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ChIP-seq: Analysis of CTCF occupancy in unaffected and DM1 patient lymphoblastoid cell lines.

ABSTRACT: ChIP-seq: Analysis of CTCF occupancy in unaffected and DM1 patient lymphoblastoid cell lines.

PROVIDER: PRJNA623380 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11490553.fastq.gz	Fastqsanger.gz
	SRR11490554.fastq.gz	Fastqsanger.gz
	SRR11490555.fastq.gz	Fastqsanger.gz
	SRR11490556.fastq.gz	Fastqsanger.gz
	SRR11490557.fastq.gz	Fastqsanger.gz

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ChIP-seq: Analysis of CTCF occupancy in unaffected and DM1 patient lymphoblastoid cell lines.

Project description:We performed CTCF ChIP-seq to determine the extent of CTCF occupancy alterations in two DM1 patient lymphoblastoid cell lines (LCLs) compared to an unaffected control LCL. Our results show that there were no large-scale changes in CTCF occupancy in the DM1 patient cells either genome-wide or in a 2 Mb region centered around the expanded repeats of DMPK.

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RNA-seq: Analysis of differential gene expression between HD and DM1 patient lymphoblastoid cell lines (LCLs) compared to unaffected LCLs.

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Project description:We performed an evolutionary comparison of the binding of the TF CTCF in human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines (LCLs). We also probes YY1 binding in human, chimpanzee, orang-utan and baboon LCLs as well as human and mouse liver.

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CGGBP1 regulates chromatin barrier activity and CTCF occupancy at repeats

Project description:To study the role of CGGBP1 in regulation of CTCF occupancy, we performed CTCF ChIP-seq in HEK293T cells with three different levels of CGGBP1: (i) endogenous levels of CGGBP1 (ii) CGGBP1 knockdown, and (iii) CGGBP1 overexpression. Here, we show that CTCF binds to repeats as well as canonical CTCF-motifs and CGGBP1 determines the CTCF occupancy preference for repeats over canonical CTCF-motif. By combining CTCF ChIP-seq with histone modifications ChIP-seq (for H3K4me3, H3K9me3 and H3K27me3) under conditions of normal or CGGBP1 knockdown, we demonstrate that CTCF binding sites regulated by CGGBP1 correspond to chromatin barrier elements with profound effects on H3K9me3 distribution. In conclusion, these finding shows that CGGBP1 is a regulator of CTCF occupancy and serve as a regulator of barrier functions of CTCF-binding sites.

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CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [MNase-seq]

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Project description:This study will look at variation in CTCF binding in humans as assayed by ChIP-seq on 60 HapMap lymphoblastoid cell lines.

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