Identification of Chimeric RNAs in Pig Skeletal Muscle and Transcriptomic Analysis of Chimeric RNA TNNI2-ACTA1 V1

Abstract

Chimeric RNA was considered a special marker of cancer. However, recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues. Here, we analyzed and predicted jointly 49 chimeric RNAs by Star-Fusion and FusionMap. One chimeric RNA, we named TNNI2-ACTA1, and its eight transcript variants were identified by reverse transcriptase–polymerase chain reaction. The overexpression of TNNI2-ACTA1 V1 inhibited the proliferation of porcine skeletal muscle satellite cells through down-regulating the mRNA expression levels of cell cycle–related genes cyclinD1. However, as parental genes, there is no such effect in the TNNI2 and ACTA1. To explore the underlying mechanism for this phenomenon, we used RNA-seq to profile the transcriptomes of PSCs with overexpression. Compared with the negative control group, 1,592 differentially expressed genes (DEGs) were upregulated and 1,077 DEGs downregulated in TNNI2 group; 1,226 DEGs were upregulated and 902 DEGs downregulated in ACTA1 group; and 13 DEGs were upregulated and 16 DEGs downregulated in TNNI2-ACTA1 V1 group, respectively. Compared with the parental gene groups, three specific genes were enriched in the TNNI2-ACTA1 V1 group (NCOA3, Radixin, and DDR2). These three genes may be the key to TNNI2-ACTA1 V1 regulating cell proliferation. Taken together, our study explores the role of chimeric RNAs in normal tissues. In addition, our study as the first research provides the foundation for the mechanism of chimeric RNAs regulating porcine skeletal muscle growth.

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

“…Cyclin T2 ( CCNT2 ), the source gene of gga_circ_0009799, is closely related to the development of skeletal muscle [ 36 ], and gga_circ_0009799 is a significant differential circRNA for the three comparison groups of W14 vs. W6, W22 vs. W6, and W30 vs. W6, which implies that gga_circ_0009799 might have an important role in skeletal muscle development in Gushi chickens. ACTA1 , the source gene of gga_circ_0006492, represses skeletal muscle satellite cell proliferation in pigs by downregulating the level of cell-cycle-related gene expression [ 37 ], and gga_circ_0006492 was a significantly different circRNA in our results for the two comparison groups W30 vs. W14, W30 vs. W22, suggesting that gga_circ_0006492 may play a key regulatory function in the later stages of skeletal muscle development in Gushi chickens. The source gene forkhead box P1 ( FOXP1 ) of gga_circ_0000808 is engaged in skeletal muscle development as a transcriptional inhibitor of gene expression [ 38 ], and gga_circ_0000808 is a significant differential circRNA of W30 vs. W14, W30 vs. W6, which predicts that gga_circ_0000808 may be involved in the skeletal muscle development process in Gushi chickens.…”

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

“…Li and colleagues examined chimeric genes for their biological effects as well as related mechanisms by weighted co-expression network analysis ( Li, Li & Ma, 2021a ). Liu et al (2021) firstly reported that the chimeric RNAs related mechanism in modulating skeletal muscle development in pigs. This work analyzed altogether 147 fusion genes in porcine GCs.…”

Chimeric RNA TNNI2-ACTA1-V1 Regulates Cell Proliferation by Regulating the Expression of NCOA3

“…To further explore the role of TA-V1 on cell proliferation, next-generation sequencing was used to perform transcriptome analysis. The results showed that three genes ( NCOA3, DDR2 and RDX ) were specifically enriched compared to the parental genes ( 12 ).…”

“…To further explore the role of TA-V1 on cell proliferation, next-generation sequencing was used to perform transcriptome analysis. The results showed that three genes (NCOA3, DDR2 and RDX) were specifically enriched compared to the parental genes (12). In order to explore TA-V1 inhibits the proliferation of PSCs potential mechanisms, we focused on the effects of NCOA3, DDR2 and RDX on the proliferation of PSCs.…”

“…Chimeric RNA TNNI2-ACTA1-V1 ( TA-V1 ), one of the TNNI2-ACTA1 transcript variants, is formed by trans-splicing of TNNI2 and ACTA1 . TA-V1 was identified by our laboratory and our previous study found that TA-V1 can inhibit the proliferation of PSCs ( 12 ). Interestingly, the parental genes do not have this function.…”