Abstract

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.

Highlights

  • The Zbtb1 family consists of a different set of transcription factors, and Zbtb1 plays an important role in lymphocyte development (Zhu et al, 2018)

  • Candidate target genes obtained by taking intersections of differentially expressed mRNAs as well as target genes that may be regulated by ceRNAs in the results of the association analysis were subjected to gene clustering, GO enrichment, and KEGG enrichment analyses

  • Twelve Long noncoding RNAs (lncRNAs) were eventually identified that may have a role in regulating the expression of mRNAs (Supplementary Table 12), of which six lncRNAs can upregulate the expression of target genes through cis ncRNA Analysis With Zbtb1 Deficiency C

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Summary

INTRODUCTION

The Zbtb family consists of a different set of transcription factors, and Zbtb plays an important role in lymphocyte development (Zhu et al, 2018). The discovery of functional noncoding transcripts from a large transcriptome is a top priority and challenge for the LNCRNA field (Kopp and Mendell, 2018). The transcriptome refers to the collection of all transcription products in a given cell in a given state, including mRNA and noncoding RNA; research on noncoding RNA has focused on small RNA, lncRNA and circRNA, which have regulatory roles (Luo et al, 2020). Whole-transcriptome sequencing study based on secondgeneration sequencing technology can analyze mRNA, lncRNA, circRNA, small RNA in the same sample at the same time and explore the transcriptional regulation behind life phenomena in greater depth (Ning et al, 2021). By studying the interaction of coding and noncoding RNAs, scientific questions can be addressed more comprehensively, and the findings can be refined

Experimental Procedure
RESULTS
Results of the Association Analysis
DISCUSSION
DATA AVAILABILITY STATEMENT

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