Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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2
INTRODUCTION
1
1
[ "b1", "b5", "b8" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
In this paper, we show that intron in the human pre-tRNA(CAA)Leu is indispensable for the C5-methylation of cytosine in the first position of the anticodon.
[ "1", "5", "8" ]
156
1,400
0
false
In this paper, we show that intron in the human pre-tRNA(CAA)Leu is indispensable for the C5-methylation of cytosine in the first position of the anticodon.
[]
In this paper, we show that intron in the human pre-tRNA(CAA)Leu is indispensable for the C5-methylation of cytosine in the first position of the anticodon.
true
true
true
true
true
242
2
INTRODUCTION
1
1
[ "b1", "b5", "b8" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
We also show that the modification of C34 depends on the nucleotide sequence surrounding the position to be modified and on the structure of intron-containing prolongated anticodon stem.
[ "1", "5", "8" ]
186
1,401
0
false
We also show that the modification of C34 depends on the nucleotide sequence surrounding the position to be modified and on the structure of intron-containing prolongated anticodon stem.
[]
We also show that the modification of C34 depends on the nucleotide sequence surrounding the position to be modified and on the structure of intron-containing prolongated anticodon stem.
true
true
true
true
true
242
3
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
Enzymes that introduce Ψ35 and m5C34 in the intron-containing pre-tRNATyr and pre-tRNALeu, respectively, have been identified in yeast (9,10).
[ "9", "10", "11", "12" ]
142
1,402
0
false
Enzymes that introduce Ψ35 and m5C34 in the intron-containing pre-tRNATyr and pre-tRNALeu, respectively, have been identified in yeast.
[ "9,10" ]
Enzymes that introduce Ψ35 and m5C34 in the intron-containing pre-tRNATyr and pre-tRNALeu, respectively, have been identified in yeast.
true
true
true
true
true
243
3
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
However, our knowledge about the corresponding enzymes in multicellular eukaryotes remains obscure.
[ "9", "10", "11", "12" ]
99
1,403
0
false
However, our knowledge about the corresponding enzymes in multicellular eukaryotes remains obscure.
[]
However, our knowledge about the corresponding enzymes in multicellular eukaryotes remains obscure.
true
true
true
true
true
243
3
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
The first human m5C methylase Dnmt2 has been reported very recently and is responsible for the modification of C38 in tRNAAsp in mice, Drosophila melanogaster and Arabidopsis thaliana.
[ "9", "10", "11", "12" ]
184
1,404
0
false
The first human m5C methylase Dnmt2 has been reported very recently and is responsible for the modification of C38 in tRNAAsp in mice, Drosophila melanogaster and Arabidopsis thaliana.
[]
The first human m5C methylase Dnmt2 has been reported very recently and is responsible for the modification of C38 in tRNAAsp in mice, Drosophila melanogaster and Arabidopsis thaliana.
true
true
true
true
true
243
3
INTRODUCTION
1
11
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
This MTase was found to be localized in cytoplasm and acts at the level of a mature tRNA molecule (11).
[ "9", "10", "11", "12" ]
103
1,405
1
false
This MTase was found to be localized in cytoplasm and acts at the level of a mature tRNA molecule.
[ "11" ]
This MTase was found to be localized in cytoplasm and acts at the level of a mature tRNA molecule.
true
true
true
true
true
243
3
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
Here, we present the characterization of a human gene encoding a methyltransferase (MTase) that is involved in the formation of m5C34 in tRNA(CAA)Leu.
[ "9", "10", "11", "12" ]
150
1,406
0
false
Here, we present the characterization of a human gene encoding a methyltransferase (MTase) that is involved in the formation of m5C34 in tRNA(CAA)Leu.
[]
Here, we present the characterization of a human gene encoding a methyltransferase (MTase) that is involved in the formation of m5C34 in tRNA(CAA)Leu.
true
true
true
true
true
243
3
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
The product of the gene, hTrm4, acts at the level of the intron-containing tRNA precursor and is localized in the nucleoplasm and nucleolus.
[ "9", "10", "11", "12" ]
140
1,407
0
false
The product of the gene, hTrm4, acts at the level of the intron-containing tRNA precursor and is localized in the nucleoplasm and nucleolus.
[]
The product of the gene, hTrm4, acts at the level of the intron-containing tRNA precursor and is localized in the nucleoplasm and nucleolus.
true
true
true
true
true
243
3
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
During the preparation of this paper, it was found that this MTase is a novel downstream Myc-target which mediates Myc-induced cell proliferation and growth.
[ "9", "10", "11", "12" ]
157
1,408
0
false
During the preparation of this paper, it was found that this MTase is a novel downstream Myc-target which mediates Myc-induced cell proliferation and growth.
[]
During the preparation of this paper, it was found that this MTase is a novel downstream Myc-target which mediates Myc-induced cell proliferation and growth.
true
true
true
true
true
243
3
INTRODUCTION
1
12
[ "b9", "b10", "b11", "b12" ]
17,071,714
pmid-14561887|pmid-10445884|pmid-16424344|pmid-16713953
Therefore, the characterization of hTrm4 substrate specificity can be essential since this MTase is a potential target for cancer therapies (12).
[ "9", "10", "11", "12" ]
145
1,409
1
false
Therefore, the characterization of hTrm4 substrate specificity can be essential since this MTase is a potential target for cancer therapies.
[ "12" ]
Therefore, the characterization of hTrm4 substrate specificity can be essential since this MTase is a potential target for cancer therapies.
true
true
true
true
true
243
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
In this article, we describe the identification, cloning and enzyme activity of the corresponding gene product encoding human Trm4 enzyme.
[ "24", "27", "12" ]
138
1,410
0
false
In this article, we describe the identification, cloning and enzyme activity of the corresponding gene product encoding human Trm4 enzyme.
[]
In this article, we describe the identification, cloning and enzyme activity of the corresponding gene product encoding human Trm4 enzyme.
true
true
true
true
true
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
This is the first report showing intron-dependent methylation of human pre-tRNA(CAA)Leu and identification of human gene encoding tRNA methylase responsible for this reaction.
[ "24", "27", "12" ]
175
1,411
0
false
This is the first report showing intron-dependent methylation of human pre-tRNA(CAA)Leu and identification of human gene encoding tRNA methylase responsible for this reaction.
[]
This is the first report showing intron-dependent methylation of human pre-tRNA(CAA)Leu and identification of human gene encoding tRNA methylase responsible for this reaction.
true
true
true
true
true
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
The hTRM4 gene was identified on the basis of its amino acid sequence similarity to a known Trm4p MTase from yeast.
[ "24", "27", "12" ]
115
1,412
0
false
The hTRM4 gene was identified on the basis of its amino acid sequence similarity to a known Trm4p MTase from yeast.
[]
The hTRM4 gene was identified on the basis of its amino acid sequence similarity to a known Trm4p MTase from yeast.
true
true
true
true
true
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
Our studies provide experimental validation of the phylogenetic analysis of RNA:m5C MTases by Bujnicki et al.
[ "24", "27", "12" ]
109
1,413
0
false
Our studies provide experimental validation of the phylogenetic analysis of RNA:m5C MTases by Bujnicki et al.
[]
Our studies provide experimental validation of the phylogenetic analysis of RNA:m5C MTases by Bujnicki et al.
true
true
true
true
true
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
who predicted the product of the NSUN2 gene as the closest human homologue of yeast Trm4p (24).
[ "24", "27", "12" ]
95
1,414
1
false
who predicted the product of the NSUN2 gene as the closest human homologue of yeast Trm4p.
[ "24" ]
who predicted the product of the NSUN2 gene as the closest human homologue of yeast Trm4p.
false
true
true
true
false
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
hTRM4 is a single-copy gene, located on the human chromosome 5, with the precise position 5p15.31.
[ "24", "27", "12" ]
98
1,415
0
false
hTRM4 is a single-copy gene, located on the human chromosome 5, with the precise position 5p15.31.
[]
hTRM4 is a single-copy gene, located on the human chromosome 5, with the precise position 5p15.31.
false
true
true
true
false
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
The hTrm4 protein is a member of an evolutionarily conserved family, which includes genuine and putative RNA:m5C MTases from all three domains of life, such as the human nucleolar proliferation-associated antigen p120 (NOL1) and its homologues.
[ "24", "27", "12" ]
244
1,416
0
false
The hTrm4 protein is a member of an evolutionarily conserved family, which includes genuine and putative RNA:m5C MTases from all three domains of life, such as the human nucleolar proliferation-associated antigen p120 (NOL1) and its homologues.
[]
The hTrm4 protein is a member of an evolutionarily conserved family, which includes genuine and putative RNA:m5C MTases from all three domains of life, such as the human nucleolar proliferation-associated antigen p120 (NOL1) and its homologues.
true
true
true
true
true
244
0
DISCUSSION
1
27
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
(27) reported that the yeast Trm4p was found to be localized in the nucleus, including the nucleolus, and was concentrated at the nuclear periphery.
[ "24", "27", "12" ]
148
1,417
1
false
reported that the yeast Trm4p was found to be localized in the nucleus, including the nucleolus, and was concentrated at the nuclear periphery.
[ "27" ]
reported that the yeast Trm4p was found to be localized in the nucleus, including the nucleolus, and was concentrated at the nuclear periphery.
false
true
true
true
false
244
0
DISCUSSION
1
24
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
Our experiments have shown that its human homologue hTrm4 is always localized in the nucleoplasm and in nucleoli of HeLa cells, and in several cases we also observed a concentration of hTrm4 at the nuclear periphery (data not shown).
[ "24", "27", "12" ]
233
1,418
0
false
Our experiments have shown that its human homologue hTrm4 is always localized in the nucleoplasm and in nucleoli of HeLa cells, and in several cases we also observed a concentration of hTrm4 at the nuclear periphery (data not shown).
[]
Our experiments have shown that its human homologue hTrm4 is always localized in the nucleoplasm and in nucleoli of HeLa cells, and in several cases we also observed a concentration of hTrm4 at the nuclear periphery (data not shown).
true
true
true
true
true
244
0
DISCUSSION
1
12
[ "b24", "b27", "b12" ]
17,071,714
pmid-15121902|pmid-9767141|pmid-16713953
These data have been recently confirmed by Frye and Watt (12).
[ "24", "27", "12" ]
62
1,419
1
false
These data have been recently confirmed by Frye and Watt.
[ "12" ]
These data have been recently confirmed by Frye and Watt.
true
true
true
true
true
244
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
The presence of an intron is required for the m5C34 formation in human pre-tRNA(CAA)Leu as demonstrated in this paper by the maturation of intron-less and intron-containing tRNA precursor in HeLa cell-free nuclear extract.
[ "21", "21", "28", "5", "10" ]
222
1,420
0
false
The presence of an intron is required for the m5C34 formation in human pre-tRNA(CAA)Leu as demonstrated in this paper by the maturation of intron-less and intron-containing tRNA precursor in HeLa cell-free nuclear extract.
[]
The presence of an intron is required for the m5C34 formation in human pre-tRNA(CAA)Leu as demonstrated in this paper by the maturation of intron-less and intron-containing tRNA precursor in HeLa cell-free nuclear extract.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
In earlier studies, Harada et al.
[ "21", "21", "28", "5", "10" ]
33
1,421
0
false
In earlier studies, Harada et al.
[]
In earlier studies, Harada et al.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
(21) showed that this position in the mature human tRNA(CAA)Leu is occupied by a hypermodified derivative.
[ "21", "21", "28", "5", "10" ]
106
1,422
1
false
showed that this position in the mature human tRNA(CAA)Leu is occupied by a hypermodified derivative.
[ "21" ]
showed that this position in the mature human tRNA(CAA)Leu is occupied by a hypermodified derivative.
false
true
true
true
false
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
The authors suggest that this is a 2′-O-methylated and further hypermodified cytidine derivative (21).
[ "21", "21", "28", "5", "10" ]
102
1,423
1
false
The authors suggest that this is a 2′-O-methylated and further hypermodified cytidine derivative.
[ "21" ]
The authors suggest that this is a 2′-O-methylated and further hypermodified cytidine derivative.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
Very similar results were obtained by Randerath et al.
[ "21", "21", "28", "5", "10" ]
54
1,424
0
false
Very similar results were obtained by Randerath et al.
[]
Very similar results were obtained by Randerath et al.
true
true
true
true
true
245
1
DISCUSSION
1
28
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
(28) when leucine tRNAs were isolated and sequenced from rat tumour, Morris hepatoma 5123D cells.
[ "21", "21", "28", "5", "10" ]
97
1,425
1
false
when leucine tRNAs were isolated and sequenced from rat tumour, Morris hepatoma 5123D cells.
[ "28" ]
when leucine tRNAs were isolated and sequenced from rat tumour, Morris hepatoma 5123D cells.
false
true
true
true
false
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
Our studies show that the first stage of C34 modification process in HeLa cells is the m5C34 formation.
[ "21", "21", "28", "5", "10" ]
103
1,426
0
false
Our studies show that the first stage of C34 modification process in HeLa cells is the m5C34 formation.
[]
Our studies show that the first stage of C34 modification process in HeLa cells is the m5C34 formation.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
However, the final chemical structure of this modification remains to be characterized.
[ "21", "21", "28", "5", "10" ]
87
1,427
0
false
However, the final chemical structure of this modification remains to be characterized.
[]
However, the final chemical structure of this modification remains to be characterized.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
In addition to intron-dependent m5C34 formation, we have shown that the activity of hTrm4 strictly depends on a specific sequence surrounding the cytosine to be modified and on the intron structure.
[ "21", "21", "28", "5", "10" ]
198
1,428
0
false
In addition to intron-dependent m5C34 formation, we have shown that the activity of hTrm4 strictly depends on a specific sequence surrounding the cytosine to be modified and on the intron structure.
[]
In addition to intron-dependent m5C34 formation, we have shown that the activity of hTrm4 strictly depends on a specific sequence surrounding the cytosine to be modified and on the intron structure.
true
true
true
true
true
245
1
DISCUSSION
1
5
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
Similar results were obtained studying the yeast Trm4p enzyme by Storbel and Abelson (5).
[ "21", "21", "28", "5", "10" ]
89
1,429
1
false
Similar results were obtained studying the yeast Trm4p enzyme by Storbel and Abelson.
[ "5" ]
Similar results were obtained studying the yeast Trm4p enzyme by Storbel and Abelson.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
However, our experiments have shown that minisubstrate composed of the anticodon stem–loop extended by the intron was not methylated at C34.
[ "21", "21", "28", "5", "10" ]
140
1,430
0
false
However, our experiments have shown that minisubstrate composed of the anticodon stem–loop extended by the intron was not methylated at C34.
[]
However, our experiments have shown that minisubstrate composed of the anticodon stem–loop extended by the intron was not methylated at C34.
true
true
true
true
true
245
1
DISCUSSION
1
10
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
In contrast, Motorin and Grosjean (10) presented data that analogous minihelix of yeast tRNA(CAA)Leu was an efficient substrate for tRNA:m5C-methyltransferase.
[ "21", "21", "28", "5", "10" ]
159
1,431
1
false
In contrast, Motorin and Grosjean presented data that analogous minihelix of yeast tRNA(CAA)Leu was an efficient substrate for tRNA:m5C-methyltransferase.
[ "10" ]
In contrast, Motorin and Grosjean presented data that analogous minihelix of yeast tRNA(CAA)Leu was an efficient substrate for tRNA:m5C-methyltransferase.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
These results imply that there are differences in the ability of enzyme–substrate recognition between the human and fungi Trm4 enzymes.
[ "21", "21", "28", "5", "10" ]
135
1,432
0
false
These results imply that there are differences in the ability of enzyme–substrate recognition between the human and fungi Trm4 enzymes.
[]
These results imply that there are differences in the ability of enzyme–substrate recognition between the human and fungi Trm4 enzymes.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
The nucleotide sequence that surrounds C34 in human tRNA precursor is more restrictive for m5C34 formation than in the case of yeast.
[ "21", "21", "28", "5", "10" ]
133
1,433
0
false
The nucleotide sequence that surrounds C34 in human tRNA precursor is more restrictive for m5C34 formation than in the case of yeast.
[]
The nucleotide sequence that surrounds C34 in human tRNA precursor is more restrictive for m5C34 formation than in the case of yeast.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
The substitution of adenosine from the middle position of the anticodon to uridine did not promote m5C34 formation in human tRNA precursor while in the case of yeast amber leucine-inserting pre-tRNA containing intron (anticodon CUA), m5C34 was formed.
[ "21", "21", "28", "5", "10" ]
251
1,434
0
false
The substitution of adenosine from the middle position of the anticodon to uridine did not promote m5C34 formation in human tRNA precursor while in the case of yeast amber leucine-inserting pre-tRNA containing intron (anticodon CUA), m5C34 was formed.
[]
The substitution of adenosine from the middle position of the anticodon to uridine did not promote m5C34 formation in human tRNA precursor while in the case of yeast amber leucine-inserting pre-tRNA containing intron (anticodon CUA), m5C34 was formed.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
Additionally, our experiments have shown that the reversion of base pair A35–Ui11 to U35–Ai11 also resulted in the m5C34 deficient pre-tRNA(CAA)Leu.
[ "21", "21", "28", "5", "10" ]
148
1,435
0
false
Additionally, our experiments have shown that the reversion of base pair A35–Ui11 to U35–Ai11 also resulted in the m5C34 deficient pre-tRNA(CAA)Leu.
[]
Additionally, our experiments have shown that the reversion of base pair A35–Ui11 to U35–Ai11 also resulted in the m5C34 deficient pre-tRNA(CAA)Leu.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
Moreover, human MTase responsible for the introduction of methyl group at the anticodon wooble cytosine (hTrm4) requires a consensus nucleotide sequence C/A/U32-U/A33-C34-A35-A36-G37 as a prerequisite for m5C34 formation.
[ "21", "21", "28", "5", "10" ]
221
1,436
0
false
Moreover, human MTase responsible for the introduction of methyl group at the anticodon wooble cytosine (hTrm4) requires a consensus nucleotide sequence C/A/U32-U/A33-C34-A35-A36-G37 as a prerequisite for m5C34 formation.
[]
Moreover, human MTase responsible for the introduction of methyl group at the anticodon wooble cytosine (hTrm4) requires a consensus nucleotide sequence C/A/U32-U/A33-C34-A35-A36-G37 as a prerequisite for m5C34 formation.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
Thus, all nucleotides from the anticodon loop that are present upstream from the intron sequence are essential for pre-tRNALeu modification.
[ "21", "21", "28", "5", "10" ]
140
1,437
0
false
Thus, all nucleotides from the anticodon loop that are present upstream from the intron sequence are essential for pre-tRNALeu modification.
[]
Thus, all nucleotides from the anticodon loop that are present upstream from the intron sequence are essential for pre-tRNALeu modification.
true
true
true
true
true
245
1
DISCUSSION
1
21
[ "b21", "b21", "b28", "b5", "b10" ]
17,071,714
pmid-6339954|pmid-3357766|pmid-1582418|pmid-3537724|NA|pmid-9869432|pmid-3537724|pmid-6514577|pmid-6514577|pmid-6773543|pmid-3537724|pmid-10445884
These results again strengthen the conclusion about the differences in the ability of enzyme–substrate recognition between human and yeast Trm4 enzymes.
[ "21", "21", "28", "5", "10" ]
152
1,438
0
false
These results again strengthen the conclusion about the differences in the ability of enzyme–substrate recognition between human and yeast Trm4 enzymes.
[]
These results again strengthen the conclusion about the differences in the ability of enzyme–substrate recognition between human and yeast Trm4 enzymes.
true
true
true
true
true
245
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
Motorin and Grosjean showed (10) that the yeast Trm4p enzyme catalysed m5C formation at four distinct sites in different tRNAs: 34, 40, 48 and 49.
[ "10", "24" ]
146
1,439
1
false
Motorin and Grosjean showed that the yeast Trm4p enzyme catalysed m5C formation at four distinct sites in different tRNAs: 34, 40, 48 and 49.
[ "10" ]
Motorin and Grosjean showed that the yeast Trm4p enzyme catalysed m5C formation at four distinct sites in different tRNAs: 34, 40, 48 and 49.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
m5C was found at positions 34 and 40 only in two yeast tRNAs [tRNA(CUA)Leu (Sup53) and tRNA(GAA)Phe, respectively], whereas most elongator tRNAs bore either m5C48 or m5C49, but never both in the same tRNA molecule.
[ "10", "24" ]
214
1,440
0
false
m5C was found at positions 34 and 40 only in two yeast tRNAs [tRNA(CUA)Leu (Sup53) and tRNA(GAA)Phe, respectively], whereas most elongator tRNAs bore either m5C48 or m5C49, but never both in the same tRNA molecule.
[]
m5C was found at positions 34 and 40 only in two yeast tRNAs [tRNA(CUA)Leu (Sup53) and tRNA(GAA)Phe, respectively], whereas most elongator tRNAs bore either m5C48 or m5C49, but never both in the same tRNA molecule.
false
true
true
true
false
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
Motorin and Grosjean concluded that yeast Trm4p
[ "10", "24" ]
47
1,441
0
false
Motorin and Grosjean concluded that yeast Trm4p
[]
Motorin and Grosjean concluded that yeast Trm4p
true
true
false
true
false
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
MTase is responsible for cytosine conversion in all yeast tRNAs and pre-tRNAs, while two other identified MTases encoded in S.cerevisiae genome are required for proper rRNA m5C modification.
[ "10", "24" ]
190
1,442
0
false
MTase is responsible for cytosine conversion in all yeast tRNAs and pre-tRNAs, while two other identified MTases encoded in S.cerevisiae genome are required for proper rRNA m5C modification.
[]
MTase is responsible for cytosine conversion in all yeast tRNAs and pre-tRNAs, while two other identified MTases encoded in S.cerevisiae genome are required for proper rRNA m5C modification.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
We transformed yeast strain BY4742 deprived of the TRM4 gene with yeast Trm4p cDNA and human Trm4 cDNA.
[ "10", "24" ]
103
1,443
0
false
We transformed yeast strain BY4742 deprived of the TRM4 gene with yeast Trm4p cDNA and human Trm4 cDNA.
[]
We transformed yeast strain BY4742 deprived of the TRM4 gene with yeast Trm4p cDNA and human Trm4 cDNA.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
In the Δtrm4 + Trm4p cDNA strain, the level of m5C in low-molecular RNA molecules was restored to that of the wild-type yeast strain (see Figure 3).
[ "10", "24" ]
148
1,444
0
false
In the Δtrm4 + Trm4p cDNA strain, the level of m5C in low-molecular RNA molecules was restored to that of the wild-type yeast strain (see Figure 3).
[]
In the Δtrm4 + Trm4p cDNA strain, the level of m5C in low-molecular RNA molecules was restored to that of the wild-type yeast strain (see Figure 3).
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
However, in the Δtrm4 + hTrm4 cDNA strain, the level of m5C was hardly detectable.
[ "10", "24" ]
82
1,445
0
false
However, in the Δtrm4 + hTrm4 cDNA strain, the level of m5C was hardly detectable.
[]
However, in the Δtrm4 + hTrm4 cDNA strain, the level of m5C was hardly detectable.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
It clearly shows that human enzyme is not able to recognize the majority of yeast tRNA substrates.
[ "10", "24" ]
98
1,446
0
false
It clearly shows that human enzyme is not able to recognize the majority of yeast tRNA substrates.
[]
It clearly shows that human enzyme is not able to recognize the majority of yeast tRNA substrates.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
Since our experiments show that yeast and human Trm4 MTases both recognize mammalian pre-tRNA(CAA)Leu containing intron, the conclusion can be drawn that the yeast enzyme has much broader substrate specificity than the human Trm4.
[ "10", "24" ]
230
1,447
0
false
Since our experiments show that yeast and human Trm4 MTases both recognize mammalian pre-tRNA(CAA)Leu containing intron, the conclusion can be drawn that the yeast enzyme has much broader substrate specificity than the human Trm4.
[]
Since our experiments show that yeast and human Trm4 MTases both recognize mammalian pre-tRNA(CAA)Leu containing intron, the conclusion can be drawn that the yeast enzyme has much broader substrate specificity than the human Trm4.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
We confirm this statement showing that hTrm4 is not able to introduce m5C48 at the level of intron-containing and intron-less human pre-tRNALeu precursor.
[ "10", "24" ]
154
1,448
0
false
We confirm this statement showing that hTrm4 is not able to introduce m5C48 at the level of intron-containing and intron-less human pre-tRNALeu precursor.
[]
We confirm this statement showing that hTrm4 is not able to introduce m5C48 at the level of intron-containing and intron-less human pre-tRNALeu precursor.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
Moreover, we show that it does not methylate different yeast tRNA precursors at positions 48 and 49.
[ "10", "24" ]
100
1,449
0
false
Moreover, we show that it does not methylate different yeast tRNA precursors at positions 48 and 49.
[]
Moreover, we show that it does not methylate different yeast tRNA precursors at positions 48 and 49.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
In the light of these observations, it is interesting to note that Bujnicki et al.
[ "10", "24" ]
82
1,450
0
false
In the light of these observations, it is interesting to note that Bujnicki et al.
[]
In the light of these observations, it is interesting to note that Bujnicki et al.
true
true
true
true
true
246
2
DISCUSSION
1
24
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
(24) identified two additional human putative orthologues of yeast Trm4p, which have probably originated from duplications and subsequent functional specializations of the original TRM4 gene in the animal lineage.
[ "10", "24" ]
213
1,451
1
false
identified two additional human putative orthologues of yeast Trm4p, which have probably originated from duplications and subsequent functional specializations of the original TRM4 gene in the animal lineage.
[ "24" ]
identified two additional human putative orthologues of yeast Trm4p, which have probably originated from duplications and subsequent functional specializations of the original TRM4 gene in the animal lineage.
false
true
true
true
false
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
One or both of these so-far uncharacterized genes may be responsible for some of the methylations carried out by the yeast Trm4p, but not exhibited by its human counterpart.
[ "10", "24" ]
173
1,452
0
false
One or both of these so-far uncharacterized genes may be responsible for some of the methylations carried out by the yeast Trm4p, but not exhibited by its human counterpart.
[]
One or both of these so-far uncharacterized genes may be responsible for some of the methylations carried out by the yeast Trm4p, but not exhibited by its human counterpart.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
This speculation can explain a very low level of m5C in the Δtrm4 + hTrm4 strain.
[ "10", "24" ]
81
1,453
0
false
This speculation can explain a very low level of m5C in the Δtrm4 + hTrm4 strain.
[]
This speculation can explain a very low level of m5C in the Δtrm4 + hTrm4 strain.
true
true
true
true
true
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
Summarizing our results concerning the hTrm4 enzyme, it can be concluded that the enzyme acts on intron-containing tRNA(CAA)Leu precursors, it is more sensitive to the nucleotide sequence that surrounds the position to be modified than its yeast homologue Trm4p
[ "10", "24" ]
261
1,454
0
false
Summarizing our results concerning the hTrm4 enzyme, it can be concluded that the enzyme acts on intron-containing tRNA(CAA)Leu precursors, it is more sensitive to the nucleotide sequence that surrounds the position to be modified than its yeast homologue Trm4p
[]
Summarizing our results concerning the hTrm4 enzyme, it can be concluded that the enzyme acts on intron-containing tRNA(CAA)Leu precursors, it is more sensitive to the nucleotide sequence that surrounds the position to be modified than its yeast homologue Trm4p
true
true
false
true
false
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
and it is equally sensitive to the anticodon prolongated, intron-containing structure.
[ "10", "24" ]
86
1,455
0
false
and it is equally sensitive to the anticodon prolongated, intron-containing structure.
[]
and it is equally sensitive to the anticodon prolongated, intron-containing structure.
false
true
true
true
false
246
2
DISCUSSION
1
10
[ "b10", "b24" ]
17,071,714
pmid-6339954|pmid-3537724|pmid-1461724|pmid-10445884|pmid-15121902
Moreover, its sensitivity to substrate specificity is more constrained than in the case of yeast homologue—Trm4p.
[ "10", "24" ]
113
1,456
0
false
Moreover, its sensitivity to substrate specificity is more constrained than in the case of yeast homologue—Trm4p.
[]
Moreover, its sensitivity to substrate specificity is more constrained than in the case of yeast homologue—Trm4p.
true
true
true
true
true
246
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Chromatin is the physiologically relevant substrate for all genetic processes in eukaryotic cells.
[ "1", "2" ]
98
1,457
0
false
Chromatin is the physiologically relevant substrate for all genetic processes in eukaryotic cells.
[]
Chromatin is the physiologically relevant substrate for all genetic processes in eukaryotic cells.
true
true
true
true
true
247
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
It represents a signal transduction platform for extracellular or intracellular signals and regulates all genome functions.
[ "1", "2" ]
123
1,458
0
false
It represents a signal transduction platform for extracellular or intracellular signals and regulates all genome functions.
[]
It represents a signal transduction platform for extracellular or intracellular signals and regulates all genome functions.
true
true
true
true
true
247
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
While DNMTs methylate DNA, histone-acetyltransferases, histone-deacetylases, histone-methyltransferases and histone-demethylases determine the acetylation and methylation state of histones, the key protein component of chromatin.
[ "1", "2" ]
229
1,459
0
false
While DNMTs methylate DNA, histone-acetyltransferases, histone-deacetylases, histone-methyltransferases and histone-demethylases determine the acetylation and methylation state of histones, the key protein component of chromatin.
[]
While DNMTs methylate DNA, histone-acetyltransferases, histone-deacetylases, histone-methyltransferases and histone-demethylases determine the acetylation and methylation state of histones, the key protein component of chromatin.
true
true
true
true
true
247
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
The specific combinations of resulting (post-translational) modifications are thought to provide transient or heritable epigenetic patterns that specify genome function.
[ "1", "2" ]
169
1,460
0
false
The specific combinations of resulting (post-translational) modifications are thought to provide transient or heritable epigenetic patterns that specify genome function.
[]
The specific combinations of resulting (post-translational) modifications are thought to provide transient or heritable epigenetic patterns that specify genome function.
true
true
true
true
true
247
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Emerging evidence causally links epigenetic alterations of chromatin to a disturbed proliferation–differentiation balance implicated in many diseases, providing the rational for the development of epigenetic treatment strategies using DNA-demethylating agents and HDAC inhibitors (1,2).
[ "1", "2" ]
286
1,461
0
false
Emerging evidence causally links epigenetic alterations of chromatin to a disturbed proliferation–differentiation balance implicated in many diseases, providing the rational for the development of epigenetic treatment strategies using DNA-demethylating agents and HDAC inhibitors.
[ "1,2" ]
Emerging evidence causally links epigenetic alterations of chromatin to a disturbed proliferation–differentiation balance implicated in many diseases, providing the rational for the development of epigenetic treatment strategies using DNA-demethylating agents and HDAC inhibitors.
true
true
true
true
true
247
1
INTRODUCTION
1
3
[ "b3", "b9", "b10", "b11" ]
17,202,157
pmid-12353038|pmid-16122420|pmid-14661024|pmid-16648823|pmid-16648823
Several studies have identified the presence of acetylated histones H3/H4 and tri-methylated histone H3 lysine 4 (H3K4me3) co-localizing at 5′ regions of active genes, suggesting that these marks together represent an active code (3–9).
[ "3", "9", "10", "11" ]
236
1,462
0
false
Several studies have identified the presence of acetylated histones H3/H4 and tri-methylated histone H3 lysine 4 co-localizing at 5′ regions of active genes, suggesting that these marks together represent an active code.
[ "H3K4me3", "3–9" ]
Several studies have identified the presence of acetylated histones H3/H4 and tri-methylated histone H3 lysine 4 co-localizing at 5′ regions of active genes, suggesting that these marks together represent an active code.
true
true
true
true
true
248
1
INTRODUCTION
1
3
[ "b3", "b9", "b10", "b11" ]
17,202,157
pmid-12353038|pmid-16122420|pmid-14661024|pmid-16648823|pmid-16648823
However, the identification of these marks also at inactive genes suggests that the presence of these marks does not necessarily correlate ongoing transcription per se (10,11), and may as well represent a poised state.
[ "3", "9", "10", "11" ]
218
1,463
0
false
However, the identification of these marks also at inactive genes suggests that the presence of these marks does not necessarily correlate ongoing transcription per se, and may as well represent a poised state.
[ "10,11" ]
However, the identification of these marks also at inactive genes suggests that the presence of these marks does not necessarily correlate ongoing transcription per se, and may as well represent a poised state.
true
true
true
true
true
248
2
INTRODUCTION
1
12
[ "b12", "b14", "b13", "b15", "b18" ]
17,202,157
pmid-11782440|pmid-12191632|pmid-12042769|pmid-9732866|pmid-16428440|pmid-11889044
Methylation of promoter CpG islands has been conceptually linked to gene silencing (12–14).
[ "12", "14", "13", "15", "18" ]
91
1,464
0
false
Methylation of promoter CpG islands has been conceptually linked to gene silencing.
[ "12–14" ]
Methylation of promoter CpG islands has been conceptually linked to gene silencing.
true
true
true
true
true
249
2
INTRODUCTION
1
12
[ "b12", "b14", "b13", "b15", "b18" ]
17,202,157
pmid-11782440|pmid-12191632|pmid-12042769|pmid-9732866|pmid-16428440|pmid-11889044
Importantly, methylation seems to function as the dominant event that seals transcriptional repression.
[ "12", "14", "13", "15", "18" ]
103
1,465
0
false
Importantly, methylation seems to function as the dominant event that seals transcriptional repression.
[]
Importantly, methylation seems to function as the dominant event that seals transcriptional repression.
true
true
true
true
true
249
2
INTRODUCTION
1
12
[ "b12", "b14", "b13", "b15", "b18" ]
17,202,157
pmid-11782440|pmid-12191632|pmid-12042769|pmid-9732866|pmid-16428440|pmid-11889044
Methyl DNA-binding (MBD) proteins such as MeCP2 and MBD2 are known to be part of co-repressor complexes that specifically associate with methylated CpGs, contain HDAC activity and establish a repressive chromatin configuration (13,15–18).
[ "12", "14", "13", "15", "18" ]
238
1,466
0
false
Methyl DNA-binding (MBD) proteins such as MeCP2 and MBD2 are known to be part of co-repressor complexes that specifically associate with methylated CpGs, contain HDAC activity and establish a repressive chromatin configuration.
[ "13,15–18" ]
Methyl DNA-binding (MBD) proteins such as MeCP2 and MBD2 are known to be part of co-repressor complexes that specifically associate with methylated CpGs, contain HDAC activity and establish a repressive chromatin configuration.
true
true
true
true
true
249
3
INTRODUCTION
1
19
[ "b19" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
We have previously shown that the erythroid-specific carbonic anhydrase II (CAII) is silenced through the action of the NCoR–SMRT co-repressor complex containing HDAC3 at an intronic enhancer and through a MeCP2–Sin3B co-repressor complex containing HDAC2 at the CAII promoter (19).
[ "19" ]
282
1,467
1
false
We have previously shown that the erythroid-specific carbonic anhydrase II (CAII) is silenced through the action of the NCoR–SMRT co-repressor complex containing HDAC3 at an intronic enhancer and through a MeCP2–Sin3B co-repressor complex containing HDAC2 at the CAII promoter.
[ "19" ]
We have previously shown that the erythroid-specific carbonic anhydrase II (CAII) is silenced through the action of the NCoR–SMRT co-repressor complex containing HDAC3 at an intronic enhancer and through a MeCP2–Sin3B co-repressor complex containing HDAC2 at the CAII promoter.
true
true
true
true
true
250
3
INTRODUCTION
1
19
[ "b19" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
Despite the presence of multiple HDAC-containing co-repressor complexes, the silenced CAII promoter was shown to be hyperacetylated.
[ "19" ]
132
1,468
0
false
Despite the presence of multiple HDAC-containing co-repressor complexes, the silenced CAII promoter was shown to be hyperacetylated.
[]
Despite the presence of multiple HDAC-containing co-repressor complexes, the silenced CAII promoter was shown to be hyperacetylated.
true
true
true
true
true
250
3
INTRODUCTION
1
19
[ "b19" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
Here we have studied the epigenetic code in detail and show that it consists of H3/H4 acetylation as well as high levels of H3K4me3 around and downstream of the transcription start site.
[ "19" ]
186
1,469
0
false
Here we have studied the epigenetic code in detail and show that it consists of H3/H4 acetylation as well as high levels of H3K4me3 around and downstream of the transcription start site.
[]
Here we have studied the epigenetic code in detail and show that it consists of H3/H4 acetylation as well as high levels of H3K4me3 around and downstream of the transcription start site.
true
true
true
true
true
250
3
INTRODUCTION
1
19
[ "b19" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
However, efficient preinitiation complex assembly takes place only after ligand-induced transcriptional activation of the promoter, and is accompanied by transient and positional changes in acetylation and local nucleosome density.
[ "19" ]
231
1,470
0
false
However, efficient preinitiation complex assembly takes place only after ligand-induced transcriptional activation of the promoter, and is accompanied by transient and positional changes in acetylation and local nucleosome density.
[]
However, efficient preinitiation complex assembly takes place only after ligand-induced transcriptional activation of the promoter, and is accompanied by transient and positional changes in acetylation and local nucleosome density.
true
true
true
true
true
250
3
INTRODUCTION
1
19
[ "b19" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
Interestingly, while the upstream part of the CpG island is highly DNA-methylated, the region of the CpG island carrying active histone marks is maintained DNA methylation-free.
[ "19" ]
177
1,471
0
false
Interestingly, while the upstream part of the CpG island is highly DNA-methylated, the region of the CpG island carrying active histone marks is maintained DNA methylation-free.
[]
Interestingly, while the upstream part of the CpG island is highly DNA-methylated, the region of the CpG island carrying active histone marks is maintained DNA methylation-free.
true
true
true
true
true
250
3
INTRODUCTION
1
19
[ "b19" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
This bipartite epigenetic code is largely unaffected by transcriptional activation of the promoter, implying that localized DNA methylation—even when adjacent to the transcription start site—is not necessarily a hallmark of gene silencing.
[ "19" ]
239
1,472
0
false
This bipartite epigenetic code is largely unaffected by transcriptional activation of the promoter, implying that localized DNA methylation—even when adjacent to the transcription start site—is not necessarily a hallmark of gene silencing.
[]
This bipartite epigenetic code is largely unaffected by transcriptional activation of the promoter, implying that localized DNA methylation—even when adjacent to the transcription start site—is not necessarily a hallmark of gene silencing.
true
true
true
true
true
250
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
In this study we characterized the epigenetic code of the CAII locus and in particular its promoter (present within a CpG island) under repressive conditions as well as upon hormone-induced activation.
[ "29" ]
201
1,473
0
false
In this study we characterized the epigenetic code of the CAII locus and in particular its promoter (present within a CpG island) under repressive conditions as well as upon hormone-induced activation.
[]
In this study we characterized the epigenetic code of the CAII locus and in particular its promoter (present within a CpG island) under repressive conditions as well as upon hormone-induced activation.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Active histone modifications including H3K9/H4 acetylation and H3K4 tri-methylation are present already under repressive conditions and are localized almost exclusively around the transcription start site.
[ "29" ]
205
1,474
0
false
Active histone modifications including H3K9/H4 acetylation and H3K4 tri-methylation are present already under repressive conditions and are localized almost exclusively around the transcription start site.
[]
Active histone modifications including H3K9/H4 acetylation and H3K4 tri-methylation are present already under repressive conditions and are localized almost exclusively around the transcription start site.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Sequential ChIP experiments showed that these histone marks are primarily present on the same nucleosomes, whereas H3K4me3-containing nucleosomes seem to be devoid of the ubiquitously present H3K9me3.
[ "29" ]
200
1,475
0
false
Sequential ChIP experiments showed that these histone marks are primarily present on the same nucleosomes, whereas H3K4me3-containing nucleosomes seem to be devoid of the ubiquitously present H3K9me3.
[]
Sequential ChIP experiments showed that these histone marks are primarily present on the same nucleosomes, whereas H3K4me3-containing nucleosomes seem to be devoid of the ubiquitously present H3K9me3.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Nevertheless, the individual active marks follow their own individual pattern upon activation of transcription.
[ "29" ]
111
1,476
0
false
Nevertheless, the individual active marks follow their own individual pattern upon activation of transcription.
[]
Nevertheless, the individual active marks follow their own individual pattern upon activation of transcription.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Within the upstream part of the CpG island active histone modifications are absent and the DNA is hypermethylated.
[ "29" ]
114
1,477
0
false
Within the upstream part of the CpG island active histone modifications are absent and the DNA is hypermethylated.
[]
Within the upstream part of the CpG island active histone modifications are absent and the DNA is hypermethylated.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
However, H3K9me3 is only slightly higher within the hypermethylated region.
[ "29" ]
75
1,478
0
false
However, H3K9me3 is only slightly higher within the hypermethylated region.
[]
However, H3K9me3 is only slightly higher within the hypermethylated region.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
DNA hypermethylation is almost completely maintained upon activation of transcription by T3 ligand.
[ "29" ]
99
1,479
0
false
DNA hypermethylation is almost completely maintained upon activation of transcription by T3 ligand.
[]
DNA hypermethylation is almost completely maintained upon activation of transcription by T3 ligand.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Even more strikingly, treatment with AZAdC does not cause drastic changes in positioning of the active histone marks, suggesting that DNA hypermethylation and the association of the previously reported MeCP2–Sin3 complex are not the critical factors in establishing or maintaining a chromatin boundary.
[ "29" ]
302
1,480
0
false
Even more strikingly, treatment with AZAdC does not cause drastic changes in positioning of the active histone marks, suggesting that DNA hypermethylation and the association of the previously reported MeCP2–Sin3 complex are not the critical factors in establishing or maintaining a chromatin boundary.
[]
Even more strikingly, treatment with AZAdC does not cause drastic changes in positioning of the active histone marks, suggesting that DNA hypermethylation and the association of the previously reported MeCP2–Sin3 complex are not the critical factors in establishing or maintaining a chromatin boundary.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
The lack of DNA methylation-spreading may instead be the consequence of a boundary formed by local and high levels of active histone marks.
[ "29" ]
139
1,481
0
false
The lack of DNA methylation-spreading may instead be the consequence of a boundary formed by local and high levels of active histone marks.
[]
The lack of DNA methylation-spreading may instead be the consequence of a boundary formed by local and high levels of active histone marks.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Indeed, chromatin boundaries between escape genes and X-inactivated genes have been shown to contain high levels of localized acetylation (29).
[ "29" ]
143
1,482
1
false
Indeed, chromatin boundaries between escape genes and X-inactivated genes have been shown to contain high levels of localized acetylation.
[ "29" ]
Indeed, chromatin boundaries between escape genes and X-inactivated genes have been shown to contain high levels of localized acetylation.
true
true
true
true
true
251
0
DISCUSSION
1
29
[ "b29" ]
17,202,157
pmid-14528273|pmid-11927287|pmid-15669143
Here, the zinc-finger protein CTCF is involved in boundary formation, and it is possible that CTCF also plays a role at the CAII locus.
[ "29" ]
135
1,483
0
false
Here, the zinc-finger protein CTCF is involved in boundary formation, and it is possible that CTCF also plays a role at the CAII locus.
[]
Here, the zinc-finger protein CTCF is involved in boundary formation, and it is possible that CTCF also plays a role at the CAII locus.
true
true
true
true
true
251
1
DISCUSSION
1
11
[ "b11" ]
17,202,157
pmid-12353038|pmid-16122420|pmid-14661024|pmid-16648823|pmid-16648823
Although H3K4 tri-methylation is generally regarded as an indicator for active chromatin transcription, the level of H3K4 tri-methylation level does not correlate with CAII promoter activity, and its presence does not necessarily signal ongoing transcription.
[ "11" ]
259
1,484
0
false
Although H3K4 tri-methylation is generally regarded as an indicator for active chromatin transcription, the level of H3K4 tri-methylation level does not correlate with CAII promoter activity, and its presence does not necessarily signal ongoing transcription.
[]
Although H3K4 tri-methylation is generally regarded as an indicator for active chromatin transcription, the level of H3K4 tri-methylation level does not correlate with CAII promoter activity, and its presence does not necessarily signal ongoing transcription.
true
true
true
true
true
252
1
DISCUSSION
1
11
[ "b11" ]
17,202,157
pmid-12353038|pmid-16122420|pmid-14661024|pmid-16648823|pmid-16648823
We have made similar observations for unexpressed genes at the human X-chromosome (11).
[ "11" ]
87
1,485
1
false
We have made similar observations for unexpressed genes at the human X-chromosome.
[ "11" ]
We have made similar observations for unexpressed genes at the human X-chromosome.
true
true
true
true
true
252
1
DISCUSSION
1
11
[ "b11" ]
17,202,157
pmid-12353038|pmid-16122420|pmid-14661024|pmid-16648823|pmid-16648823
Moreover, H3K4 tri-methylation is not subjected to significant alteration upon transcriptional activation, but instead is high in both the repressive and active state.
[ "11" ]
167
1,486
0
false
Moreover, H3K4 tri-methylation is not subjected to significant alteration upon transcriptional activation, but instead is high in both the repressive and active state.
[]
Moreover, H3K4 tri-methylation is not subjected to significant alteration upon transcriptional activation, but instead is high in both the repressive and active state.
true
true
true
true
true
252
1
DISCUSSION
1
11
[ "b11" ]
17,202,157
pmid-12353038|pmid-16122420|pmid-14661024|pmid-16648823|pmid-16648823
Next to marking active chromatin, H3K4 tri-methylation may well mark promoters that become activated and provide the epigenetic setting to facilitate such future activation.
[ "11" ]
173
1,487
0
false
Next to marking active chromatin, H3K4 tri-methylation may well mark promoters that become activated and provide the epigenetic setting to facilitate such future activation.
[]
Next to marking active chromatin, H3K4 tri-methylation may well mark promoters that become activated and provide the epigenetic setting to facilitate such future activation.
true
true
true
true
true
252
2
DISCUSSION
1
19
[ "b19" ]
17,202,157
pmid-11782440|pmid-12191632|pmid-12042769|pmid-9732866|pmid-16428440|pmid-11889044
Our results show that PIC assembly is inhibited notwithstanding the active histone modifications at the CAII promoter.
[ "19" ]
118
1,488
0
false
Our results show that PIC assembly is inhibited notwithstanding the active histone modifications at the CAII promoter.
[]
Our results show that PIC assembly is inhibited notwithstanding the active histone modifications at the CAII promoter.
true
true
true
true
true
253
2
DISCUSSION
1
19
[ "b19" ]
17,202,157
pmid-11782440|pmid-12191632|pmid-12042769|pmid-9732866|pmid-16428440|pmid-11889044
This indicates that the establishment of an active epigenetic code alone is insufficient to establish productive transcription.
[ "19" ]
127
1,489
0
false
This indicates that the establishment of an active epigenetic code alone is insufficient to establish productive transcription.
[]
This indicates that the establishment of an active epigenetic code alone is insufficient to establish productive transcription.
true
true
true
true
true
253
2
DISCUSSION
1
19
[ "b19" ]
17,202,157
pmid-11782440|pmid-12191632|pmid-12042769|pmid-9732866|pmid-16428440|pmid-11889044
It seems likely that PIC assembly at the promoter is critically regulated through communication with the +7 kb HS2 enhancer which recruits the v-ErbA/NCoR-HDAC complex during repression, and the TRAPP220 co-activator upon activation (19).
[ "19" ]
238
1,490
1
false
It seems likely that PIC assembly at the promoter is critically regulated through communication with the +7 kb HS2 enhancer which recruits the v-ErbA/NCoR-HDAC complex during repression, and the TRAPP220 co-activator upon activation.
[ "19" ]
It seems likely that PIC assembly at the promoter is critically regulated through communication with the +7 kb HS2 enhancer which recruits the v-ErbA/NCoR-HDAC complex during repression, and the TRAPP220 co-activator upon activation.
true
true
true
true
true
253
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
Hormone-induced activation of CAII transcription is associated with changes in H3/H4 acetylation, H3K4 tri-methylation, but also nucleosome density, as measured through the association of histone H3.
[ "26", "19", "26" ]
199
1,491
0
false
Hormone-induced activation of CAII transcription is associated with changes in H3/H4 acetylation, H3K4 tri-methylation, but also nucleosome density, as measured through the association of histone H3.
[]
Hormone-induced activation of CAII transcription is associated with changes in H3/H4 acetylation, H3K4 tri-methylation, but also nucleosome density, as measured through the association of histone H3.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
At the transcriptional start site, nucleosome depletion or eviction most likely occurs.
[ "26", "19", "26" ]
87
1,492
0
false
At the transcriptional start site, nucleosome depletion or eviction most likely occurs.
[]
At the transcriptional start site, nucleosome depletion or eviction most likely occurs.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
This explains why H3/H4ac and H3K4me3 locally decrease during induction, and implicates that the levels of H3K9-Ac and H3K4me3 themselves do not decrease but are—at least partially—maintained.
[ "26", "19", "26" ]
192
1,493
0
false
This explains why H3/H4ac and H3K4me3 locally decrease during induction, and implicates that the levels of H3K9-Ac and H3K4me3 themselves do not decrease but are—at least partially—maintained.
[]
This explains why H3/H4ac and H3K4me3 locally decrease during induction, and implicates that the levels of H3K9-Ac and H3K4me3 themselves do not decrease but are—at least partially—maintained.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
Furthermore, the initial increase in H4 acetylation is in fact even more pronounced.
[ "26", "19", "26" ]
84
1,494
0
false
Furthermore, the initial increase in H4 acetylation is in fact even more pronounced.
[]
Furthermore, the initial increase in H4 acetylation is in fact even more pronounced.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
A lowered nucleosome density at the transcriptional start is consistent with our previous observations that ligand induces a DNase I hypersensitive site around the transcriptional start site (26).
[ "26", "19", "26" ]
196
1,495
1
false
A lowered nucleosome density at the transcriptional start is consistent with our previous observations that ligand induces a DNase I hypersensitive site around the transcriptional start site.
[ "26" ]
A lowered nucleosome density at the transcriptional start is consistent with our previous observations that ligand induces a DNase I hypersensitive site around the transcriptional start site.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
Since the pan-H3 antiserum does not discriminate between histone H3 and H3.3 histone replacement cannot be excluded.
[ "26", "19", "26" ]
116
1,496
0
false
Since the pan-H3 antiserum does not discriminate between histone H3 and H3.3 histone replacement cannot be excluded.
[]
Since the pan-H3 antiserum does not discriminate between histone H3 and H3.3 histone replacement cannot be excluded.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
At +7 kb H3 was initially low and slightly decreased even further during T3-induction.
[ "26", "19", "26" ]
86
1,497
0
false
At +7 kb H3 was initially low and slightly decreased even further during T3-induction.
[]
At +7 kb H3 was initially low and slightly decreased even further during T3-induction.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
This position corresponds with the HS2 DNase I hypersensitive site (19,26).
[ "26", "19", "26" ]
75
1,498
0
false
This position corresponds with the HS2 DNase I hypersensitive site.
[ "19,26" ]
This position corresponds with the HS2 DNase I hypersensitive site.
true
true
true
true
true
254
3
DISCUSSION
1
26
[ "b26", "b19", "b26" ]
17,202,157
pmid-11889044|pmid-9857194|pmid-11889044|pmid-9857194
The low levels of H3 measured at the HS2 enhancer strongly suggest that this position is locally devoid of nucleosomes, and explain the low levels of all tested histone modifications at this position (see Figures 2, 3 and 8).
[ "26", "19", "26" ]
225
1,499
0
false
The low levels of H3 measured at the HS2 enhancer strongly suggest that this position is locally devoid of nucleosomes, and explain the low levels of all tested histone modifications at this position (see Figures 2, 3 and 8).
[]
The low levels of H3 measured at the HS2 enhancer strongly suggest that this position is locally devoid of nucleosomes, and explain the low levels of all tested histone modifications at this position.
true
true
true
true
true
254