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Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (RNA-seq)

ABSTRACT: Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (RNA-seq)

PROVIDER: PRJNA644004 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12144000_1.fastq.gz	Fastqsanger.gz
	SRR12144000_2.fastq.gz	Fastqsanger.gz
	SRR12144001_1.fastq.gz	Fastqsanger.gz
	SRR12144001_2.fastq.gz	Fastqsanger.gz
	SRR12144002_1.fastq.gz	Fastqsanger.gz

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Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)

Project description:Transcription factor binding to DNA is a central mechanism regulating cellular gene expression. Thus, thorough characterization of this process is essential for understanding cellular biology in both health and disease. In this study, we combined data from three sequencing-based methods to unravel the DNA binding function of the novel zinc finger protein ZNF414 in cells representing two tumor types. ChIP-exo served to map protein binding sites in the genome, ATAC-seq allowed identification of open chromatin, and RNA-seq examined the transcriptome.

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Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (RNA-seq)

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Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)

Project description:Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)

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Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

Project description:Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

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Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ATAC-seq)

Project description:Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ATAC-seq)

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Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation

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Genomic targets of the KRAB and scan domain-containing zinc finger protein 263 (ZNF263).

Project description:Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger factor (ZNF). However, very few studies have performed genome-wide analyses of ZNF binding patterns and thus it is not clear if the binding code developed in vitro will be useful for identifying target genes of a particular ZNF. We performed genome-wide ChIP-seq for ZNF263, a C2H2 ZNF that contains 9 finger domains, a KRAB repression domain, and a SCAN domain and identified more than 5000 binding sites in K562 cells. Our results suggest that ZNF263 binds to a 24 nt site which differs from the motif predicted by the zinc finger code in several positions. Interestingly, many of the ZNF263 binding sites are located within the transcribed region of the target gene. Although ZNFs containing a KRAB domain are thought to function mainly as transcriptional repressors, many of the ZNF263 target genes are expressed at high levels. To address the biological role of ZNF263, we identified genes whose expression was altered by treatment of cells with ZNF263-specific siRNAs. Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of ZNF263 ChIP-seq in K562 cells.

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