Construction and functional analysis of circular RNA interaction network based on open chromatin in breast cancer

doi:10.3969/j.issn.1006-7795.2019.06.017

Abstract

Abstract: Objective To identify some important circular RNAs (circRNAs) in breast cancer and the molecular biological processes in which they participate. Methods Genome-wide analysis of three breast cancer cell lines:Dnase Ⅰ hypersensitive sites sequencing data (DNase-seq) and assay for transposase accessible chromatin with high-throughput sequencing data, (ATAC-seq) of MCF-7, T-47D, MDA-MB-231,and screening out the corresponding activated circRNA on the sequence of the captured gene encoding were done. Then the activated circRNA gene was enriched and screened based on KEGG pathway. In this result, the activated circRNA gene shared in three cell lines was selected, and the interaction network of activated circRNA gene in breast cancer was constructed according to the molecular biological process of Gene Ontology. Results The expression regulatory network identified 111 key functional modules, which were mainly divided into regulation and response categories, and included some important signaling pathways. In the active circRNA gene interaction network, the activated circRNA gene with connectivity greater than 50 was defined as hub gene, and the corresponding circRNA of hub gene was defined as hub circRNA, including PTK2B, PDCD6IP, ABL1, EGFR, RHOA, MTOR, NRP1, ATR, CTNNB1, ILK, NF1, PRKCA, HNRNPK, MEF2C, PMAIP1, LYN, NR4A3, SRF, AREG, PML, PTK2, ROCK2, TGFBR2, VEGFA, DLG1, HRAS, ITGA2, CREB1, STAT3, RUNX2 and TIAM1.Conclusion Activated circRNA in the chromatin of breast cancer cells is mainly involved in positive and negative regulation of cell cycle, apoptosis, proliferation, differentiation and other important cellular biological processes, which indicates that circRNA plays an important role in the occurrence and development of breast cancer.

Key words: breast cancer, circular RNA, open chromatin localization, high throughput sequencing, circRNA interaction network

CLC Number:

Zhang Yunxian, Wang Yamei, Zhou Ping. Construction and functional analysis of circular RNA interaction network based on open chromatin in breast cancer[J]. Journal of Capital Medical University, 2019, 40(6): 901-910.

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URL: https://journal03.magtech.org.cn/Jweb_sdykdxxb/EN/10.3969/j.issn.1006-7795.2019.06.017

https://journal03.magtech.org.cn/Jweb_sdykdxxb/EN/Y2019/V40/I6/901

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