Comprehensive Analysis of lncRNA and mRNA Reveals the Effect of ZBED6 on Spleen Growth in Pigs

Abstract

Transcription factor zinc-finger BED domain-containing protein 6 (ZBED6) is unique to placental mammals and regulates insulin-like growth factor 2 (IGF2) expression, which lead to muscle growth. However, the effect of ZBED6 on the growth of spleen is still elusive. In this study, we explored the regulation of ZBED6 on spleen growth, and the results showed ZBED6 knockout (ZBED6 KO) pigs had heavier spleens than wild-type (WT) pigs. To analyze the mechanism of increased spleen weight in ZBED6 KO pigs, long noncoding RNAs (lncRNAs) and mRNAs in the spleen samples (WT:ZBED6 KO pigs = 3:3) were analyzed to identify differentially expressed lncRNAs (DE-lncRNAs) and genes (DEGs) based on the RNA sequencing (RNA-seq) method. Then, 142 DEGs and 82 DE-lncRNAs were obtained. The qRT-PCR results were consistent with those of the RNA-seq, indicating that the data were reliable. The heavier spleen weight of ZBED6 KO pigs coincided with the significantly upregulated IGF2 mRNA. Functional enrichment analysis of DEGs showed enrichment mainly in myofibril assembly and sarcomere. In addition, 252 cis- and 109 trans-acting target genes of 82 DE-lncRNAs were predicted. By conjoint analysis of lncRNA and mRNA revealed that IGF2, DE-lnRNAs (XLOC_113021, XLOC_078852, NONSUSG004057.1, NONSUSG014354.1, and NONSUSG009750.1), and their target gene ACTN2 may be the key candidate genes in promoting spleen growth in ZBED6 KO pigs. This study provides new directions to understand the global functions of ZBED6 and lncRNAs in spleen growth in pigs.