Transcriptome Sequencing Analysis of circRNA in Skeletal Muscle between Fast- and Slow-Growing Chickens at Embryonic Stages

SIMPLE SUMMARY: Broilers provide a large amount of protein for human every year, in which skeletal muscle contribute a major role. In recent years, circRNAs have been found to be involved in skeletal muscle development, and more significant circRNAs in the process need to be revealed. In the study, transcriptome sequencing technology was used to obtain differentially expressed circRNAs (DECs) between fast- and slow-growing chickens. A variety of bioinformatics analysis were then used to identify the key circRNAs including novel_circ_0004547, novel_circ_0003578, novel_circ_0010289 and novel_circ_0003082. In addition, some candidate circRNA-miRNA pairs related to skeletal muscle were also obtained such as novel_circ_0002153-miR-12219-5p, novel_circ_0003578-miR-3064-3p and novel_circ_0010661-miR-12260-3p. This study would help to improve the regulation mechanism of circRNAs in skeletal muscle and also provide reference for broiler breeding. ABSTRACT: Skeletal muscle growth has always been the focus of the broiler industry, and circRNAs play a significant role in this process. We collected leg muscles of slow- and fast-growing Bian chicken embryos in the study at 14 (S14 and F14) and 20 (S20 and F20) days for RNA-seq. Finally, 123 and 121 differentially expressed circRNAs (DECs) were identified in S14 vs. F14 and S20 vs. F20, respectively. GO enrichment analysis for DECs obtained important biological process (BP) terms including nicotinate nucleotide biosynthetic process, nicotinate nucleotide salvage, and NAD salvage in S20 vs. F20 and protein mannosylation in S14 vs. F14. KEGG pathway analysis showed Wnt signaling pathway, Tight junction, Ubiquitin mediated proteolysis, and Notch signaling pathway were enriched in the top 20. Based on the GO and KEGG analysis results, we found some significant host genes and circRNAs such as NAPRT and novel_circ_0004547, DVL1 and novel_circ_0003578, JAK2 and novel_circ_0010289, DERA and novel_circ_0003082, etc. Further analysis found 19 co-differentially expressed circRNAs between the two comparison groups. We next constructed a circRNA-miRNA network for them, and some candidate circRNA-miRNA pairs related to skeletal muscle were obtained, such as novel_circ_0002153-miR-12219-5p, novel_circ_0003578-miR-3064-3p, and novel_circ_0010661-miR-12260-3p. These results would help to reveal the mechanism for circRNAs in skeletal muscle and also provide some guidance for the breeding of broilers.