Decoding regulatory associations of G-quadruplex with epigenetic and transcriptomic functional components.

Autor:	Fang S; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States., Liu S; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.; The Collaborative Core for Cancer Bioinformatics (C3B) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, Indianapolis, IN, United States., Yang D; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States.; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States., Yang L; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States.; Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States.; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States., Hu CD; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States.; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States., Wan J; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.; The Collaborative Core for Cancer Bioinformatics (C3B) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, Indianapolis, IN, United States.; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in genetics [Front Genet] 2022 Aug 25; Vol. 13, pp. 957023. Date of Electronic Publication: 2022 Aug 25 (Print Publication: 2022).
DOI:	10.3389/fgene.2022.957023
Abstrakt:	G-quadruplex (G4) has been previously observed to be associated with gene expression. In this study, we performed integrative analysis on G4 multi-omics data from in-silicon prediction and ChIP-seq in human genome. Potential G4 sites were classified into three distinguished groups, such as one group of high-confidence G4-forming locations (G4-II) and groups only containing either ChIP-seq detected G4s (G4-I) or predicted G4 motif candidates (G4-III). We explored the associations of different-confidence G4 groups with other epigenetic regulatory elements, including CpG islands, chromatin status, enhancers, super-enhancers, G4 locations compared to the genes, and DNA methylation. Our elastic net regression model revealed that G4 structures could correlate with gene expression in two opposite ways depending on their locations to the genes as well as G4-forming DNA strand. Some transcription factors were identified to be over-represented with G4 emergence. The motif analysis discovered distinct consensus sequences enriched in the G4 feet, the flanking regions of two groups of G4s. We found high GC content in the feet of high-confidence G4s (G4-II) when compared to high TA content in solely predicted G4 feet of G4-III. Overall, we uncovered the comprehensive associations of G4 formations or predictions with other epigenetic and transcriptional elements which potentially coordinate gene transcription. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Fang, Liu, Yang, Yang, Hu and Wan.)
Databáze:	MEDLINE
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