Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions

Garcia, Jennifer F.; Dumesic, Phillip A.; Hartley, Philip; El-Samad, Hana; Madhani, Hiten D.

doi:10.1101/gad.1946410

Cited by 59 publications

(98 citation statements)

References 60 publications

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“…This is consistent with the H3 ChIP-seq and nucleosome positioning data that show a nucleosome-free region between SPAC212.10 and SPAC212.09c in caf1Δdcr1Δ (Fig. 3B) and clr4Δ cells (Garcia et al 2010). Northern blot analysis confirms that tlh RNA is longer in caf1Δdcr1Δ and caf1Δago1Δ cells than in ago1Δ or caf1Δ cells (Fig.…”

Section: Absence Of Rna Degradation Leads To Changes In Chromatin Orgsupporting

confidence: 77%

Accumulation of RNA on chromatin disrupts heterochromatic silencing

Brönner¹,

Salvi²,

Zocco³

et al. 2017

Genome Res.

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Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochromatin is lost at transcribed regions in the absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA: RNA hybrids, and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing. The Ccr4-Not complex is localized to chromatin independently of H3K9me and degrades chromatin-associated transcripts, which is required for transcriptional silencing. Overexpression of heterochromatic RNA, but not euchromatic RNA, leads to chromatin localization and loss of silencing of a distant ade6 reporter in wild-type cells. Our results demonstrate that chromatin-bound RNAs disrupt heterochromatin organization and need to be degraded in a process of heterochromatin formation.

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Section: Absence Of Rna Degradation Leads To Changes In Chromatin Orgsupporting

confidence: 77%

Accumulation of RNA on chromatin disrupts heterochromatic silencing

Brönner¹,

Salvi²,

Zocco³

et al. 2017

Genome Res.

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“…Previous studies have implicated a role for Mit1 in positioning nucleosomes (19,20). In this study, we demonstrated that Mit1 is indeed a nucleosome remodeling factor capable of mobilizing histone octamers in vitro, with characteristics similar to those of Mi-2 remodelers.…”

mentioning

confidence: 50%

“…One mechanism by which heterochromatin can restrict RNA polymerase II accessibility is through altering nucleosomal occupancy to prevent access of transcription factors to their target sequences. Heterochromatin prevents the appearance of nucleosome-free regions (NFRs) at various locations in silenced regions of the genome, and nucleosome occupancy at some of these sites has been shown to depend on Mit1/SHREC (7,9,20,39). Interestingly, the sites that most depend on Mit1 do not map to sites of transcription initiation or to regions particularly enriched for RNA Pol II.…”

Section: ⌬Phd and Mit1mentioning

confidence: 99%

The Mi-2 Homolog Mit1 Actively Positions Nucleosomes within Heterochromatin To Suppress Transcription

Creamer

Job

Shanker

et al. 2014

Molecular and Cellular Biology

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Mit1 is the putative chromatin remodeling subunit of the fission yeast Snf2/histone deacetylase (HDAC) repressor complex (SHREC) and is known to repress transcription at regions of heterochromatin. However, how Mit1 modifies chromatin to silence transcription is largely unknown. Here we report that Mit1 mobilizes histone octamers in vitro and requires ATP hydrolysis and conserved chromatin tethering domains, including a previously unrecognized chromodomain, to remodel nucleosomes and silence transcription. Loss of Mit1 remodeling activity results in nucleosome depletion at specific DNA sequences that display low intrinsic affinity for the histone octamer, but its contribution to antagonizing RNA polymerase II (Pol II) access and transcription is not restricted to these sites. Genetic epistasis analyses demonstrate that SHREC subunits and the transcriptioncoupled Set2 histone methyltransferase, which is involved in suppression of cryptic transcription at actively transcribed regions, cooperate to silence heterochromatic transcripts. In addition, we have demonstrated that Mit1's remodeling activity contributes to SHREC function independently of Clr3's histone deacetylase activity on histone H3 K14. We propose that Mit1 is a chromatin remodeling factor that cooperates with the Clr3 histone deacetylase of SHREC and other chromatin modifiers to stabilize heterochromatin structure and to prevent access to the transcriptional machinery.

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“…The recent finding that different NDRs depend on the binding of different proteins and epigenetic modifications in S. pombe (Garcia et al, 2010) and in S. cerevisiae (Bai et al, 2011) suggests that only some combinations of them would make a NDR competent for recruiting the recombination machinery.…”

Section: Specification Of Meiotic Dsb Sites In S Pombementioning

confidence: 99%

Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

et al. 2011

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In Schizosaccharomyces pombe, DNA replication origins (ORIs) and meiotic recombination hotspots lack consensus sequences and show a bias towards mapping to large intergenic regions (IGRs). To explore whether this preference depended on underlying chromatin features, we have generated genome-wide nucleosome profiles during mitosis and meiosis. We have found that meiotic double-strand break sites (DSBs) colocalize with nucleosome-depleted regions (NDRs) and that large IGRs include clusters of NDRs that overlap with almost half of all DSBs. By contrast, ORIs do not colocalize with NDRs and they are regulated independently of DSBs. Physical relocation of NDRs at ectopic loci or modification of their genomic distribution during meiosis was paralleled by the generation of new DSB sites. Over 80% of all meiotic DSBs colocalize with NDRs that are also present during mitosis, indicating that the recombination pattern is largely dependent on constitutive properties of the genome and, to a lesser extent, on the transcriptional profile during meiosis. The organization of ORIs and of DSBs regions in S. pombe reveals similarities and differences relative to Saccharomyces cerevisiae.

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Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions

Cited by 59 publications

References 60 publications

Accumulation of RNA on chromatin disrupts heterochromatic silencing

Accumulation of RNA on chromatin disrupts heterochromatic silencing

The Mi-2 Homolog Mit1 Actively Positions Nucleosomes within Heterochromatin To Suppress Transcription

Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

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