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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...

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Autores principales: Wang, Junhong, Li, Xiaoxu, Lu, Yiyuan, Huang, Quntao, Sun, Yu, Cheng, Mingyang, Li, Fengdi, Shi, Chunwei, Zeng, Yan, Wang, Chunfeng, Cao, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8695857/
https://www.ncbi.nlm.nih.gov/pubmed/34956935
http://dx.doi.org/10.3389/fcimb.2021.806290
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author Wang, Junhong
Li, Xiaoxu
Lu, Yiyuan
Huang, Quntao
Sun, Yu
Cheng, Mingyang
Li, Fengdi
Shi, Chunwei
Zeng, Yan
Wang, Chunfeng
Cao, Xin
author_facet Wang, Junhong
Li, Xiaoxu
Lu, Yiyuan
Huang, Quntao
Sun, Yu
Cheng, Mingyang
Li, Fengdi
Shi, Chunwei
Zeng, Yan
Wang, Chunfeng
Cao, Xin
author_sort Wang, Junhong
collection PubMed
description 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.
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spelling pubmed-86958572021-12-24 Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs Wang, Junhong Li, Xiaoxu Lu, Yiyuan Huang, Quntao Sun, Yu Cheng, Mingyang Li, Fengdi Shi, Chunwei Zeng, Yan Wang, Chunfeng Cao, Xin Front Cell Infect Microbiol Cellular and Infection Microbiology 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. Frontiers Media S.A. 2021-12-09 /pmc/articles/PMC8695857/ /pubmed/34956935 http://dx.doi.org/10.3389/fcimb.2021.806290 Text en Copyright © 2021 Wang, Li, Lu, Huang, Sun, Cheng, Li, Shi, Zeng, Wang and Cao https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Wang, Junhong
Li, Xiaoxu
Lu, Yiyuan
Huang, Quntao
Sun, Yu
Cheng, Mingyang
Li, Fengdi
Shi, Chunwei
Zeng, Yan
Wang, Chunfeng
Cao, Xin
Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs
title Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs
title_full Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs
title_fullStr Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs
title_full_unstemmed Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs
title_short Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs
title_sort analysis of lncrnas and mrna expression in the zbtb1 knockout monoclonal el4 cell line and combined analysis with mirnas and circrnas
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8695857/
https://www.ncbi.nlm.nih.gov/pubmed/34956935
http://dx.doi.org/10.3389/fcimb.2021.806290
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