4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells (Q33813311)

29 July 2017

title

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells (English)

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29 July 2017

Ido Amit

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29 July 2017

Gilad Fuchs

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29 July 2017

Yoav Voichek

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29 July 2017

Sima Benjamin

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29 July 2017

Shlomit Gilad

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29 July 2017

Moshe Oren

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29 July 2017

publication date

9 May 2014

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29 July 2017

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29 July 2017

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29 July 2017

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29 July 2017

page(s)

R69

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Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

29 July 2017

cites work

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Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses

4 July 2018

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Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

4 July 2018

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Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

4 July 2018

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Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells

4 July 2018

1 reference

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HDAC inhibitors induce transcriptional repression of high copy number genes in breast cancer through elongation blockade

4 July 2018

1 reference

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Precise maps of RNA polymerase reveal how promoters direct initiation and pausing

4 July 2018

1 reference

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Transcriptional amplification in tumor cells with elevated c-Myc.

4 July 2018

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Expression noise and acetylation profiles distinguish HDAC functions

4 July 2018

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RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation

4 July 2018

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Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

4 July 2018

1 reference

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Complexity of RNA polymerase II elongation dynamics

4 July 2018

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Suppression of the antiviral response by an influenza histone mimic

4 July 2018

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A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster

4 July 2018

1 reference

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Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner

4 July 2018

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RNA polymerase II kinetics in polo polyadenylation signal selection.

4 July 2018

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

4 July 2018

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New Insights into the Control of HIV-1 Transcription: When Tat Meets the 7SK snRNP and Super Elongation Complex (SEC)

4 July 2018

1 reference

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Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

4 July 2018

1 reference

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ENCODE whole-genome data in the UCSC genome browser (2011 update)

4 July 2018

1 reference

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HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Rates of in situ transcription and splicing in large human genes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Defining mechanisms that regulate RNA polymerase II transcription in vivo

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

RNA polymerase is poised for activation across the genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

A chromatin landmark and transcription initiation at most promoters in human cells

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

A slow RNA polymerase II affects alternative splicing in vivo

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

On the importance of being co-transcriptional

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Integrating mRNA processing with transcription

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Phosphorylated RNA polymerase II stimulates pre-mRNA splicing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

RNA polymerase II is an essential mRNA polyadenylation factor

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4072947

Tracking rates of transcription and splicing in vivo.

4 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FGB-2014-15-5-R69

Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FGB-2014-15-5-R69

A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FGB-2014-15-5-R69

21 January 2018

Identifiers

DOI

10.1186/GB-2014-15-5-R69

1 reference

Dimensions Publication ID

29 July 2017

1036790059

0 references

Fatcat ID

release_nz2vwgmsyve5jhppdg5zw6hlre

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/nz2vwgmsyve5jhppdg5zw6hlre

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

4072947

1 reference

29 July 2017

1 reference