Genomics

Dataset Information

299

Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq]


ABSTRACT: CTCF and CTCFL DNA binding profile in CTCFL induced and non-induced ES cells.CTCF is a highly conserved and essential zinc finger protein that in conjunction with cohesin organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the testis-specific paralogue of CTCF, is less clear. Here, we show that CTCFL is only transiently present during spermatogenesis, prior to the onset of meiosis, when the protein co-localizes in nuclei with ubiquitously expressed CTCF. Our data show that CTCFL is functionally different from CTCF and its absence in mice causes sub-fertility due to a partially penetrant testicular atrophy. Genome-wide studies reveal that CTCFL and CTCF bind similar consensus sequences. However, only ~2000 out of the ~5,700 CTCFL and ~31,000 CTCF binding sites overlap. CTCFL binds promoters with loosely assembled nucleosomes, whereas CTCF favors consensus sites surrounded by phased nucleosomes. Thus, nucleosome dynamics specifies the genome-wide binding of CTCFL and CTCF. We propose that the transient expression of CTCFL in spermatogonia and preleptotene spermatocytes serves to occupy a subset of promoters and maintain the expression of male germ cell genes ChIP-seq for CTCF (with CTCF antibody) and CTCFL (with V5 antibody) in CTCFL_V5_GFP induced and non-induced ES cells

ORGANISM(S): Mus musculus  

SUBMITTER: Lisa Caesar   Frank Grosveld  Sven Dienstbach  Wilfred van Ijcken  Manuel Rosa-Garrido  Widia Soochit  Vedran Franke  Suzanne van de Nobelen  Michael van der Reijden  M D Delgado  Jan Christian Bryne  Philipp Bergmaier  Marek Bartkuhn  Boris Lenhard  J A Grootegoed  Frank Sleutels  Niels Galjart  frank sleutels  Rainer Renkawitz  Helen Heath 

PROVIDER: E-GEOD-34094 | ArrayExpress | 2012-07-25

SECONDARY ACCESSION(S): SRP009541GSE34094PRJNA156497

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


BACKGROUND: CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the testis-specific paralog of CTCF, is less clear. RESULTS: Using immunohistochemistry on testis sections and fluorescence-based microscopy on intact live seminiferous tubules, we show that CTCFL is only transiently present during sp  ...[more]

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