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Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

ABSTRACT: Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

PROVIDER: PRJNA589339 | ENA |

REPOSITORIES: ENA

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Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

Project description:We analyzed the impact of CTCFL and CTCF-CTCFL fusion proteins in the presence and absence of CTCF to obtain insight into the individual functional contributions of the zinc finger and N/C terminal domains

2020-04-14 | GSE140363 | GEO

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation.

Project description:BACKGROUND:Ubiquitously expressed CTCF is involved in numerous cellular functions, such as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally only present in the testis. However, it is also aberrantly expressed in many cancers. While it is known that shared and unique zinc finger sequences in CTCF and CTCFL enable CTCFL to bind competitively to a subset of CTCF binding sites as well as its own unique locations, the impact of CTCFL on chromosome organization and gene expression has not been comprehensively analyzed in the context of CTCF function. Using an inducible complementation system, we analyze the impact of expressing CTCFL and CTCF-CTCFL chimeric proteins in the presence or absence of endogenous CTCF to clarify the relative and combined contribution of CTCF and CTCFL to chromosome organization and transcription. RESULTS:We demonstrate that the N terminus of CTCF interacts with cohesin which explains the requirement for convergent CTCF binding sites in loop formation. By analyzing CTCF and CTCFL binding in tandem, we identify phenotypically distinct sites with respect to motifs, targeting to promoter/intronic intergenic regions and chromatin folding. Finally, we reveal that the N, C, and zinc finger terminal domains play unique roles in targeting each paralog to distinct binding sites to regulate transcription, chromatin looping, and insulation. CONCLUSION:This study clarifies the unique and combined contribution of CTCF and CTCFL to chromosome organization and transcription, with direct implications for understanding how their co-expression deregulates transcription in cancer.

| S-EPMC7212617 | biostudies-literature

CTCFL

Project description:CTCFL

| PRJNA400477 | ENA

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

Project description: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

2012-07-25 | E-GEOD-34094 | biostudies-arrayexpress

Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [MoGene-1_0 Expression]

Project description:CTCFL binding to DNA and the effect of CTCFL expression in ES cells RNA extracted from CTCFL induced and non-induced ES cells was hybridized on Affymetrix Mouse Gene 1.0ST arrays

2012-07-24 | E-GEOD-34092 | biostudies-arrayexpress

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

Project description:This SuperSeries is composed of the following subset Series: GSE34091: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression] GSE34092: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [MoGene-1_0 Expression] GSE34094: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq] Refer to individual Series

2012-07-24 | E-GEOD-34093 | biostudies-arrayexpress

Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression]

Project description:The effect of CTCFL mutation on the transcriptional program in testes Testis RNA extracted from CTCFL wildtype and mutant mice was hybridized on Affymetrix Mouse430_2 arrays

2012-07-24 | E-GEOD-34091 | biostudies-arrayexpress

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

2012-07-25 | GSE34094 | GEO

Mapping of CTCF and CTCFL binding sites in 3T3 and p19 cells

Project description:Study of the differential binding behavior of the paralogous factors CTCF and CTCFL by ChIP-seq in mouse NIH3T3 and p19 cells.

2018-05-30 | GSE103198 | GEO

Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [MoGene-1_0 Expression]

Project description:CTCFL binding to DNA and the effect of CTCFL expression in ES cells

2012-07-25 | GSE34092 | GEO