CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin

Burke, Les J.; Zhang, Ru; Bartkuhn, Marek; Tiwari, Vijay; Tavoosidana, Gholamreza; Kurukuti, Sreenivasulu; Weth, Christine; Leers, Joerg; Galjart, Niels; Ohlsson, Rolf; Renkawitz, Rainer

doi:10.1038/sj.emboj.7600793

Cited by 120 publications

(125 citation statements)

References 62 publications

Supporting

Mentioning

115

Contrasting

Order By: Relevance

“…S6). Our results confirm previous reports that a large fraction of CTCF remains associated with chromosomes during metaphase (24). Seventy of 147 CTCF sites detected in asynchronously growing HBL100 cells were also found in chromatin of mitotic HBL100 cells (Fig.…”

Section: Detection Of Ctcf Interacting Proteins By Isotope Coded Affisupporting

confidence: 82%

See 1 more Smart Citation

CTCF physically links cohesin to chromatin

Rubio¹,

Reiss

Welcsh³

et al. 2008

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

448

382

View full text Add to dashboard Cite

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

show abstract

Section: Detection Of Ctcf Interacting Proteins By Isotope Coded Affisupporting

confidence: 82%

“…6A, Table S4, and ref. 24). Thus, in combination, our data suggest that CTCF is required for cohesin binding in interphase and mitotic cells.…”

Section: Discussionsupporting

confidence: 53%

CTCF physically links cohesin to chromatin

Rubio¹,

Reiss

Welcsh³

et al. 2008

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

448

382

View full text Add to dashboard Cite

show abstract

“…At least in the instance of the ICR-DMR1 complex, this interaction survives mitosis, suggesting that it is part of an epigenetic memory (39). It is important to realize that our analysis and therefore the model arising from it ( Fig.…”

Section: Discussionmentioning

confidence: 99%

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

Kurukuti

Tiwari²,

Tavoosidana³

et al. 2006

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

Self Cite

481

420

View full text Add to dashboard Cite

It is thought that the H19 imprinting control region (ICR) directs the silencing of the maternally inherited Igf2 allele through a CTCFdependent chromatin insulator. The ICR has been shown to interact physically with a silencer region in Igf2, differentially methylated region (DMR)1, but the role of CTCF in this chromatin loop and whether it restricts the physical access of distal enhancers to Igf2 is not known. We performed systematic chromosome conformation capture analyses in the Igf2͞H19 region over >160 kb, identifying sequences that interact physically with the distal enhancers and the ICR. We found that, on the paternal chromosome, enhancers interact with the Igf2 promoters but that, on the maternal allele, this is prevented by CTCF binding within the H19 ICR. CTCF binding in the maternal ICR regulates its interaction with matrix attachment region (MAR)3 and DMR1 at Igf2, thus forming a tight loop around the maternal Igf2 locus, which may contribute to its silencing. Mutation of CTCF binding sites in the H19 ICR leads to loss of CTCF binding and de novo methylation of a CTCF target site within Igf2 DMR1, showing that CTCF can coordinate regional epigenetic marks. This systematic chromosome conformation capture analysis of an imprinting cluster reveals that CTCF has a critical role in the epigenetic regulation of higher-order chromatin structure and gene silencing over considerable distances in the genome.genomic imprinting ͉ insulators ͉ chromosome biology A variety of control elements, such as enhancers, silencers, and chromatin insulators, are thought to establish and maintain domains of gene expression or repression in the genome. Insulators, for example, are needed to keep genes in silent domains, away from the influence of neighboring enhancers. The prototypical insulator from the chicken ␤-globin locus contains binding sites for the 11-zinc-finger protein CTCF, and binding of CTCF is necessary for insulator function, not only in the chicken but also in many mammalian insulators (1-4). How CTCF confers chromatin insulation is not clear, but recent work shows that DNA-bound CTCF molecules can dimerize in a binding site-specific fashion (5) and that CTCF binds nucleophosmin and may be tethered to the nuclear matrix (6). CTCF emerges, therefore, as a potential mediator of long-range interactions that are involved in establishing repressed domains.Regional coordination of gene expression and repression is found in many imprinted gene clusters in the mammalian genome and is regulated by imprinting centers or imprinting control regions (ICRs) (7-10). A well characterized cluster is that containing the paternally expressed Igf2 and maternally expressed H19. Both genes share enhancers, and the ICR is located in the 5Ј flank of the H19 gene (11). The deletion of this ICR results in biallelic expression of both Igf2 and H19, demonstrating a role of the ICR to repress the maternal Igf2 allele, which is located Ͼ80 kb away (12). The mechanism underlying this function has been proposed to involve a CTCF-dependent...

show abstract

“…The very similar outcome of co-localization analysis for omoWeak with CTCF signals and flexible regions would suggest a relationship of these words with some aspects of chromatin structure. Indeed CTCF binding sites regulate chromatin domains activity [8] whilst flexible regions mediate DNAprotein binding processes and specific interactions of DNA metabolism [17]. Interestingly, both these sequence-dependent parameters that are not related to specific sequences, colocalize with words along the whole genes independently of sequence identity.…”

Section: Final Remarksmentioning

confidence: 99%

A top-down linguistic approach to the analysis of genomic sequences: The metabotropic glutamate receptors 1 and 5 in human and in mouse as a case study

Menconi

Puliti

Sbrana

et al. 2011

Journal of Theoretical Biology

View full text Add to dashboard Cite

. A top-down linguistic approach to the analysis of genomic sequences: The metabotropic glutamate receptors 1 and 5 in human and in mouse as a case study. Journal of Theoretical Biology, Elsevier, 2011, 270 (1) This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.A top-down linguistic approach to the analysis of genomic sequences: The metabotropic Glutamate receptors 1 and 5 in Human and in Mouse as a case study AbstractThis paper presents a top-down strategy to detect features in genomic sequences. The strategy's core is to exploit dictionary-based compression algorithms and analyze the content of the automatically generated dictionary. We classify the different over-represented words and in the case study we correlate them to experimentally identified or theoretically forecasted biological features. A large spectrum analysis reveals that the only feature co-located with the a priori extracted words is the torsional flexibility of DNA, while non-B DNA configurations are anti-localized and other features are mostly independent of the extracted words. This analysis unravels complex relationships between the linguistic structures investigated under our approach and some known biological features.

show abstract

CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin

Cited by 120 publications

References 62 publications

CTCF physically links cohesin to chromatin

CTCF physically links cohesin to chromatin

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

A top-down linguistic approach to the analysis of genomic sequences: The metabotropic glutamate receptors 1 and 5 in human and in mouse as a case study

Contact Info

Product

Resources

About