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Links from GEO DataSets

Items: 20

1.

Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-Seq

(Submitter supplied) Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription by Pol II in embryonic stem (ES) cells, and thus an additional step where regulation of gene expression may occur. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
17 Samples
Download data: TXT, WIG
Series
Accession:
GSE20530
ID:
200020530
2.

Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-chip

(Submitter supplied) Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription by Pol II in embryonic stem (ES) cells, and thus an additional step where regulation of gene expression may occur. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10099
8 Samples
Download data: TXT
Series
Accession:
GSE20529
ID:
200020529
3.

Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10099 GPL9185
25 Samples
Download data: TXT
Series
Accession:
GSE20485
ID:
200020485
4.

ZFP281 recruits MYC to active promoters in regulating transcriptional initiation and elongation

(Submitter supplied) In this study, we analyzed the function of ZFP281 in transcription control by genome wide ChIP-Seq analyses in mouse embryonic stem cells.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
4 Samples
Download data: BW
Series
Accession:
GSE125435
ID:
200125435
5.

The histone deacetylase SIRT6 restrains transcription elongation via promoter-proximal pausing

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
46 Samples
Download data: BW
Series
Accession:
GSE130692
ID:
200130692
6.

The histone deacetylase SIRT6 controls transcription elongation via promoter-proximal pausing (PRO-Seq)

(Submitter supplied) Transcriptional regulation in eukaryotes commonly occurs at promoter-proximal regions wherein transcriptionally engaged RNA Polymerase II (Pol II) pauses before proceeding towards productive elongation. The roles of chromatin in this process remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 regulates transcription elongation by binding to Pol II and anchoring the Negative ELongation Factor NELF, thereby preventing the release of Pol II towards elongation. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
8 Samples
Download data: BW
Series
Accession:
GSE130691
ID:
200130691
7.

The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal pausing (RNA-Seq)

(Submitter supplied) Transcriptional regulation in eukaryotes commonly occurs at promoter-proximal regions wherein transcriptionally engaged RNA Polymerase II (Pol II) pauses before proceeding towards productive elongation. The roles of chromatin in this process remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 regulates transcription elongation by binding to Pol II and anchoring the Negative ELongation Factor NELF, thereby preventing the release of Pol II towards elongation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
9 Samples
Download data: TXT
Series
Accession:
GSE130690
ID:
200130690
8.

The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal pausing (ChIP-Seq)

(Submitter supplied) Transcriptional regulation in eukaryotes commonly occurs at promoter-proximal regions wherein transcriptionally engaged RNA Polymerase II (Pol II) pauses before proceeding towards productive elongation. The roles of chromatin in this process remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 regulates transcription elongation by binding to Pol II and anchoring the Negative ELongation Factor NELF, thereby preventing the release of Pol II towards elongation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
29 Samples
Download data: BW
Series
Accession:
GSE130689
ID:
200130689
9.

Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
19 Samples
Download data: TXT, WIG
Series
Accession:
GSE59833
ID:
200059833
10.

Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (ChIP-seq)

(Submitter supplied) Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
5 Samples
Download data: WIG
Series
Accession:
GSE59828
ID:
200059828
11.

Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (RNA-seq)

(Submitter supplied) Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
14 Samples
Download data: TXT
Series
Accession:
GSE59813
ID:
200059813
12.

Integrative analysis of RNA Polymerase II and transcriptional dynamics upon Myc activation

(Submitter supplied) Over-expression of the Myc transcription factor causes its widespread interaction with regulatory domains in the genome, but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following Myc activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing and mathematical modeling. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
81 Samples
Download data: TXT
Series
Accession:
GSE98420
ID:
200098420
13.

Integrative analysis of RNA Polymerase II and transcriptional dynamics upon Myc activation [ChIP-seq]

(Submitter supplied) Over-expression of the Myc transcription factor causes its widespread interaction with regulatory domains in the genome, but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following Myc activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing and mathematical modeling. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
15 Samples
Download data: TXT
Series
Accession:
GSE98419
ID:
200098419
14.

Integrative analysis of RNA Polymerase II and transcriptional dynamics upon Myc activation [RNA-seq]

(Submitter supplied) Over-expression of the Myc transcription factor causes its widespread interaction with regulatory domains in the genome, but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following Myc activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing and mathematical modeling. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
66 Samples
Download data: TXT
Series
Accession:
GSE98418
ID:
200098418
15.

RNAPol2 accounts for tumor cells liability to JQ1

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL11154 GPL6244
28 Samples
Download data: BED, CEL, XLS
Series
Accession:
GSE76192
ID:
200076192
16.

RNAPol2 accounts for tumor cells liability to JQ1 [ChIP-Seq]

(Submitter supplied) We here use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
22 Samples
Download data: BED, XLS
Series
Accession:
GSE76191
ID:
200076191
17.

RNAPol2 accounts for tumor cells liability to JQ1 [Affymetrix]

(Submitter supplied) We here use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
6 Samples
Download data: CEL, XLS
Series
Accession:
GSE76188
ID:
200076188
18.

Association with Aurora-A controls N-MYC-dependent promoter escape and pause release of RNA polymerase II during the cell cycle

(Submitter supplied) MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (RNAPII). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of RNAPII promoters and intergenic regions. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL10999
50 Samples
Download data: BEDGRAPH, TXT, WIG
19.

Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy

(Submitter supplied) The super elongation complex (SEC) is required for robust and productive transcription through release of RNA polymerase II (Pol II) with its P-TEFb module and promoting transcriptional processivity with its ELL2 subunit. Malfunction of SEC contributes to multiple human diseases including cancer. Here, we identify peptidomimetic lead compounds, KL-1 and its structural homolog KL-2, which disrupt the interaction between the SEC scaffolding protein AFF4 and P-TEFb, resulting in impaired release of Pol II from promoter-proximal pause sites and a reduced average rate of processive transcription elongation. more...
Organism:
Drosophila melanogaster; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL18573 GPL19132
111 Samples
Download data: BW
Series
Accession:
GSE112608
ID:
200112608
20.

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

(Submitter supplied) The MYC oncoprotein binds to promoter-proximal regions of virtually all transcribed genes and is expressed in a strictly growth factor-dependent manner in non-tumor cells. Here we show that MYC directly binds SPT5, a subunit of the RNA polymerase II (POL2) elongation factor DSIF. MYC recruits SPT5 to genes and enables the CDK7-dependent transfer of SPT5 onto POL2. Consistent with known functions of SPT5, MYC is required for fast and processive transcription elongation. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL18573
47 Samples
Download data: BEDGRAPH
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