Intergenic transcription causes repression by directing nucleosome assembly (Q27930707)

GOA release 2020-03-11

author name string

Sarah J Hainer

1

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Robin M Monteverde

4

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Rachel D Mitchell

3

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Justin A Pruneski

2

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Joseph A Martens

Most "dark matter" transcripts are associated with known genes

5

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language of work or name

English

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publication date

1 January 2011

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1 reference

1 December 2016

25

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issue

1

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page(s)

29-40

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cites work

1 reference

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20 March 2017

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20 March 2017

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20 March 2017

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20 March 2017

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20 March 2017

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Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions

20 March 2017

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Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation

20 March 2017

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Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex

20 March 2017

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

20 March 2017

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Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements.

20 March 2017

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Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene

20 March 2017

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Transcription elongation factors repress transcription initiation from cryptic sites.

20 March 2017

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Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN.

20 March 2017

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20 March 2017

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20 March 2017

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SPT10 and SPT21 are required for transcription of particular histone genes in Saccharomyces cerevisiae

20 March 2017

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Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C

20 March 2017

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20 March 2017

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FACT facilitates transcription-dependent nucleosome alteration

20 March 2017

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

20 March 2017

1 reference

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20 March 2017

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Genome-wide map of nucleosome acetylation and methylation in yeast

7 April 2017

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Non-coding RNAs: Meet thy masters

7 April 2017

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The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

29 September 2017

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Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiae

29 September 2017

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Regulation of proto-oncogene transcription, cell proliferation, and tumorigenesis in mice by PSF protein and a VL30 noncoding RNA.

29 September 2017

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Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

29 September 2017

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Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome

29 September 2017

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Pervasive transcription constitutes a new level of eukaryotic genome regulation

29 September 2017

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Role of human noncoding RNAs in the control of tumorigenesis

29 September 2017

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Divergent transcription: a new feature of active promoters

29 September 2017

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What controls nucleosome positions?

29 September 2017

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

29 September 2017

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29 September 2017

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

The DNA-encoded nucleosome organization of a eukaryotic genome

29 September 2017

1 reference

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Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

29 September 2017

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Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs

29 September 2017

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Non-coding RNAs in imprinted gene clusters

29 September 2017

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A high-resolution atlas of nucleosome occupancy in yeast

29 September 2017

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Transcriptional interference: an unexpected layer of complexity in gene regulation

29 September 2017

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29 September 2017

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Nucleosome positioning signals in genomic DNA

29 September 2017

1 reference

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state

29 September 2017

1 reference

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A site to remember: H3K36 methylation a mark for histone deacetylation

29 September 2017

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Transcriptional noise and the fidelity of initiation by RNA polymerase II.

29 September 2017

1 reference

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Repression of ADH1 and ADH3 during zinc deficiency by Zap1-induced intergenic RNA transcripts.

29 September 2017

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Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae.

29 September 2017

1 reference

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29 September 2017

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The Snf1 protein kinase and Sit4 protein phosphatase have opposing functions in regulating TATA-binding protein association with the Saccharomyces cerevisiae INO1 promoter

29 September 2017

1 reference

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Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II.

29 September 2017

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Spt10-dependent transcriptional activation in Saccharomyces cerevisiae requires both the Spt10 acetyltransferase domain and Spt21

29 September 2017

1 reference

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The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo

29 September 2017

1 reference

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Evidence that Swi/Snf directly represses transcription in S. cerevisiae

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

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29 September 2017

1 reference

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Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.

29 September 2017

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Intergenic transcription and transinduction of the human beta-globin locus

29 September 2017

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Organization of theGAL1–GAL10intergeaic control region chromatin

29 September 2017

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29 September 2017

1 reference

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H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Antisense transcription controls cell fate in Saccharomyces cerevisiae

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Antagonistic forces that position nucleosomes in vivo.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Intergenic transcription through a polycomb group response element counteracts silencing

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Histone chaperone spt16 promotes redeposition of the original h3-h4 histones evicted by elongating RNA polymerase.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

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

27 November 2018

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Evidence for nucleosome depletion at active regulatory regions genome-wide

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012934

From bacteria to humans, chromatin to elongation, and activation to repression: The expanding roles of noncoding RNAs in regulating transcription

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21156811

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21156811

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Nucleosome positions predicted through comparative genomics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21156811

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GAD.1975011

1 reference

1338415

1338415

1 reference

1 reference

1 reference