The c-<i>myc</i> Insulator Element and Matrix Attachment Regions Definethe c-<i>myc</i> ChromosomalDomain

Gombert, Wendy M.; Farris, Stephen; Rubio, Eric D.; Morey-Rosler, Kristin M.; Schubach, William H.; Krumm, Anton

doi:10.1128/mcb.23.24.9338-9348.2003

Cited by 72 publications

(91 citation statements)

References 50 publications

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“…The results demonstrate that H2A.Z associates with the c-myc promoter in both resting and stimulated CTLL-2 cells. H2A.Z decorates the entire promoter region (ϳ2.5 kb) up to the binding site of CTCF, which we have shown to be part of the c-myc insulator element MINE located upstream of the transcription start site (15). Thus, consistent with the hypothesis that H2A.Z inhibits the spreading of silent heterochromatin, this histone variant demarcates the c-myc gene domain.…”

Section: Histone Subdomains Across Transcribed Regions Of Mamma-supporting

confidence: 69%

“…RNA Analysis-Nuclease S1 protection assays were performed as described previously (15), Northern analysis followed the previously published protocol (14).…”

Section: Methodsmentioning

confidence: 99%

“…Chromatin Immunoprecipitation-Chromatin immunoprecipitation (ChIP) experiments were performed as described (15). The total amount of antibody used in one chromatin immunoprecipitation was 10 g.…”

Section: Methodsmentioning

confidence: 99%

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Transcription-induced Chromatin Remodeling at the c-myc Gene Involves the Local Exchange of Histone H2A.Z

Farris

Rubio

Moon

et al. 2005

Journal of Biological Chemistry

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The post-translational modification of histones and the incorporation of core histone variants play key roles in governing gene expression. Many eukaryotic genes regulate their expression by limiting the escape of RNA polymerase from promoter-proximal pause sites. Here we report that elongating RNA polymerase II complexes encounter distinct chromatin landscapes that are marked by methylation of lysine residues Lys 4 , Lys 79 , and Lys 36 of histone H3. However, neither histone methylation nor acetylation directly regulates the release of elongation complexes stalled at promoter-proximal pause sites of the c-myc gene. In contrast, transcriptional activation is associated with local displacement of the histone variant H2A.Z within the transcribed region and incorporation of the major histone variant H2A. This result indicates that transcribing RNA polymerase II remodels chromatin in part through coincident displacement of H2A.Z-H2B dimers and incorporation of H2A-H2B dimers. In combination, these results suggest a new model in which the incorporation of H2A.Z into nucleosomes down-regulates transcription; at the same time it may act as a cellular memory for transcriptionally poised gene domains. RNA pol II1 encounters nucleosomes and other multiprotein complexes during transcription. Conceptually, any mechanism that destabilizes the DNA-histone interaction or removes part or all of the histone octamer potentially increases the elongation efficiency of RNA polymerases. Protein complexes such as FACT, Elongator, and Swi/Snf have been proposed to alleviate barriers that are imposed by chromatin (1-3). For instance, the protein complex FACT assists RNA polymerase during elongation by altering the nucleosomal conformation and destabilizing the interaction between the H2A/H2B dimer and the (H3/H4) 2 tetramer (4). After the transcription complex has passed the nucleosome, FACT participates in the reassembly of the nucleosome. In addition to the FACT-mediated catalytic remodeling of nucleosomes, the post-translational modification of histones, and/or the incorporation of histone variants also may facilitate the passage of the transcription complex through nucleosomes (5-7). For example, the identification of the acetyltransferase activity in the Elp3 subunit of the RNA pol II-associated Elongator complex suggests that histone acetylation is an important component in the regulation of transcription elongation (8,9). Indeed, previous studies demonstrated that the yeast Elongator complex is associated with nascent transcripts (2). In addition to histone acetylation, methylation of H3 lysine residues Lys -specific histone demethylase LSD1 suggests a model in which RNA polymerase II elongation is regulated by the antagonistic action of histone methyltransferases and histone demethylases (12). Alternatively, a replication-independent histone exchange pathway in which variant forms of histones are incorporated during active transcription may provide an opportunity to continuously exchange histones with either hyper-or hypomethyl...

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Section: Histone Subdomains Across Transcribed Regions Of Mamma-supporting

confidence: 69%

“…RNA Analysis-Nuclease S1 protection assays were performed as described previously (15), Northern analysis followed the previously published protocol (14).…”

Section: Methodsmentioning

confidence: 99%

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Transcription-induced Chromatin Remodeling at the c-myc Gene Involves the Local Exchange of Histone H2A.Z

Farris

Rubio

Moon

et al. 2005

Journal of Biological Chemistry

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“…Chromatin corresponding to 2 ϫ 10 7 cells was immunoprecipitated with anti-CTCF antibody (Upstate Biotechnology, 06-917), anti-Scc3/SA1 antibody (Abcam, #4457), or antitrimethyl-Histone-H3 (3MK9, Upstate Biotechnology, #07-442). Immunoprecipitates were washed, the DNA-protein cross-links reversed, and the recovered DNA was tested in regular conventional quantitative PCR as described (13). Sequences of primers specific for gene loci under study and reference primers (␤-globin) are available upon request.…”

Section: Lc-ms/ms and Datamentioning

confidence: 99%

“…CTCF is present at the boundary between genes that are subject to X inactivation and genes that escape this silencing (11,12). CTCF is also an integral component of the c-myc insulator element MINE that separates the transcriptionally active c-myc gene from surrounding chromatin that bears features typical for heterochromatin (13). The mode of action of CTCF at this genomic region, however, is unclear.…”

mentioning

confidence: 99%

CTCF physically links cohesin to chromatin

Rubio¹,

Reiss

Welcsh³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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448

382

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Cohesin is required to prevent premature dissociation of sister chromatids after DNA replication. Although its role in chromatid cohesion is well established, the functional significance of cohesin's association with interphase chromatin is not clear. Using a quantitative proteomics approach, we show that the STAG1 (Scc3/ SA1) subunit of cohesin interacts with the CCTC-binding factor CTCF bound to the c-myc insulator element. Both allele-specific binding of CTCF and Scc3/SA1 at the imprinted IGF2/H19 gene locus and our analyses of human DM1 alleles containing base substitutions at CTCF-binding motifs indicate that cohesin recruitment to chromosomal sites depends on the presence of CTCF. A large-scale genomic survey using ChIP-Chip demonstrates that Scc3/SA1 binding strongly correlates with the CTCF-binding site distribution in chromosomal arms. However, some chromosomal sites interact exclusively with CTCF, whereas others interact with Scc3/SA1 only. Furthermore, immunofluorescence microscopy and ChIP-Chip experiments demonstrate that CTCF associates with both centromeres and chromosomal arms during metaphase. These results link cohesin to gene regulatory functions and suggest an essential role for CTCF during sister chromatid cohesion. These results have implications for the functional role of cohesin subunits in the pathogenesis of Cornelia de Lange syndrome and Roberts syndromes.cohesion ͉ transcription ͉ insulator ͉ centromere ͉ metaphase

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Chromatin Insulators and Epigenetic Inheritance in Health and Disease

Yang

Corcés

2012

Toxicology and Epigenetics

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The c-myc Insulator Element and Matrix Attachment Regions Definethe c-myc ChromosomalDomain

Cited by 72 publications

References 50 publications

Transcription-induced Chromatin Remodeling at the c-myc Gene Involves the Local Exchange of Histone H2A.Z

Transcription-induced Chromatin Remodeling at the c-myc Gene Involves the Local Exchange of Histone H2A.Z

CTCF physically links cohesin to chromatin

Chromatin Insulators and Epigenetic Inheritance in Health and Disease

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