Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

Liang, Jun; Lacroix, Laurent; Gamot, Adrien; Cuddapah, Suresh; Queillé, Sophie; Lhoumaud, Priscillia; Lepetit, Pierre; Martin, Pascal G.P.; Vogelmann, Jutta; Court, Franck; Hennion, Magali; Micas, Gaël; Urbach, Serge; Bouchez, Olivier; Nöllmann, Marcelo; Zhao, Keji; Emberly, Eldon; Cuvier, Olivier

doi:10.1016/j.molcel.2013.12.029

Cited by 115 publications

(172 citation statements)

References 41 publications

(104 reference statements)

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“…PRDM9 could thus interact indirectly with DNA sequences located on the axis, and the allele specificity of these sites favors a model where PRDM9 molecules bound to class 1 sites are involved in these interactions, as discussed above. An example of such indirect interactions involves the insulator protein BEAF-32 (Liang et al 2014). According to this model, the class 2B signal uncovered by our analysis reveals an interaction between two genomic loci: one DSB site and one axis-associated region (Fig.…”

Section: Dom2mentioning

confidence: 67%

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

et al. 2017

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In mouse and human meiosis, DNA double-strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence-specific DNA binding domain of the PRDM9 histone methyl transferase. Here, we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a noncanonical recruitment of PRDM9 to sites that lack recombination activity and the PRDM9 binding consensus motif. These sites include gene promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset reveals DSB-independent interactions between PRDM9 and genomic sites, such as the binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic sequences located on the chromosome axis.

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Section: Dom2mentioning

confidence: 67%

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

et al. 2017

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“…The subtelomeric clustering and Tf2 LTR proximity of the majority of Nts1, and many Clr6, coregulated loci could support such a model, given that these genomic features are organized in transcriptionally repressive subnuclear domains (e.g., see reference 12). In this regard, long-range interactions mediated by complex I== are a possibility (48,49). Alternatively, complex I== may dynamically associate with the genes deregulated by deleting Nts1, and the threshold for significance in our ChIP-seq analyses may have obscured such associations.…”

Section: Discussionmentioning

confidence: 97%

A Novel Histone Deacetylase Complex in the Control of Transcription and Genome Stability

Zilio

Codlin

Vashisht

et al. 2014

Molecular and Cellular Biology

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The acetylation state of histones, controlled by histone acetyltransferases (HATs) and deacetylases (HDACs), profoundly affects DNA transcription and repair by modulating chromatin accessibility to the cellular machinery. The Schizosaccharomyces pombe HDAC Clr6 (human HDAC1) binds to different sets of proteins that define functionally distinct complexes: I, I=, and II. Here, we determine the composition, architecture, and functions of a new Clr6 HDAC complex, I==, delineated by the novel proteins Nts1, Mug165, and Png3. Deletion of nts1 causes increased sensitivity to genotoxins and deregulated expression of Tf2 elements, long noncoding RNA, and subtelomeric and stress-related genes. Similar, but more pervasive, phenotypes are observed upon Clr6 inactivation, supporting the designation of complex I== as a mediator of a key subset of Clr6 functions. We also reveal that with the exception of Tf2 elements, the genome-wide loading sites and loci regulated by Clr6 I؆ do not correlate. Instead, Nts1 loads at genes that are expressed in midmeiosis, following oxidative stress, or are periodically expressed. Collective data suggest that Clr6 I== has (i) indirect effects on gene expression, conceivably by mediating higher-order chromatin organization of subtelomeres and Tf2 elements, and (ii) direct effects on the transcription of specific genes in response to certain cellular or environmental stimuli.

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“…The Su(Hw), dCTCF, and BEAF-32 proteins interact with Centrosomal Protein 190 kD, named CP190 (Pai et al 2004;Gerasimova et al 2007;Mohan et al 2007;Bartkuhn et al 2009;Oliver et al 2010;Liang et al 2014). CP190 (1096 amino acids) contains an N-terminal BTB/POZ domain, an aspartic-acid-rich D-region, four C2H2 zinc-finger motifs, and a C-terminal E-rich domain (Oliver et al 2010;Ahanger et al 2013).…”

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confidence: 99%

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

et al. 2014

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Insulators are multiprotein-DNA complexes that regulate the nuclear architecture. The Drosophila CP190 protein is a cofactor for the DNA-binding insulator proteins Su(Hw), CTCF, and BEAF-32. The fact that CP190 has been found at genomic sites devoid of either of the known insulator factors has until now been unexplained. We have identified two DNA-binding zinc-finger proteins, Pita, and a new factor named ZIPIC, that interact with CP190 in vivo and in vitro at specific interaction domains. Genomic binding sites for these proteins are clustered with CP190 as well as with CTCF and BEAF-32. Model binding sites for Pita or ZIPIC demonstrate a partial enhancer-blocking activity and protect gene expression from PRE-mediated silencing. The function of the CTCF-bound MCP insulator sequence requires binding of Pita. These results identify two new insulator proteins and emphasize the unifying function of CP190, which can be recruited by many DNA-binding insulator proteins.

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Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

Cited by 115 publications

References 41 publications

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

A Novel Histone Deacetylase Complex in the Control of Transcription and Genome Stability

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

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