transcription depending on the position of the methylated residues.
[ "6" ]
Lysine residues may also be modified by methylation, which can stimulate or repress transcription depending on the position of the methylated residues.
true
true
true
true
true
524
1
INTRODUCTION
1
4
[ "b4", "b5", "b6", "b7" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
In general, methylation of histone H3K9, H3K27 and H4K20 in combination with histone hypoacetylation and DNA methylation, is associated with heterochromatin and gene silencing.
[ "4", "5", "6", "7" ]
176
3,118
0
false
In general, methylation of histone H3K9, H3K27 and H4K20 in combination with histone hypoacetylation and DNA methylation, is associated with heterochromatin and gene silencing.
[]
In general, methylation of histone H3K9, H3K27 and H4K20 in combination with histone hypoacetylation and DNA methylation, is associated with heterochromatin and gene silencing.
true
true
true
true
true
524
1
INTRODUCTION
1
7
[ "b4", "b5", "b6", "b7" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
Euchromatin on the other hand, contains elevated levels of histone H3 lysine methylation at positions 4, 36 and 79 as well as hyperacetylation of histone H4 (7).
[ "4", "5", "6", "7" ]
161
3,119
1
false
Euchromatin on the other hand, contains elevated levels of histone H3 lysine methylation at positions 4, 36 and 79 as well as hyperacetylation of histone H4.
[ "7" ]
Euchromatin on the other hand, contains elevated levels of histone H3 lysine methylation at positions 4, 36 and 79 as well as hyperacetylation of histone H4.
true
true
true
true
true
524
2
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
The ability to methylate lysine residues on the histone tails resides in proteins containing the evolutionarily conserved 130 amino acid SET domain named after the three Drosophila proteins SUPPRESSOR OF VARIEGATION 3-9
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
219
3,120
0
false
The ability to methylate lysine residues on the histone tails resides in proteins containing the evolutionarily conserved 130 amino acid SET domain named after the three Drosophila proteins SUPPRESSOR OF VARIEGATION 3-9
[]
The ability to methylate lysine residues on the histone tails resides in proteins containing the evolutionarily conserved 130 amino acid SET domain named after the three Drosophila proteins SUPPRESSOR OF VARIEGATION 3-9
true
true
false
true
false
525
2
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
[SU(VAR)3-9], ENHANCER OF ZESTE [E(Z)] and TRITHORAX (TRX) (8).
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
63
3,121
1
false
, ENHANCER OF ZESTE [E(Z)] and TRITHORAX (TRX).
[ "SU(VAR)3-9", "8" ]
, ENHANCER OF ZESTE [E(Z)] and TRITHORAX (TRX).
false
false
true
true
false
525
2
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
In the Arabidopsis thaliana genome there are at least 29 actively transcribed genes encoding SET-domain proteins, that can be divided into four major evolutionarily conserved classes (9,10).
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
190
3,122
0
false
In the Arabidopsis thaliana genome there are at least 29 actively transcribed genes encoding SET-domain proteins, that can be divided into four major evolutionarily conserved classes.
[ "9,10" ]
In the Arabidopsis thaliana genome there are at least 29 actively transcribed genes encoding SET-domain proteins, that can be divided into four major evolutionarily conserved classes.
true
true
true
true
true
525
2
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
The diversity of these proteins suggests that they exert specific functions during Arabidopsis development.
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
107
3,123
0
false
The diversity of these proteins suggests that they exert specific functions during Arabidopsis development.
[]
The diversity of these proteins suggests that they exert specific functions during Arabidopsis development.
true
true
true
true
true
525
2
INTRODUCTION
1
9
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
For example, MEDEA (MEA) is a Polycomb group protein homologous to E(Z) (9), which in Arabidopsis regulates seed development after fertilization (11,12).
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
153
3,124
1
false
For example, MEDEA (MEA) is a Polycomb group protein homologous to E(Z), which in Arabidopsis regulates seed development after fertilization.
[ "9", "11,12" ]
For example, MEDEA (MEA) is a Polycomb group protein homologous to E(Z), which in Arabidopsis regulates seed development after fertilization.
true
true
true
true
true
525
2
INTRODUCTION
1
13
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
The ATX1 protein, a homologue to TRX, positively regulates the expression of several flower homeotic genes in Arabidopsis, and in vitro results suggest that the protein is a histone H3K4 methyltransferase (13).
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
210
3,125
1
false
The ATX1 protein, a homologue to TRX, positively regulates the expression of several flower homeotic genes in Arabidopsis, and in vitro results suggest that the protein is a histone H3K4 methyltransferase.
[ "13" ]
The ATX1 protein, a homologue to TRX, positively regulates the expression of several flower homeotic genes in Arabidopsis, and in vitro results suggest that the protein is a histone H3K4 methyltransferase.
true
true
true
true
true
525
2
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b9", "b11", "b12", "b13", "b14", "b15" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
The protein product of the ASHH2 gene (At1g77300), similar to Drosophila ASH1, is involved in control of flowering time and may act as an H3K4 and/or H3K36 HMTase (14,15).
[ "8", "9", "10", "9", "11", "12", "13", "14", "15" ]
171
3,126
0
false
The protein product of the ASHH2 gene (At1g77300), similar to Drosophila ASH1, is involved in control of flowering time and may act as an H3K4 and/or H3K36 HMTase.
[ "14,15" ]
The protein product of the ASHH2 gene (At1g77300), similar to Drosophila ASH1, is involved in control of flowering time and may act as an H3K4 and/or H3K36 HMTase.
true
true
true
true
true
525
3
INTRODUCTION
1
16
[ "b16", "b19", "b18", "b16", "b20" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
The two SU(VAR)3-9 homologues KRYPTONITE (KYP)/SUVH4 and SUVH2 have been studied in more detail and both have been shown to control heterochromatic H3K9 dimethylation and to function in vivo as heterochromatin-specific H3K9 HMTases (16–19).
[ "16", "19", "18", "16", "20" ]
240
3,127
0
false
The two SU(VAR)3-9 homologues KRYPTONITE (KYP)/SUVH4 and SUVH2 have been studied in more detail and both have been shown to control heterochromatic H3K9 dimethylation and to function in vivo as heterochromatin-specific H3K9 HMTases.
[ "16–19" ]
The two SU(VAR)3-9 homologues KRYPTONITE (KYP)/SUVH4 and SUVH2 have been studied in more detail and both have been shown to control heterochromatic H3K9 dimethylation and to function in vivo as heterochromatin-specific H3K9 HMTases.
true
true
true
true
true
526
3
INTRODUCTION
1
18
[ "b16", "b19", "b18", "b16", "b20" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
The most severe effects of this histone methylation mark were found in suvh2 null mutants, and a dosage dependent effect of SUVH2 on heterochromatic gene silencing has been demonstrated (18).
[ "16", "19", "18", "16", "20" ]
191
3,128
1
false
The most severe effects of this histone methylation mark were found in suvh2 null mutants, and a dosage dependent effect of SUVH2 on heterochromatic gene silencing has been demonstrated.
[ "18" ]
The most severe effects of this histone methylation mark were found in suvh2 null mutants, and a dosage dependent effect of SUVH2 on heterochromatic gene silencing has been demonstrated.
true
true
true
true
true
526
3
INTRODUCTION
1
16
[ "b16", "b19", "b18", "b16", "b20" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
Two other SUVH proteins, SUVH5 and SUVH6, also show in vitro H3K9 HMTase activity and together with SUVH4 these HMTases control non-CpG DNA methylation and gene silencing at heterochromatic loci (16,20).
[ "16", "19", "18", "16", "20" ]
203
3,129
0
false
Two other SUVH proteins, SUVH5 and SUVH6, also show in vitro H3K9 HMTase activity and together with SUVH4 these HMTases control non-CpG DNA methylation and gene silencing at heterochromatic loci.
[ "16,20" ]
Two other SUVH proteins, SUVH5 and SUVH6, also show in vitro H3K9 HMTase activity and together with SUVH4 these HMTases control non-CpG DNA methylation and gene silencing at heterochromatic loci.
true
true
true
true
true
526
3
INTRODUCTION
1
16
[ "b16", "b19", "b18", "b16", "b20" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
Therefore, all data available strongly suggest that proteins belonging to the SU(VAR)3-9 group of SET-domain proteins are involved in multiple controls of heterochromatic H3K9 methylation and gene silencing in Arabidopsis.
[ "16", "19", "18", "16", "20" ]
222
3,130
0
false
Therefore, all data available strongly suggest that proteins belonging to the SU(VAR)3-9 group of SET-domain proteins are involved in multiple controls of heterochromatic H3K9 methylation and gene silencing in Arabidopsis.
[]
Therefore, all data available strongly suggest that proteins belonging to the SU(VAR)3-9 group of SET-domain proteins are involved in multiple controls of heterochromatic H3K9 methylation and gene silencing in Arabidopsis.
true
true
true
true
true
526
4
INTRODUCTION
1
9
[ "b9", "b18", "b9", "b10" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
In addition to nine active SUVH genes, there are five SU(VAR)3-9 related SUVR genes in Arabidopsis.
[ "9", "18", "9", "10" ]
99
3,131
0
false
In addition to nine active SUVH genes, there are five SU(VAR)3-9 related SUVR genes in Arabidopsis.
[]
In addition to nine active SUVH genes, there are five SU(VAR)3-9 related SUVR genes in Arabidopsis.
true
true
true
true
true
527
4
INTRODUCTION
1
9
[ "b9", "b18", "b9", "b10" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
The encoded proteins have a SET domain with pre- and post-SET domains most similar to the SU(VAR)3-9 group, but are lacking the YDG domain of the SUVH proteins (9) that appears to be involved in directing DNA methylation to target sequences (18).
[ "9", "18", "9", "10" ]
246
3,132
1
false
The encoded proteins have a SET domain with pre- and post-SET domains most similar to the SU(VAR)3-9 group, but are lacking the YDG domain of the SUVH proteins that appears to be involved in directing DNA methylation to target sequences.
[ "9", "18" ]
The encoded proteins have a SET domain with pre- and post-SET domains most similar to the SU(VAR)3-9 group, but are lacking the YDG domain of the SUVH proteins that appears to be involved in directing DNA methylation to target sequences.
true
true
true
true
true
527
4
INTRODUCTION
1
9
[ "b9", "b18", "b9", "b10" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
To elucidate whether SUVR proteins differ in function from SUVH proteins we have focused the present work on SUVR1, SUVR2 and SUVR4 that constitute a subgroup amongst the SUVR proteins (9,10).
[ "9", "18", "9", "10" ]
192
3,133
0
false
To elucidate whether SUVR proteins differ in function from SUVH proteins we have focused the present work on SUVR1, SUVR2 and SUVR4 that constitute a subgroup amongst the SUVR proteins.
[ "9,10" ]
To elucidate whether SUVR proteins differ in function from SUVH proteins we have focused the present work on SUVR1, SUVR2 and SUVR4 that constitute a subgroup amongst the SUVR proteins.
true
true
true
true
true
527
4
INTRODUCTION
1
9
[ "b9", "b18", "b9", "b10" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
We present their particular domain structure and splice variants.
[ "9", "18", "9", "10" ]
65
3,134
0
false
We present their particular domain structure and splice variants.
[]
We present their particular domain structure and splice variants.
true
true
true
true
true
527
4
INTRODUCTION
1
9
[ "b9", "b18", "b9", "b10" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
In contrast to other SET-domain proteins these SUVR proteins were mainly found localized in the nucleolus or nuclear bodies, and we have identified a short amino acid sequence that can direct proteins to the nucleolus.
[ "9", "18", "9", "10" ]
218
3,135
0
false
In contrast to other SET-domain proteins these SUVR proteins were mainly found localized in the nucleolus or nuclear bodies, and we have identified a short amino acid sequence that can direct proteins to the nucleolus.
[]
In contrast to other SET-domain proteins these SUVR proteins were mainly found localized in the nucleolus or nuclear bodies, and we have identified a short amino acid sequence that can direct proteins to the nucleolus.
true
true
true
true
true
527
4
INTRODUCTION
1
9
[ "b9", "b18", "b9", "b10" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
The recombinant SUVR4 protein, but not SUVR1 and SUVR2, has HMTase activity with specificity for monomethylated H3K9 in vitro.
[ "9", "18", "9", "10" ]
126
3,136
0
false
The recombinant SUVR4 protein, but not SUVR1 and SUVR2, has HMTase activity with specificity for monomethylated H3K9 in vitro.
[]
The recombinant SUVR4 protein, but not SUVR1 and SUVR2, has HMTase activity with specificity for monomethylated H3K9 in vitro.
true
true
true
true
true
527
0
DISCUSSION
1
9
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
Based on domain composition and sequence alignments of the SET domains, we have earlier classified the SUVR1, SUVR2 and SUVR4 proteins as SU(VAR)3-9 related proteins most similar to the human G9a (9).
[ "9", "10", "29", "35", "36" ]
200
3,137
1
false
Based on domain composition and sequence alignments of the SET domains, we have earlier classified the SUVR1, SUVR2 and SUVR4 proteins as SU(VAR)3-9 related proteins most similar to the human G9a.
[ "9" ]
Based on domain composition and sequence alignments of the SET domains, we have earlier classified the SUVR1, SUVR2 and SUVR4 proteins as SU(VAR)3-9 related proteins most similar to the human G9a.
true
true
true
true
true
528
0
DISCUSSION
1
10
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
Later this small sub-group has been referred to as class V-6 SET-domain proteins (10).
[ "9", "10", "29", "35", "36" ]
86
3,138
1
false
Later this small sub-group has been referred to as class V-6 SET-domain proteins.
[ "10" ]
Later this small sub-group has been referred to as class V-6 SET-domain proteins.
true
true
true
true
true
528
0
DISCUSSION
1
9
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
SUVR1, SUVR2 and SUVR4 diverge from the Arabidopsis SUVH members of the SU(VAR)3-9 class both in the SET domain itself and in the pre-SET region (Supplementary Figure 1).
[ "9", "10", "29", "35", "36" ]
170
3,139
0
false
SUVR1, SUVR2 and SUVR4 diverge from the Arabidopsis SUVH members of the SU(VAR)3-9 class both in the SET domain itself and in the pre-SET region (Supplementary Figure 1).
[]
SUVR1, SUVR2 and SUVR4 diverge from the Arabidopsis SUVH members of the SU(VAR)3-9 class both in the SET domain itself and in the pre-SET region (Supplementary Figure 1).
true
true
true
true
true
528
0
DISCUSSION
1
29
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
The importance of the SET flanking regions for enzyme activity has been demonstrated for other SET-domain proteins (29).
[ "9", "10", "29", "35", "36" ]
120
3,140
1
false
The importance of the SET flanking regions for enzyme activity has been demonstrated for other SET-domain proteins.
[ "29" ]
The importance of the SET flanking regions for enzyme activity has been demonstrated for other SET-domain proteins.
true
true
true
true
true
528
0
DISCUSSION
1
35
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
The SUVR pre-SET adds three invariant cysteines to the triangular zinc-binding cluster of nine invariant cysteines found in the pre-SET of the rest of the SU(VAR)3-9 group (35).
[ "9", "10", "29", "35", "36" ]
177
3,141
1
false
The SUVR pre-SET adds three invariant cysteines to the triangular zinc-binding cluster of nine invariant cysteines found in the pre-SET of the rest of the SU(VAR)3-9 group.
[ "35" ]
The SUVR pre-SET adds three invariant cysteines to the triangular zinc-binding cluster of nine invariant cysteines found in the pre-SET of the rest of the SU(VAR)3-9 group.
true
true
true
true
true
528
0
DISCUSSION
1
36
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
Thus, the SUVR pre-SET may confer a new type of binding, or be involved in substrate specificity (36).
[ "9", "10", "29", "35", "36" ]
102
3,142
1
false
Thus, the SUVR pre-SET may confer a new type of binding, or be involved in substrate specificity.
[ "36" ]
Thus, the SUVR pre-SET may confer a new type of binding, or be involved in substrate specificity.
true
true
true
true
true
528
0
DISCUSSION
1
9
[ "b9", "b10", "b29", "b35", "b36" ]
17,020,925
pmid-12419240|pmid-11498575|pmid-12648673|pmid-11691919|pmid-12805620|pmid-14675547|pmid-15869391|pmid-12575990
Notably, the variable SET-I region of the SET domain also contains SUVR-specific conserved motifs (Supplementary Figure 1).
[ "9", "10", "29", "35", "36" ]
123
3,143
0
false
Notably, the variable SET-I region of the SET domain also contains SUVR-specific conserved motifs (Supplementary Figure 1).
[]
Notably, the variable SET-I region of the SET domain also contains SUVR-specific conserved motifs (Supplementary Figure 1).
true
true
true
true
true
528
1
DISCUSSION
1
37
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
These SUVR-specific pre-SET and SET-I regions were only found in plant proteins (Supplementary Figure 1), as was also the case for the novel N-terminal WIYLD domain (Figure 3B).
[ "37", "38", "18", "39", "40" ]
177
3,144
0
false
These SUVR-specific pre-SET and SET-I regions were only found in plant proteins (Supplementary Figure 1), as was also the case for the novel N-terminal WIYLD domain (Figure 3B).
[]
These SUVR-specific pre-SET and SET-I regions were only found in plant proteins (Supplementary Figure 1), as was also the case for the novel N-terminal WIYLD domain.
true
true
true
true
true
529
1
DISCUSSION
1
37
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
Secondary structure prediction indicates that this domain consists of three alpha helices with four conserved Leu/Ile residues (Figure 3B), suggesting that it may be involved in dimerization, as is the case for the N-terminal region of SU(VAR)3-9 (37).
[ "37", "38", "18", "39", "40" ]
252
3,145
1
false
Secondary structure prediction indicates that this domain consists of three alpha helices with four conserved Leu/Ile residues (Figure 3B), suggesting that it may be involved in dimerization, as is the case for the N-terminal region of SU(VAR)3-9.
[ "37" ]
Secondary structure prediction indicates that this domain consists of three alpha helices with four conserved Leu/Ile residues, suggesting that it may be involved in dimerization, as is the case for the N-terminal region of SU(VAR)3-9.
true
true
true
true
true
529
1
DISCUSSION
1
37
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
SUVR4 histone H3 binding is independent of the WIYLD domain, and the nucleolar localization of the SUVR1a splice variant, lacking this domain, excludes a major role for this domain in nucleolar localization.
[ "37", "38", "18", "39", "40" ]
207
3,146
0
false
SUVR4 histone H3 binding is independent of the WIYLD domain, and the nucleolar localization of the SUVR1a splice variant, lacking this domain, excludes a major role for this domain in nucleolar localization.
[]
SUVR4 histone H3 binding is independent of the WIYLD domain, and the nucleolar localization of the SUVR1a splice variant, lacking this domain, excludes a major role for this domain in nucleolar localization.
true
true
true
true
true
529
1
DISCUSSION
1
38
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
However, structural similarity to the RuvA C-terminal domain (38) (Rein Aasland, personal communication), may point to a role in binding of DNA.
[ "37", "38", "18", "39", "40" ]
144
3,147
1
false
However, structural similarity to the RuvA C-terminal domain (Rein Aasland, personal communication), may point to a role in binding of DNA.
[ "38" ]
However, structural similarity to the RuvA C-terminal domain (Rein Aasland, personal communication), may point to a role in binding of DNA.
true
true
true
true
true
529
1
DISCUSSION
1
18
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
The YDG domain of the Arabidopsis SUVH2 protein appears to be involved in directing DNA methylation to target sequences (18).
[ "37", "38", "18", "39", "40" ]
125
3,148
1
false
The YDG domain of the Arabidopsis SUVH2 protein appears to be involved in directing DNA methylation to target sequences.
[ "18" ]
The YDG domain of the Arabidopsis SUVH2 protein appears to be involved in directing DNA methylation to target sequences.
true
true
true
true
true
529
1
DISCUSSION
1
37
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
Similarly, the WIYLD domain may be involved in directing proteins to their targets, or conversely be directed to its targets through interactions with the WIYLD domain.
[ "37", "38", "18", "39", "40" ]
168
3,149
0
false
Similarly, the WIYLD domain may be involved in directing proteins to their targets, or conversely be directed to its targets through interactions with the WIYLD domain.
[]
Similarly, the WIYLD domain may be involved in directing proteins to their targets, or conversely be directed to its targets through interactions with the WIYLD domain.
true
true
true
true
true
529
1
DISCUSSION
1
37
[ "b37", "b38", "b18", "b39", "b40" ]
17,020,925
pmid-11437231|pmid-10694882|pmid-12067650|pmid-11893494|pmid-15035645|pmid-7885479|pmid-15775980|pmid-15145577|pmid-15102374
The plant dialect of chromatin modulation differ from other phyla in several aspects (39,40), and the SUVR proteins may play a role in some of these processes.
[ "37", "38", "18", "39", "40" ]
159
3,150
0
false
The plant dialect of chromatin modulation differ from other phyla in several aspects, and the SUVR proteins may play a role in some of these processes.
[ "39,40" ]
The plant dialect of chromatin modulation differ from other phyla in several aspects, and the SUVR proteins may play a role in some of these processes.
true
true
true
true
true
529
2
DISCUSSION
1
6
[ "b6", "b16", "b18" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
All the SUVR-GFP fusion proteins were exclusively localized to the nucleus, with no expression in the cytoplasm.
[ "6", "16", "18" ]
112
3,151
0
false
All the SUVR-GFP fusion proteins were exclusively localized to the nucleus, with no expression in the cytoplasm.
[]
All the SUVR-GFP fusion proteins were exclusively localized to the nucleus, with no expression in the cytoplasm.
true
true
true
true
true
530
2
DISCUSSION
1
6
[ "b6", "b16", "b18" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
SUVR1a and SUVR4a were almost exclusively found within the nucleolus, and only a weak GFP signal was detectable in the nucleoplasm, while SUVR2a was associated with the nucleolus and other subnuclear regions (Figure 2A–E).
[ "6", "16", "18" ]
222
3,152
0
false
SUVR1a and SUVR4a were almost exclusively found within the nucleolus, and only a weak GFP signal was detectable in the nucleoplasm, while SUVR2a was associated with the nucleolus and other subnuclear regions (Figure 2A–E).
[]
SUVR1a and SUVR4a were almost exclusively found within the nucleolus, and only a weak GFP signal was detectable in the nucleoplasm, while SUVR2a was associated with the nucleolus and other subnuclear regions (Figure 2A–E).
true
true
true
true
true
530
2
DISCUSSION
1
6
[ "b6", "b16", "b18" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
When expressed in the nucleoplasm, however, the SUVR-GFP signals were excluded from densely DAPI stained heterochromatin and localized to euchromatin.
[ "6", "16", "18" ]
150
3,153
0
false
When expressed in the nucleoplasm, however, the SUVR-GFP signals were excluded from densely DAPI stained heterochromatin and localized to euchromatin.
[]
When expressed in the nucleoplasm, however, the SUVR-GFP signals were excluded from densely DAPI stained heterochromatin and localized to euchromatin.
true
true
true
true
true
530
2
DISCUSSION
1
6
[ "b6", "b16", "b18" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
Altogether, the subnuclear localization to the nucleolus and weakly DAPI-stained subdomains suggest that the SUVR proteins are associated with rDNA and/or euchromatin.
[ "6", "16", "18" ]
167
3,154
0
false
Altogether, the subnuclear localization to the nucleolus and weakly DAPI-stained subdomains suggest that the SUVR proteins are associated with rDNA and/or euchromatin.
[]
Altogether, the subnuclear localization to the nucleolus and weakly DAPI-stained subdomains suggest that the SUVR proteins are associated with rDNA and/or euchromatin.
true
true
true
true
true
530
2
DISCUSSION
1
6
[ "b6", "b16", "b18" ]
17,020,925
pmid-9487389|pmid-11691919|pmid-12805620|pmid-11691919|pmid-12815071|pmid-12970192|pmid-12699618|pmid-16258034|NA|pmid-12067650|pmid-15014946|pmid-15775980
This is in contrast to many SU(VAR)3-9 class proteins that function as heterochromatic stabilizers at the chromocenters (6,16,18).
[ "6", "16", "18" ]
130
3,155
0
false
This is in contrast to many SU(VAR)3-9 class proteins that function as heterochromatic stabilizers at the chromocenters.
[ "6,16,18" ]
This is in contrast to many SU(VAR)3-9 class proteins that function as heterochromatic stabilizers at the chromocenters.
true
true
true
true
true
530
3
DISCUSSION
1
41
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
The primary function of the nucleolus is rDNA transcription, pre-rRNA processing and modification, and ribosome assembly (41,42).
[ "41", "42", "43", "9" ]
129
3,156
0
false
The primary function of the nucleolus is rDNA transcription, pre-rRNA processing and modification, and ribosome assembly.
[ "41,42" ]
The primary function of the nucleolus is rDNA transcription, pre-rRNA processing and modification, and ribosome assembly.
true
true
true
true
true
531
3
DISCUSSION
1
43
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
Moreover, the activity and availability of proteins involved in cell-cycle progression may be regulated by sequestration in the nucleolus (43).
[ "41", "42", "43", "9" ]
143
3,157
1
false
Moreover, the activity and availability of proteins involved in cell-cycle progression may be regulated by sequestration in the nucleolus.
[ "43" ]
Moreover, the activity and availability of proteins involved in cell-cycle progression may be regulated by sequestration in the nucleolus.
true
true
true
true
true
531
3
DISCUSSION
1
9
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
The SUVH genes of Arabidopsis, with the exception of SUVH4, are intronless, suggesting that they have evolved via retrotransposition (9).
[ "41", "42", "43", "9" ]
137
3,158
1
false
The SUVH genes of Arabidopsis, with the exception of SUVH4, are intronless, suggesting that they have evolved via retrotransposition.
[ "9" ]
The SUVH genes of Arabidopsis, with the exception of SUVH4, are intronless, suggesting that they have evolved via retrotransposition.
true
true
true
true
true
531
3
DISCUSSION
1
41
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
In contrast, the SUVR genes all have introns and alternative splicing results in formation of protein isoforms (Figure 1B and C) that may regulate subnuclear spatial distribution.
[ "41", "42", "43", "9" ]
179
3,159
0
false
In contrast, the SUVR genes all have introns and alternative splicing results in formation of protein isoforms (Figure 1B and C) that may regulate subnuclear spatial distribution.
[]
In contrast, the SUVR genes all have introns and alternative splicing results in formation of protein isoforms that may regulate subnuclear spatial distribution.
true
true
true
true
true
531
3
DISCUSSION
1
41
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
We have demonstrated that the extended N-terminus in SUVR1a compared to SUVR1b is responsible for localization of GFP-fusion proteins to the nucleolus (Figure 2A and B), and that 40 amino acid of this terminus encompassing the 17 amino acid NLS1 is sufficient for the nucleolar targeting (Figure 2F).
[ "41", "42", "43", "9" ]
300
3,160
0
false
We have demonstrated that the extended N-terminus in SUVR1a compared to SUVR1b is responsible for localization of GFP-fusion proteins to the nucleolus (Figure 2A and B), and that 40 amino acid of this terminus encompassing the 17 amino acid NLS1 is sufficient for the nucleolar targeting (Figure 2F).
[]
We have demonstrated that the extended N-terminus in SUVR1a compared to SUVR1b is responsible for localization of GFP-fusion proteins to the nucleolus (Figure 2A and B), and that 40 amino acid of this terminus encompassing the 17 amino acid NLS1 is sufficient for the nucleolar targeting (Figure 2F).
true
true
true
true
true
531
3
DISCUSSION
1
41
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
The SUVR4 C-terminus containing a predicted NLS similar to NLS1 of SUVR1a (Figure 3A), could also direct GFP to the nucleolus, although the GFP signal was also seen in the rest of the nucleus (Figure 2G).
[ "41", "42", "43", "9" ]
204
3,161
0
false
The SUVR4 C-terminus containing a predicted NLS similar to NLS1 of SUVR1a (Figure 3A), could also direct GFP to the nucleolus, although the GFP signal was also seen in the rest of the nucleus (Figure 2G).
[]
The SUVR4 C-terminus containing a predicted NLS similar to NLS1 of SUVR1a (Figure 3A), could also direct GFP to the nucleolus, although the GFP signal was also seen in the rest of the nucleus (Figure 2G).
true
true
true
true
true
531
3
DISCUSSION
1
41
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
Interestingly, the GFP signal of the SUVR4 NLS and the full-length SUVR4 was sometimes seen in a spot within or close to the nucleolus (Figure 2E and G).
[ "41", "42", "43", "9" ]
153
3,162
0
false
Interestingly, the GFP signal of the SUVR4 NLS and the full-length SUVR4 was sometimes seen in a spot within or close to the nucleolus (Figure 2E and G).
[]
Interestingly, the GFP signal of the SUVR4 NLS and the full-length SUVR4 was sometimes seen in a spot within or close to the nucleolus (Figure 2E and G).
true
true
true
true
true
531
3
DISCUSSION
1
41
[ "b41", "b42", "b43", "b9" ]
17,020,925
pmid-15014946|pmid-11898023|pmid-15775980|pmid-15014946|pmid-16582009|pmid-12034767|pmid-10754561|pmid-11063944|pmid-11691919
The nature of these spots as well as the subnuclear foci in the nucleoplasm observed for SUVR2 remains to be determined.
[ "41", "42", "43", "9" ]
120
3,163
0
false
The nature of these spots as well as the subnuclear foci in the nucleoplasm observed for SUVR2 remains to be determined.
[]
The nature of these spots as well as the subnuclear foci in the nucleoplasm observed for SUVR2 remains to be determined.
true
true
true
true
true
531
4
DISCUSSION
1
9
[ "b9", "b18", "b19", "b44", "b45" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
Alignment of the SET-domain sequences [Supplementary Figure 1 and (9)] show that the SUVR proteins are most closely related to G9a, SUVH2, SUVH6 and SUVH4 of the known HMTases.
[ "9", "18", "19", "44", "45" ]
176
3,164
0
false
Alignment of the SET-domain sequences show that the SUVR proteins are most closely related to G9a, SUVH2, SUVH6 and SUVH4 of the known HMTases.
[ "Supplementary Figure 1 and (9)" ]
Alignment of the SET-domain sequences show that the SUVR proteins are most closely related to G9a, SUVH2, SUVH6 and SUVH4 of the known HMTases.
true
true
true
true
true
532
4
DISCUSSION
1
9
[ "b9", "b18", "b19", "b44", "b45" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
These proteins methylate H3K9 and H3K27, H3K9 and H4K20 or H3K9, respectively (18,19,44).
[ "9", "18", "19", "44", "45" ]
89
3,165
0
false
These proteins methylate H3K9 and H3K27, H3K9 and H4K20 or H3K9, respectively.
[ "18,19,44" ]
These proteins methylate H3K9 and H3K27, H3K9 and H4K20 or H3K9, respectively.
true
true
true
true
true
532
4
DISCUSSION
1
9
[ "b9", "b18", "b19", "b44", "b45" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
We were not able to identify any in vitro HMTase activity for SUVR1 and SUVR2.
[ "9", "18", "19", "44", "45" ]
78
3,166
0
false
We were not able to identify any in vitro HMTase activity for SUVR1 and SUVR2.
[]
We were not able to identify any in vitro HMTase activity for SUVR1 and SUVR2.
true
true
true
true
true
532
4
DISCUSSION
1
9
[ "b9", "b18", "b19", "b44", "b45" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
This may reflect the need for a cofactor or for a particular molecular context of a presumptive target histone peptide, as demonstrated for the mammalian EED-EZH2 complex.
[ "9", "18", "19", "44", "45" ]
171
3,167
0
false
This may reflect the need for a cofactor or for a particular molecular context of a presumptive target histone peptide, as demonstrated for the mammalian EED-EZH2 complex.
[]
This may reflect the need for a cofactor or for a particular molecular context of a presumptive target histone peptide, as demonstrated for the mammalian EED-EZH2 complex.
true
true
true
true
true
532
4
DISCUSSION
1
45
[ "b9", "b18", "b19", "b44", "b45" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
H3K27 methylation by this complex requires a minimum of three components including EZH2, EED and SUZ12 (45).
[ "9", "18", "19", "44", "45" ]
108
3,168
1
false
H3K27 methylation by this complex requires a minimum of three components including EZH2, EED and SUZ12.
[ "45" ]
H3K27 methylation by this complex requires a minimum of three components including EZH2, EED and SUZ12.
true
true
true
true
true
532
4
DISCUSSION
1
9
[ "b9", "b18", "b19", "b44", "b45" ]
17,020,925
pmid-11691919|pmid-15775980|pmid-11691919|pmid-12805620|pmid-11691919|pmid-15775980|pmid-11898023|pmid-11316813|pmid-15225548
Therefore, we cannot exclude that the SUVR1 and SUVR2 proteins may function as HMTases in vivo at the nucleolar/euchromatic sites specified by our GFP data.
[ "9", "18", "19", "44", "45" ]
156
3,169
0
false
Therefore, we cannot exclude that the SUVR1 and SUVR2 proteins may function as HMTases in vivo at the nucleolar/euchromatic sites specified by our GFP data.
[]
Therefore, we cannot exclude that the SUVR1 and SUVR2 proteins may function as HMTases in vivo at the nucleolar/euchromatic sites specified by our GFP data.
true
true
true
true
true
532
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
We have, however, demonstrated that at least SUVR4 acts on H3K9.
[ "16", "20", "35", "46", "28", "20", "28" ]
64
3,170
0
false
We have, however, demonstrated that at least SUVR4 acts on H3K9.
[]
We have, however, demonstrated that at least SUVR4 acts on H3K9.
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
In vitro SUVR4 has a novel specificity, in that it acts as an efficient dimethyltransferase specifically adding the second methyl group to monomethylated H3K9 (Figure 4C and D), but not to monomethylated H3K27 (Supplementary Figure 2A).
[ "16", "20", "35", "46", "28", "20", "28" ]
236
3,171
0
false
In vitro SUVR4 has a novel specificity, in that it acts as an efficient dimethyltransferase specifically adding the second methyl group to monomethylated H3K9 (Figure 4C and D), but not to monomethylated H3K27 (Supplementary Figure 2A).
[]
In vitro SUVR4 has a novel specificity, in that it acts as an efficient dimethyltransferase specifically adding the second methyl group to monomethylated H3K9 (Figure 4C and D), but not to monomethylated H3K27 (Supplementary Figure 2A).
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
Only very weak HMTase activity was seen when unmethylated H3 protein or tail peptides were used as substrates.
[ "16", "20", "35", "46", "28", "20", "28" ]
110
3,172
0
false
Only very weak HMTase activity was seen when unmethylated H3 protein or tail peptides were used as substrates.
[]
Only very weak HMTase activity was seen when unmethylated H3 protein or tail peptides were used as substrates.
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
Other known HMTases, e.g.
[ "16", "20", "35", "46", "28", "20", "28" ]
25
3,173
0
false
Other known HMTases, e.g.
[]
Other known HMTases, e.g.
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
SUVH4, SUVH5 and SUVH6, are in contrast very efficient monomethyltransferases but moderately efficient dimethyltransferases in vitro (16,20).
[ "16", "20", "35", "46", "28", "20", "28" ]
141
3,174
0
false
SUVH4, SUVH5 and SUVH6, are in contrast very efficient monomethyltransferases but moderately efficient dimethyltransferases in vitro.
[ "16,20" ]
SUVH4, SUVH5 and SUVH6, are in contrast very efficient monomethyltransferases but moderately efficient dimethyltransferases in vitro.
true
true
true
true
true
533
5
DISCUSSION
1
35
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
These proteins have a tyrosine (Y) in position 4 of SET motif IV (ELx[FYW]DY) (35), while the SUVR proteins have a tryptophan (W) (arrowhead in Figure 1C) like the SETDB1/ESET protein, which is a di/tri HMTase (46).
[ "16", "20", "35", "46", "28", "20", "28" ]
215
3,175
1
false
These proteins have a tyrosine (Y) in position 4 of SET motif IV (ELx[FYW]DY), while the SUVR proteins have a tryptophan (W) (arrowhead in Figure 1C) like the SETDB1/ESET protein, which is a di/tri HMTase.
[ "35", "46" ]
These proteins have a tyrosine (Y) in position 4 of SET motif IV (ELx[FYW]DY), while the SUVR proteins have a tryptophan (W) (arrowhead in Figure 1C) like the SETDB1/ESET protein, which is a di/tri HMTase.
true
true
true
true
true
533
5
DISCUSSION
1
28
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
The DIM-5 of Neurospora crassa and human G9a that have phenylalanine (F) in this position can add three methyl groups to unmethylated H3K9 (28).
[ "16", "20", "35", "46", "28", "20", "28" ]
144
3,176
1
false
The DIM-5 of Neurospora crassa and human G9a that have phenylalanine (F) in this position can add three methyl groups to unmethylated H3K9.
[ "28" ]
The DIM-5 of Neurospora crassa and human G9a that have phenylalanine (F) in this position can add three methyl groups to unmethylated H3K9.
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
However, conversion of the SUVR4 tryptophan to either tyrosine or phenylalanine both resulted in total loss of HMTase activity.
[ "16", "20", "35", "46", "28", "20", "28" ]
127
3,177
0
false
However, conversion of the SUVR4 tryptophan to either tyrosine or phenylalanine both resulted in total loss of HMTase activity.
[]
However, conversion of the SUVR4 tryptophan to either tyrosine or phenylalanine both resulted in total loss of HMTase activity.
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
In contrast, conversions from phenylalanine to tyrosine or vice versa in other SET-domain proteins only change the product specificity (20,28).
[ "16", "20", "35", "46", "28", "20", "28" ]
143
3,178
0
false
In contrast, conversions from phenylalanine to tyrosine or vice versa in other SET-domain proteins only change the product specificity.
[ "20,28" ]
In contrast, conversions from phenylalanine to tyrosine or vice versa in other SET-domain proteins only change the product specificity.
true
true
true
true
true
533
5
DISCUSSION
1
16
[ "b16", "b20", "b35", "b46", "b28", "b20", "b28" ]
17,020,925
pmid-15014946|pmid-16582009|pmid-15869391|pmid-14536086|pmid-15590646|pmid-16582009|pmid-15590646
Possibly, other particularities in the SUVR4 SET domain, for instance the amino acid DAN instead of PLN close to the important NH[RSH]C motif (Figure 1C) may impose a 3D conformation that is incompatible with substrate binding or methyl transfer when the W is exchanged with Y or F.
[ "16", "20", "35", "46", "28", "20", "28" ]
282
3,179
0
false
Possibly, other particularities in the SUVR4 SET domain, for instance the amino acid DAN instead of PLN close to the important NH[RSH]C motif (Figure 1C) may impose a 3D conformation that is incompatible with substrate binding or methyl transfer when the W is exchanged with Y or F.
[]
Possibly, other particularities in the SUVR4 SET domain, for instance the amino acid DAN instead of PLN close to the important NH[RSH]C motif may impose a 3D conformation that is incompatible with substrate binding or methyl transfer when the W is exchanged with Y or F.
true
true
true
true
true
533
6
DISCUSSION
1
3
[ "b3", "b20" ]
17,020,925
pmid-12648673|pmid-16582009
SUVR4 was able to bind both core and recombinant histone H3 in vitro (Figure 5) indicating that the binding to the histone substrate itself is independent of posttranslational modifications.
[ "3", "20" ]
190
3,180
0
false
SUVR4 was able to bind both core and recombinant histone H3 in vitro (Figure 5) indicating that the binding to the histone substrate itself is independent of posttranslational modifications.
[]
SUVR4 was able to bind both core and recombinant histone H3 in vitro (Figure 5) indicating that the binding to the histone substrate itself is independent of posttranslational modifications.
true
true
true
true
true
534
6
DISCUSSION
1
3
[ "b3", "b20" ]
17,020,925
pmid-12648673|pmid-16582009
The monomethylation at H3K9 thus seems to be important for the methyltransferase activity of SUVR4, but not for substrate binding.
[ "3", "20" ]
130
3,181
0
false
The monomethylation at H3K9 thus seems to be important for the methyltransferase activity of SUVR4, but not for substrate binding.
[]
The monomethylation at H3K9 thus seems to be important for the methyltransferase activity of SUVR4, but not for substrate binding.
true
true
true
true
true
534
6
DISCUSSION
1
3
[ "b3", "b20" ]
17,020,925
pmid-12648673|pmid-16582009
Thus, binding to histone H3 and HMTase activity may be separate functions of the same protein.
[ "3", "20" ]
94
3,182
0
false
Thus, binding to histone H3 and HMTase activity may be separate functions of the same protein.
[]
Thus, binding to histone H3 and HMTase activity may be separate functions of the same protein.
true
true
true
true
true
534
6
DISCUSSION
1
3
[ "b3", "b20" ]
17,020,925
pmid-12648673|pmid-16582009
If SUVR4 HMTase activity is dependent on a monomethylated histone H3 at position K9 in vivo, this suggests that SUVR4 is reliant on the cooperative action of another monomethyltransferase.
[ "3", "20" ]
188
3,183
0
false
If SUVR4 HMTase activity is dependent on a monomethylated histone H3 at position K9 in vivo, this suggests that SUVR4 is reliant on the cooperative action of another monomethyltransferase.
[]
If SUVR4 HMTase activity is dependent on a monomethylated histone H3 at position K9 in vivo, this suggests that SUVR4 is reliant on the cooperative action of another monomethyltransferase.
true
true
true
true
true
534
6
DISCUSSION
1
3
[ "b3", "b20" ]
17,020,925
pmid-12648673|pmid-16582009
Several examples of interdependency of posttranslational modifications have been reported [reviewed in (3)].
[ "3", "20" ]
108
3,184
0
false
Several examples of interdependency of posttranslational modifications have been reported.
[ "reviewed in (3)" ]
Several examples of interdependency of posttranslational modifications have been reported.
true
true
true
true
true
534
6
DISCUSSION
1
20
[ "b3", "b20" ]
17,020,925
pmid-12648673|pmid-16582009
Furthermore, recent data shows that the DNA-methylating activity of CMT3 is regulated by the combined activity of three HMTases (20).
[ "3", "20" ]
133
3,185
1
false
Furthermore, recent data shows that the DNA-methylating activity of CMT3 is regulated by the combined activity of three HMTases.
[ "20" ]
Furthermore, recent data shows that the DNA-methylating activity of CMT3 is regulated by the combined activity of three HMTases.
true
true
true
true
true
534
7
DISCUSSION
1
18
[ "b18", "b20", "b47", "b48", "b49" ]
17,020,925
pmid-15775980|pmid-16582009|pmid-12130538|pmid-15753565|pmid-14992728
All available data for the SUVH proteins show that these HMTases associate with heterochromatin and are involved in heterochromatic gene silencing (18–20).
[ "18", "20", "47", "48", "49" ]
155
3,186
0
false
All available data for the SUVH proteins show that these HMTases associate with heterochromatin and are involved in heterochromatic gene silencing.
[ "18–20" ]
All available data for the SUVH proteins show that these HMTases associate with heterochromatin and are involved in heterochromatic gene silencing.
true
true
true
true
true
535
7
DISCUSSION
1
18
[ "b18", "b20", "b47", "b48", "b49" ]
17,020,925
pmid-15775980|pmid-16582009|pmid-12130538|pmid-15753565|pmid-14992728
In contrast, the localization of the SUVR proteins to the nucleolus or non-condensed nuclear bodies suggests that these proteins are not involved in heterochromatic gene silencing.
[ "18", "20", "47", "48", "49" ]
180
3,187
0
false
In contrast, the localization of the SUVR proteins to the nucleolus or non-condensed nuclear bodies suggests that these proteins are not involved in heterochromatic gene silencing.
[]
In contrast, the localization of the SUVR proteins to the nucleolus or non-condensed nuclear bodies suggests that these proteins are not involved in heterochromatic gene silencing.
true
true
true
true
true
535
7
DISCUSSION
1
47
[ "b18", "b20", "b47", "b48", "b49" ]
17,020,925
pmid-15775980|pmid-16582009|pmid-12130538|pmid-15753565|pmid-14992728
This is also suggested by the close sequence similarity of the SUVR proteins to the G9a HMTase, which function as a repressor in euchromatin (47).
[ "18", "20", "47", "48", "49" ]
146
3,188
1
false
This is also suggested by the close sequence similarity of the SUVR proteins to the G9a HMTase, which function as a repressor in euchromatin.
[ "47" ]
This is also suggested by the close sequence similarity of the SUVR proteins to the G9a HMTase, which function as a repressor in euchromatin.
true
true
true
true
true
535
7
DISCUSSION
1
18
[ "b18", "b20", "b47", "b48", "b49" ]
17,020,925
pmid-15775980|pmid-16582009|pmid-12130538|pmid-15753565|pmid-14992728
Similarly, the SUVR proteins may function as regulators in euchromatin or in the nucleolus.
[ "18", "20", "47", "48", "49" ]
91
3,189
0
false
Similarly, the SUVR proteins may function as regulators in euchromatin or in the nucleolus.
[]
Similarly, the SUVR proteins may function as regulators in euchromatin or in the nucleolus.
true
true
true
true
true
535
7
DISCUSSION
1
48
[ "b18", "b20", "b47", "b48", "b49" ]
17,020,925
pmid-15775980|pmid-16582009|pmid-12130538|pmid-15753565|pmid-14992728
Although the rDNA is mainly decondensed in the nucleolus, untranscribed foci of condensed rDNA may also be found inside the nucleolus (48).
[ "18", "20", "47", "48", "49" ]
139
3,190
1
false
Although the rDNA is mainly decondensed in the nucleolus, untranscribed foci of condensed rDNA may also be found inside the nucleolus.
[ "48" ]
Although the rDNA is mainly decondensed in the nucleolus, untranscribed foci of condensed rDNA may also be found inside the nucleolus.
true
true
true
true
true
535
7
DISCUSSION
1
49
[ "b18", "b20", "b47", "b48", "b49" ]
17,020,925
pmid-15775980|pmid-16582009|pmid-12130538|pmid-15753565|pmid-14992728
Based on the specific dimethylation of H3K9 in vitro, which is a marker of repressive chromatin domains, we suggest that SUVR4 may function as a repressor of rDNA gene clusters in the decondensed part of the nucleolus, and possibly act to regulate rDNA expression together with HDACs also present in this compartment (49...
[ "18", "20", "47", "48", "49" ]
322
3,191
1
false
Based on the specific dimethylation of H3K9 in vitro, which is a marker of repressive chromatin domains, we suggest that SUVR4 may function as a repressor of rDNA gene clusters in the decondensed part of the nucleolus, and possibly act to regulate rDNA expression together with HDACs also present in this compartment.
[ "49" ]
Based on the specific dimethylation of H3K9 in vitro, which is a marker of repressive chromatin domains, we suggest that SUVR4 may function as a repressor of rDNA gene clusters in the decondensed part of the nucleolus, and possibly act to regulate rDNA expression together with HDACs also present in this compartment.
true
true
true
true
true
535
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,966,337
pmid-15513989|pmid-10195282
Recent advances in large-scale genome sequencing have resulted in the huge accumulation of protein amino acid sequences (1).
[ "1", "2" ]
124
3,192
1
false
Recent advances in large-scale genome sequencing have resulted in the huge accumulation of protein amino acid sequences.
[ "1" ]
Recent advances in large-scale genome sequencing have resulted in the huge accumulation of protein amino acid sequences.
true
true
true
true
true
536
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,966,337
pmid-15513989|pmid-10195282
Currently, many researchers are trying either to discover or to clarify the unknown functions of these proteins.
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Currently, many researchers are trying either to discover or to clarify the unknown functions of these proteins.
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Currently, many researchers are trying either to discover or to clarify the unknown functions of these proteins.
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Since knowing the subcellular localization where a protein resides can give important insight into its possible functions (2), it is indispensable to identify the subcellular localization of a protein.
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Since knowing the subcellular localization where a protein resides can give important insight into its possible functions, it is indispensable to identify the subcellular localization of a protein.
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Since knowing the subcellular localization where a protein resides can give important insight into its possible functions, it is indispensable to identify the subcellular localization of a protein.
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INTRODUCTION
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However, it is time consuming and costly to identify the subcellular localizations of newly found proteins entirely by performing experimental tests.
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However, it is time consuming and costly to identify the subcellular localizations of newly found proteins entirely by performing experimental tests.
[]
However, it is time consuming and costly to identify the subcellular localizations of newly found proteins entirely by performing experimental tests.
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Thus, a reliable and efficient computational method is highly required to directly extract localization information.
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Thus, a reliable and efficient computational method is highly required to directly extract localization information.
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Thus, a reliable and efficient computational method is highly required to directly extract localization information.
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INTRODUCTION
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From a machine learning point of view, a task that predicts the subcellular localizations of given proteins has several characteristics which demonstrate the task's complexity (see Table 1).
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From a machine learning point of view, a task that predicts the subcellular localizations of given proteins has several characteristics which demonstrate the task's complexity.
[ "see Table 1" ]
From a machine learning point of view, a task that predicts the subcellular localizations of given proteins has several characteristics which demonstrate the task's complexity.
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First, there are too many localizations in a cell.
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First, there are too many localizations in a cell.
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First, there are too many localizations in a cell.
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INTRODUCTION
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For example, according to the work of Huh et al.
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For example, according to the work of Huh et al.
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For example, according to the work of Huh et al.
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