Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs

In previous experiments, we identified the effect of deletion of the Zbtb1 gene on circRNAs and microRNAs. In this study, we examined the expression profiles of lncRNAs and mRNAs using the RNA-seq method for Zbtb1-deficient EL4 cells and performed a clustering analysis of differentially expressed ln...

Full description

Saved in:
Bibliographic Details
Published in:Frontiers in cellular and infection microbiology 2021-12, Vol.11, p.806290-806290
Main Authors: Wang, Junhong, Li, Xiaoxu, Lu, Yiyuan, Huang, Quntao, Sun, Yu, Cheng, Mingyang, Li, Fengdi, Shi, Chunwei, Zeng, Yan, Wang, Chunfeng, Cao, Xin
Format: Article
Language:English
Subjects:
Cell Line
Cellular and Infection Microbiology
EL4
Gene Regulatory Networks
lncRNA
MicroRNAs - genetics
mRNA
RNA, Circular
RNA, Long Noncoding - genetics
RNA, Messenger - genetics
RNA-seq
Zbtb1
Citations: Items that this one cites
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:In previous experiments, we identified the effect of deletion of the Zbtb1 gene on circRNAs and microRNAs. In this study, we examined the expression profiles of lncRNAs and mRNAs using the RNA-seq method for Zbtb1-deficient EL4 cells and performed a clustering analysis of differentially expressed lncRNAs and mRNAs. GO term histograms and KEGG scatter plots were drawn. For the experimental results, a joint analysis was performed, which predicted the regulatory relationships among lncRNAs, mRNAs, microRNAs and circRNAs. For the regulatory relationship between lncRNAs and target genes, the chromatin structure and the degree of openness were verified for the possible target gene locations regulated by lncRNA using experimental methods such as Hi-C and ATAC-seq. Ultimately, the possible differential regulation of the Brcal and Dennd5d genes by lncRNAs and the differential changes in transcription factor binding sites in the promoter region were identified. For neRNA-regulated target genes with significantly differentially expressed mRNAs, a combined screen was performed, and the final obtained candidate target genes were subjected to GO and KEGG term enrichment analyses. Our results illustrate that the Zbtb1 gene can not only function as a regulatory factor but also regulate EL4 cells from multiple perspectives based on ceRNA theory.
ISSN:2235-2988
2235-2988
DOI:10.3389/fcimb.2021.806290