Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture

Cell Reports
Matteo Vietri RudanSuzana Hadjur

Abstract

Topological domains are key architectural building blocks of chromosomes, but their functional importance and evolutionary dynamics are not well defined. We performed comparative high-throughput chromosome conformation capture (Hi-C) in four mammals and characterized the conservation and divergence of chromosomal contact insulation and the resulting domain architectures within distantly related genomes. We show that the modular organization of chromosomes is robustly conserved in syntenic regions and that this is compatible with conservation of the binding landscape of the insulator protein CTCF. Specifically, conserved CTCF sites are co-localized with cohesin, are enriched at strong topological domain borders, and bind to DNA motifs with orientations that define the directionality of CTCF's long-range interactions. Conversely, divergent CTCF binding between species is correlated with divergence of internal domain structure, likely driven by local CTCF binding sequence changes, demonstrating how genome evolution can be linked to a continuous flux of local conformation changes. We also show that large-scale domains are reorganized during genome evolution as intact modules.

References

Mar 27, 2001·Molecular Biology and Evolution·E T Dermitzakis, A G Clark
Aug 11, 2007·Science·Anthony R BornemanMichael Snyder
Feb 2, 2008·Cell·Vania ParelhoMatthias Merkenschlager
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 27, 2009·The EMBO Journal·Tsuyoshi MishiroMitsuyoshi Nakao
Sep 11, 2012·Nature Methods·Harmen J G van de WerkenWouter de Laat
May 28, 2013·Cell·Jennifer E Phillips-CreminsVictor G Corces
Nov 5, 2013·The EMBO Journal·Sevil SofuevaSuzana Hadjur
Dec 18, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jessica ZuinKerstin S Wendt

❮ Previous
Next ❯

Citations

Oct 9, 2015·Critical Reviews in Biochemistry and Molecular Biology·Lijing YaoPeggy J Farnham
Feb 11, 2016·Trends in Genetics : TIG·Darío G LupiáñezStefan Mundlos
Jan 25, 2016·Current Opinion in Genetics & Development·Celia Pilar Martinez-Jimenez, Duncan T Odom
Jan 24, 2016·Current Opinion in Genetics & Development·Tamer AliMarek Bartkuhn
Dec 22, 2015·Cell Stem Cell·Xiong JiRichard A Young
Feb 8, 2016·Current Opinion in Cell Biology·M Jordan Rowley, Victor G Corces
Nov 13, 2015·Wiley Interdisciplinary Reviews. Developmental Biology·Silvia RemeseiroFrançois Spitz
Jun 10, 2015·FEBS Letters·Ivan JunierFrançois le Dily
May 27, 2015·FEBS Letters·Caelin Cubeñas-Potts, Victor G Corces
Sep 15, 2015·FEBS Letters·Maxim V ImakaevLeonid A Mirny
Sep 9, 2015·FEBS Letters·Job Dekker, Edith Heard
Apr 29, 2015·FEBS Letters·Andreas Hofmann, Dieter W Heermann
Jul 21, 2015·Journal of Cellular Biochemistry·Andrew FritzGary S Stein
Sep 30, 2015·Nucleus·Caelin Cubeñas-Potts, Victor G Corces
Mar 5, 2016·Current Opinion in Cell Biology·Irina SoloveiYana Feodorova
Dec 15, 2015·Seminars in Cell & Developmental Biology·Chenhuan Xu, Victor G Corces
Dec 18, 2015·Seminars in Cell & Developmental Biology·Ignacio Maeso, Juan J Tena
Nov 4, 2015·Molecular Cell·Elzo de WitWouter de Laat
Mar 12, 2016·Cell·Job Dekker, Leonid Mirny
Oct 7, 2015·Trends in Genetics : TIG·Matteo Vietri Rudan, Suzana Hadjur
Mar 24, 2016·BMC Genomics·Martin OtiHuiqing Zhou
May 24, 2016·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Haiyan Huang, Qiang Wu
Mar 31, 2016·Biophysical Journal·Guido TianaLuca Giorgetti
Aug 16, 2015·Cell·Michael H Nichols, Victor G Corces
Aug 27, 2015·Genome Biology·Takashi NaganoPeter Fraser
Apr 1, 2015·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Ignacio Maeso
Jul 25, 2015·Briefings in Functional Genomics·Clara Lopes Novo, Peter J Rugg-Gunn
Jun 26, 2015·Epigenomics·Pedro P RochaJane A Skok
Apr 22, 2016·Cellular and Molecular Life Sciences : CMLS·Sonia YuWen H Shen
Apr 26, 2016·Current Opinion in Genetics & Development·Anne-Laure Valton, Job Dekker
Dec 1, 2015·PloS One·Giorgio Bernardi
May 21, 2016·Trends in Cell Biology·Marianne EntrevanGiacomo Cavalli
May 24, 2016·Cell Reports·Geoffrey FudenbergLeonid A Mirny
Jun 4, 2016·Molecular Cell·Jesse R DixonBing Ren
Jun 7, 2016·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Jonathan A Beagan, Jennifer E Phillips-Cremins
Jun 12, 2016·Chromosoma·Sergey V Razin, Yegor S Vassetzky
Jun 18, 2016·Trends in Genetics : TIG·Adriana Gonzalez-Sandoval, Susan M Gasser
Jul 2, 2016·Seminars in Cell & Developmental Biology·François Spitz

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSM769019

Methods Mentioned

BETA
Hi-C
immunoprecipitation
ChIP-seq
Hi-seq
ChIP

Software Mentioned

liftOver
Bowtie

Related Concepts

Related Feeds

Autoimmune Polyendocrine Syndromes

This feed focuses on a rare genetic condition called Autoimmune Polyendocrine Syndromes, which are characterized by autoantibodies against multiple endocrine organs. This can lead to Type I Diabetes.

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

Autoimmune Polyendocrinopathies

Autoimmune polyendocrinopathies, also called polyglandular autoimmune syndromes (PGASs), or polyendocrine autoimmune syndromes(PASs), are a heterogeneous group of rare diseases characterized by autoimmune activity against more than one endocrine organ, although non-endocrine organs can be affected. Discover the latest research on autoimmune polyendocrinopathies here.