CTCF and HOXs

由 sufang 在 四, 11/20/2014 - 12:53 發表 EBV and KSHV CTCF

Mol Cell Biol. 2014 Oct;34(20):3867-79. doi: 10.1128/MCB.00567-14. Epub 2014 Aug 18.
CTCF controls HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure in NT2/D1 cells.
Xu M1, Zhao GN1, Lv X1, Liu G1, Wang LY2, Hao DL1, Wang J3, Liu DP4, Liang CC1.
Author information
Abstract

HOX cluster genes are activated sequentially in their positional order along the chromosome during vertebrate development. This phenomenon, known as temporal colinearity, depends on transcriptional silencing of 5' HOX genes. Chromatin looping was recently identified as a conserved feature of silent HOX clusters, with CCCTC-binding factor (CTCF) binding sites located at the loop bases. However, the potential contribution of CTCF to HOX cluster silencing and the underlying mechanism have not been established. Here, we demonstrate that the HOXA locus is organized by CTCF into chromatin loops and that CTCF depletion causes significantly enhanced activation of HOXA3 to -A7, -A9 to -A11, and -A13 in response to retinoic acid, with the highest effect observed for HOXA9. Our subsequent analyses revealed that CTCF facilitates the stabilization of Polycomb repressive complex 2 (PRC2) and trimethylated lysine 27 of histone H3 (H3K27me3) at the human HOXA locus. Our results reveal that CTCF functions as a controller of HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure.

Copyright © 2014, American Society for Microbiology. All Rights Reserved.

很玄但是非常重要的文章 CTCF

由 sufang 在 四, 05/15/2014 - 15:44 發表 EBV and KSHV chromosome conformation capture (3C) cohesion CTCF Topologically associated domain (TAD)

Cell. 2014 May 8;157(4):950-63. doi: 10.1016/j.cell.2014.03.025.

 

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.

Giorgetti L1, Galupa R1, Nora EP2, Piolot T1, Lam F1, Dekker J3, Tiana G4, Heard E5.
Author information

    1Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France.
    2Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.
    3Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA.
    4Dipartimento di Fisica, Università degli Studi di Milano and INFN, Via Celoria 16, 20133 Milano, Italy. Electronic address: guido.tiana@unimi.it.
    5Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France; Collège de France, 11 place Marcelin-Berthelot, Paris 75005, France. Electronic address: edith.heard@curie.fr.

Abstract

A new level of chromosome organization, topologically associating domains (TADs), was recently uncovered by chromosome conformation capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model's predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation. Copyright © 2014 Elsevier Inc. All rights reserved. PMID: 24813616

EVKV genome comparison

EVKV genome comparison

由 sufang 在 四, 12/13/2012 - 16:39 發表 

• EBV and KSHV
 
• EBV1
 
• KSHV_rc

捨不得丟掉的老圖