The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by deep-sequencing and high-density tiling arrays, and we discovered an array of well-positioned nucleosomes flanking sites occupied by the insulator binding protein CTCF across the human genome. These nucleosomes are highly enriched for the histone variant H2A.Z and 11 histone modifications. The distances between the center positions of the neighboring nucleosomes are largely invariant, and we estimate them to be 185 bp on average. Surprisingly, subsets of nucleosomes that are enriched in different histone modifications vary greatly in the lengths of DNA protected from micrococcal nuclease cleavage (106–164 bp). The nucleosomes enriched in those histone modifications previously implicated to be correlated with active transcription tend to contain less protected DNA, indicating that these modifications are correlated with greater DNA accessibility. Another striking result obtained from our analysis is that nucleosomes flanking CTCF sites are much better positioned than those downstream of transcription start sites, the only genomic feature previously known to position nucleosomes genome-wide. This nucleosome-positioning phenomenon is not observed for other transcriptional factors for which we had genome-wide binding data. We suggest that binding of CTCF provides an anchor point for positioning nucleosomes, and chromatin remodeling is an important component of CTCF function.

[1]  B D Athey,et al.  Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. , 1986, Biophysical journal.

[2]  L. Stryer,et al.  Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. , 1988, Nucleic acids research.

[3]  Victor V Lobanenkov,et al.  A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. , 1990, Oncogene.

[4]  The eukaryotic genome : organisation and regulation : Fiftieth Symposium of the Society for General Microbiology held at UMIST, April 1993 , 1993 .

[5]  P. Neiman,et al.  CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms , 1993, Molecular and cellular biology.

[6]  S. Oliver,et al.  The eukaryotic genome: organisation and regulation. , 1993 .

[7]  P. Neiman,et al.  An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes , 1996, Molecular and cellular biology.

[8]  Victor V Lobanenkov,et al.  Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF , 1997, Molecular and cellular biology.

[9]  M. Groudine,et al.  Looping versus linking: toward a model for long-distance gene activation. , 1999, Genes & development.

[10]  T. Richmond,et al.  Expression and purification of recombinant histones and nucleosome reconstitution. , 1999, Methods in molecular biology.

[11]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[12]  D. Timm,et al.  Asymmetries in the nucleosome core particle at 2.5 A resolution. , 2000, Acta crystallographica. Section D, Biological crystallography.

[13]  R Ohlsson,et al.  CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. , 2001, Trends in genetics : TIG.

[14]  Victor G. Levitsky,et al.  Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis , 2001, Bioinform..

[15]  S. Tapscott,et al.  CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus , 2001, Nature Genetics.

[16]  C. Kanduri,et al.  Multiple Nucleosome Positioning Sites Regulate the CTCF-Mediated Insulator Function of the H19 Imprinting Control Region† , 2002, Molecular and Cellular Biology.

[17]  Jeannie T. Lee.  Molecular Links between X-Inactivation and Autosomal Imprinting: X-Inactivation as a Driving Force for the Evolution of Imprinting? , 2003, Current Biology.

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

[19]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  J. Lieb,et al.  Evidence for nucleosome depletion at active regulatory regions genome-wide , 2004, Nature Genetics.

[21]  M. Beato,et al.  DNA instructed displacement of histones H2A and H2B at an inducible promoter. , 2004, Molecular cell.

[22]  B. Cairns,et al.  Genome-Wide Dynamics of Htz1, a Histone H2A Variant that Poises Repressed/Basal Promoters for Activation through Histone Loss , 2005, Cell.

[23]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[24]  Kevin Struhl,et al.  Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. , 2005, Molecular cell.

[25]  Mathieu Blanchette,et al.  Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning , 2005, PLoS biology.

[26]  S. Schreiber,et al.  Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin , 2006, Cell.

[27]  J. Workman,et al.  Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[29]  Rolf Ohlsson,et al.  CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Michael Q. Zhang,et al.  BMC Bioinformatics Methodology article Statistical significance of cis-regulatory modules , 2007 .

[31]  Z. Weng,et al.  A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome , 2006, Cell.

[32]  David J Segal,et al.  Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. , 2006, Journal of molecular biology.

[33]  Jun S. Song,et al.  High-throughput mapping of the chromatin structure of human promoters , 2007, Nature Biotechnology.

[34]  Ronald W. Davis,et al.  A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.

[35]  Jane M J Lin,et al.  Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome , 2007, PLoS genetics.

[36]  G. Felsenfeld,et al.  Critical DNA Binding Interactions of the Insulator Protein CTCF , 2007, Journal of Biological Chemistry.

[37]  Nir Friedman,et al.  Dynamics of Replication-Independent Histone Turnover in Budding Yeast , 2007, Science.

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

[39]  I. Albert,et al.  Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome , 2007, Nature.

[40]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

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

[42]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

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

[44]  S. Henikoff,et al.  Histone Replacement Marks the Boundaries of cis-Regulatory Domains , 2007, Science.

[45]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[46]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.