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

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.

Genome-Wide Analysis of the KLF Gene Family in Chicken: Characterization and Expression Profile

“…These primers were synthesized by Sangon (Shanghai, China). The qPCR experiments were conducted on Applied Biosystems 7500 (ABI, Los Angeles, California, USA) using SYBR qPCR Master Mix (Vazyme, Nanjing, China), and β-actin was used as housekeeping gene [46], with three technical repetitions for each sample. The 2 −∆∆CT method was used to calculate the relative expression of KLFs [47].…”

MeRIP sequencing reveals the regulation of N6-methyladenosine in muscle development between hypertrophic and leaner broilers

“…The RNA-seq results showed that the body weight differences between XH and WRR chicken are mainly reflected in metabolism, catalytic activity, and fatty acid metabolism according to the GO term and KEGG pathway analysis ( Figures 2 C– 2 D). Studies have shown that the weight difference of poultry after birth is mainly manifested in energy metabolism ( Kong et al, 2017 ), the host genes of differentially expressed circRNAs in late embryonic stage of slow- and fast-growing chicken muscle were also mainly enriched in metabolic pathways ( Zhang et al, 2022 ), proved that the difference in metabolic levels before and after birth is an important reason for the differences in muscle mass and growing speed in poultry.…”

Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development

“…We use the intersection of circRNA predicted by find_circ and CIRC software can improve the accuracy of circRNA. This method has been used in mice [ 52 ], cattle [ 53 ], sheep [ 54 ], chicken [ 55 ] and other species [ 56 ]. We identified a total of 16,990 expressed circRNAs, which is much higher than the number reported in one recent study.…”