Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

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Rodriguez-Martinez , A , Vuorinen , E M , Shcherban , A , Uusi-Mäkelä , J , Rajala , N K M , Nykter , M & Kallioniemi , A 2022 , ' Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data ' , Biochimica et Biophysica Acta. Gene Regulatory Mechanisms , vol. 1865 , no. 3 , 194811 . https://doi.org/10.1016/j.bbagrm.2022.194811

Title: Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data
Author: Rodriguez-Martinez, Alejandra; Vuorinen, Elisa M.; Shcherban, Anastasia; Uusi-Mäkelä, Joonas; Rajala, Nina K. M.; Nykter, Matti; Kallioniemi, Anne
Contributor organization: Institute for Molecular Medicine Finland
Date: 2022-04
Language: eng
Number of pages: 9
Belongs to series: Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
ISSN: 1874-9399
DOI: https://doi.org/10.1016/j.bbagrm.2022.194811
URI: http://hdl.handle.net/10138/343695
Abstract: Transcription factor binding to DNA is a central mechanism regulating gene expression. Thus, thorough characterization of this process is essential for understanding cellular biology in both health and disease. We combined data from three sequencing-based methods to unravel the DNA binding function of the novel ZNF414 protein in cells representing two tumor types. ChIP-exo served to map protein binding sites, ATAC-seq allowed identification of open chromatin, and RNA-seq examined the transcriptome. We show that ZNF414 is a DNAbinding protein that both induces and represses gene expression. This transcriptional response has an impact on cellular processes related to proliferation and other malignancy-associated functions, such as cell migration and DNA repair. Approximately 20% of the differentially expressed genes harbored ZNF414 binding sites in their promoters in accessible chromatin, likely representing direct targets of ZNF414. De novo motif discovery revealed several putative ZNF414 binding sequences, one of which was validated using EMSA. In conclusion, this study illustrates a highly efficient integrative approach for the characterization of the DNA binding and transcriptional activity of transcription factors.
Subject: ZNF414
ChIP-exo
Transcription factor
Gene regulation
ATAC-seq
PROTEOME-SCALE MAP
DNA-BINDING
GLUCOCORTICOID-RECEPTOR
READ ALIGNMENT
PROTEINS
RECOGNITION
EVOLUTION
KPNA7
1182 Biochemistry, cell and molecular biology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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