(Q34430701)

2 August 2017

title

ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape (English)

1 reference

2 August 2017

Eric A Alcid

1

1 reference

2 August 2017

Toshio Tsukiyama

series ordinal

2

1 reference

2 August 2017

publication date

1 November 2014

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2 August 2017

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2 August 2017

volume

28

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2 August 2017

issue

21

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2 August 2017

page(s)

2348-2360

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

2 August 2017

cites work

1 reference

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6 July 2018

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Long noncoding RNAs in cell-fate programming and reprogramming

6 July 2018

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6 July 2018

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6 July 2018

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Transcriptome surveillance by selective termination of noncoding RNA synthesis.

6 July 2018

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Genomic organization of human transcription initiation complexes

6 July 2018

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Bimodal expression of PHO84 is modulated by early termination of antisense transcription.

6 July 2018

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6 July 2018

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X-inactivation, imprinting, and long noncoding RNAs in health and disease

6 July 2018

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Long noncoding RNAs: cellular address codes in development and disease

6 July 2018

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Is junk DNA bunk? A critique of ENCODE

6 July 2018

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A role for the nucleoporin Nup170p in chromatin structure and gene silencing

6 July 2018

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Genome-wide nucleosome positioning during embryonic stem cell development

6 July 2018

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Landscape of transcription in human cells

6 July 2018

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Genome-wide nucleosome specificity and directionality of chromatin remodelers.

6 July 2018

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A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods

6 July 2018

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Genome-wide structure and organization of eukaryotic pre-initiation complexes

6 July 2018

1 reference

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Compatibility with killer explains the rise of RNAi-deficient fungi

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Nascent transcript sequencing visualizes transcription at nucleotide resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Differential expression analysis for sequence count data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Long noncoding RNA as modular scaffold of histone modification complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

BEDTools: a flexible suite of utilities for comparing genomic features

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

6 July 2018

RNAi in budding yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Transcriptome analysis by strand-specific sequencing of complementary DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

The Sequence Alignment/Map format and SAMtools

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Mechanisms that specify promoter nucleosome location and identity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Bidirectional promoters generate pervasive transcription in yeast

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Long intronic noncoding RNA transcription: expression noise or expression choice?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

The transcriptional landscape of the yeast genome defined by RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Chromatin remodelling at promoters suppresses antisense transcription

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Antisense transcription controls cell fate in Saccharomyces cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Systematic genetic analysis with ordered arrays of yeast deletion mutants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

The Sequence of the Human Genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4215180

27 October 2018

Identifiers

DOI

10.1101/GAD.250902.114

1 reference

2 August 2017

1 reference

2 August 2017

1 reference