(Q35969015)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

title

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

author name string

L Stirling Churchman

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

publication date

24 March 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

volume

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

page(s)

813-833

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

30 March 2020

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5326677/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1038/nprot.2016.047

0 references

cites work

Protein-DNA binding in high-resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II-transcribed genes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Getting up to speed with transcription elongation by RNA polymerase II

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

HTSeq--a Python framework to work with high-throughput sequencing data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Interactions between RNA polymerase and the "core recognition element" counteract pausing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Dealing with pervasive transcription.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Gene regulation by antisense transcription

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

STAR: ultrafast universal RNA-seq aligner

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Defining the status of RNA polymerase at promoters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Landscape of transcription in human cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

NIH Image to ImageJ: 25 years of image analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Native elongating transcript sequencing (NET-seq).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Nascent transcript sequencing visualizes transcription at nucleotide resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Integrative genomics viewer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Uniform transitions of the general RNA polymerase II transcription complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Chemical-genomic dissection of the CTD code.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

A large fraction of extragenic RNA pol II transcription sites overlap enhancers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

c-Myc regulates transcriptional pause release

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Widespread transcription at neuronal activity-regulated enhancers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Co-transcriptional splicing of constitutive and alternative exons

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Divergent transcription: a new feature of active promoters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Divergent transcription from active promoters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

RNA exosome depletion reveals transcription upstream of active human promoters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Poised RNA polymerase II gives pause for thought

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

RNA polymerase is poised for activation across the genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Controlling the elongation phase of transcription with P-TEFb

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Positive transcription elongation factor B phosphorylates hSPT5 and RNA polymerase II carboxyl-terminal domain independently of cyclin-dependent kinase-activating kinase.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Transcriptional activation by recruitment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Physical Isolation of Nascent RNA Chains Transcribed by RNA Polymerase II: Evidence for Cotranscriptional Splicing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Gene-specific RNA polymerase II phosphorylation and the CTD code

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

ChIP-Seq: a method for global identification of regulatory elements in the genome.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

Detecting transcriptionally engaged RNA polymerase in eukaryotic cells with permanganate genomic footprinting.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5326677

The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2016.047

Specific Inhibition of Nuclear RNA Polymerase II by α-Amanitin

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2016.047

A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2016.047

31 March 2020

Identifiers

DOI

10.1038/NPROT.2016.047

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27010758%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

PubMed publication ID

27010758

1 reference