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| Status |
Public on Jul 25, 2012 |
| Title |
Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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
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| Overall design |
ChIP-seq for CTCF (with CTCF antibody) and CTCFL (with V5 antibody) in CTCFL_V5_GFP induced and non-induced ES cells
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| Contributor(s) |
Sleutels F, Soochit W, Bartkuhn M, Heath H, Dienstbach S, Bergmaier P, Franke V, Rosa-Garrido M, van de Nobelen S, Caesar L, van der Reijden M, Christian Bryne J, van Ijcken W, Grootegoed JA, Delgado MD, Lenhard B, Renkawitz R, Grosveld F, Galjart N |
| Citation(s) |
22709888 |
| Submission date |
Dec 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
frank sleutels |
| Organization name |
ErasmusMC
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| Department |
cell biology and genetics
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| Street address |
Dr Molewaterplein 50
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| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE34093 |
Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF |
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| Relations |
| SRA |
SRP009541 |
| BioProject |
PRJNA156497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34094_ES_DOX_mm9_peaks.bed.gz |
64.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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