Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions (Q36118451)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22817891%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

title

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

1 reference

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8 February 2020

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1 reference

4

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8 February 2020

Gioacchino Natoli

6

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8 February 2020

author name string

Dev M Bhatt

1

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8 February 2020

Amy Pandya-Jones

2

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8 February 2020

Ann-Jay Tong

3

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8 February 2020

Michelle M Lissner

5

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8 February 2020

Douglas L Black

7

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8 February 2020

Stephen T Smale

8

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8 February 2020

language of work or name

English

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publication date

1 July 2012

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8 February 2020

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8 February 2020

volume

150

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8 February 2020

issue

2

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8 February 2020

page(s)

279-290

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Mechanisms establishing TLR4-responsive activation states of inflammatory response genes.

8 February 2020

cites work

1 reference

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

2 October 2017

1 reference

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Single-molecule imaging of transcriptionally coupled and uncoupled splicing

2 October 2017

1 reference

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Regulation of primary response genes

2 October 2017

1 reference

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Nuclear quality control of RNA polymerase II transcripts

2 October 2017

1 reference

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Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells

2 October 2017

1 reference

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A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells

2 October 2017

1 reference

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

2 October 2017

1 reference

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The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing

2 October 2017

1 reference

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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=3405548

Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

2 October 2017

1 reference

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Comprehensive comparative analysis of strand-specific RNA sequencing methods

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Selective transcription in response to an inflammatory stimulus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

BEDTools: a flexible suite of utilities for comparing genomic features

2 October 2017

1 reference

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Transcriptional control of the inflammatory response

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

"Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Metabolic tagging and purification of nascent RNA: implications for transcriptomics.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Rates of in situ transcription and splicing in large human 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=3405548

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

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=3405548

Control of inducible gene expression by signal-dependent transcriptional elongation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

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=3405548

Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Mapping and quantifying mammalian transcriptomes by RNA-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=3405548

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Exon tethering in transcription by RNA polymerase II

2 October 2017

1 reference

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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

2 October 2017

1 reference

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Toll-like receptors and innate antiviral responses

2 October 2017

1 reference

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Chromatin-remodelling factor BRG1 selectively activates a subset of interferon-alpha-inducible 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=3405548

Maximal induction of a subset of interferon target genes requires the chromatin-remodeling activity of the BAF 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=3405548

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=3405548

Identification of a common nucleotide sequence in the 3'-untranslated region of mRNA molecules specifying inflammatory mediators

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Steps in the processing of Ad2 mRNA: poly(A)+ nuclear sequences are conserved and poly(A) addition precedes 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=3405548

A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405548

10.1016/J.CELL.2012.05.043

23 September 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22817891%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22817891%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

PubMed publication ID

22817891

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22817891%20AND%20SRC:MED&resulttype=core&format=json