CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.

[1]  A. West,et al.  The Protein CTCF Is Required for the Enhancer Blocking Activity of Vertebrate Insulators , 1999, Cell.

[2]  Dirk Schübeler,et al.  Nuclear compartmentalization and gene activity , 2000, Nature Reviews Molecular Cell Biology.

[3]  S. Fiering,et al.  To be or not to be active: the stochastic nature of enhancer action. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[4]  G. Felsenfeld,et al.  Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene , 2000, Nature.

[5]  John T. Dimos,et al.  A Stem Cell Molecular Signature , 2002, Science.

[6]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[7]  G. Felsenfeld,et al.  CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. , 2004, Molecular cell.

[8]  K. O'Shea,et al.  Self-renewal vs. Differentiation of Mouse Embryonic Stem Cells1 , 2004, Biology of reproduction.

[9]  R. Ghirlando,et al.  Chromatin boundaries and chromatin domains. , 2004, Cold Spring Harbor symposia on quantitative biology.

[10]  Wolf Reik,et al.  Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops , 2004, Nature Genetics.

[11]  R. Eils,et al.  Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes , 2005, PLoS biology.

[12]  Hui Ling Chen,et al.  CTCF Mediates Interchromosomal Colocalization Between Igf2/H19 and Wsb1/Nf1 , 2006, Science.

[13]  Tom Misteli,et al.  Chromatin in pluripotent embryonic stem cells and differentiation , 2006, Nature Reviews Molecular Cell Biology.

[14]  N. Galjart,et al.  CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. , 2007, Genes & development.

[15]  R. Kamakaka,et al.  Chromatin insulators. , 2006, Annual review of genetics.

[16]  Wouter de Laat,et al.  CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. , 2006, Genes & development.

[17]  K. Sandhu,et al.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions , 2006, Nature Genetics.

[18]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[19]  Wouter de Laat,et al.  Quantitative analysis of chromosome conformation capture assays (3C-qPCR) , 2007, Nature Protocols.

[20]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[21]  Guillaume J. Filion,et al.  Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic , 2007, Science.

[22]  J. Chung,et al.  Analysis of the H19ICR Insulator , 2007, Molecular and Cellular Biology.

[23]  Michael Q. Zhang,et al.  Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome , 2007, Cell.

[24]  W. Reik Stability and flexibility of epigenetic gene regulation in mammalian development , 2007, Nature.

[25]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[26]  T. Misteli Beyond the Sequence: Cellular Organization of Genome Function , 2011 .

[27]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[28]  M. Vigneron,et al.  CTCF Interacts with and Recruits the Largest Subunit of RNA Polymerase II to CTCF Target Sites Genome-Wide , 2007, Molecular and Cellular Biology.

[29]  Weiwei Zhang,et al.  Zic3 is required for maintenance of pluripotency in embryonic stem cells. , 2007, Molecular biology of the cell.

[30]  N. D. Clarke,et al.  Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.

[31]  W. de Laat,et al.  Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription , 2008, PloS one.

[32]  L. Wessels,et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions , 2008, Nature.

[33]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[34]  B. Chadwick,et al.  The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions , 2008, The Journal of experimental medicine.

[35]  H. Aburatani,et al.  Cohesin mediates transcriptional insulation by CCCTC-binding factor , 2008, Nature.

[36]  Z. Weng,et al.  The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome , 2008, PLoS genetics.

[37]  Stephan Sauer,et al.  Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms , 2008, Cell.

[38]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[39]  Dustin E. Schones,et al.  Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. , 2008, Genome research.

[40]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[41]  T. Misteli,et al.  The emerging role of nuclear architecture in DNA repair and genome maintenance , 2009, Nature Reviews Molecular Cell Biology.

[42]  Wing-Kin Sung,et al.  Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries , 2009, PloS one.

[43]  K. Sandhu,et al.  Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. , 2009, Genes & development.

[44]  A. Visel,et al.  ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.

[45]  J. Zlatanova,et al.  CTCF and its protein partners: divide and rule? , 2009, Journal of Cell Science.

[46]  W. Sung,et al.  ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing , 2010, Genome Biology.

[47]  P. Fraser,et al.  Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus , 2009, Nature.

[48]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[49]  Petra C. Schwalie,et al.  A CTCF-independent role for cohesin in tissue-specific transcription. , 2010, Genome research.

[50]  Jennifer A. Mitchell,et al.  Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.

[51]  William Stafford Noble,et al.  A Three-Dimensional Model of the Yeast Genome , 2010, Nature.

[52]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[53]  P. Flicek,et al.  Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. , 2010, Molecular cell.

[54]  Feng Lin,et al.  A signal-noise model for significance analysis of ChIP-seq with negative control , 2010, Bioinform..