Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

Abstract

Background The growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. To better understand the regulatory mechanism of circRNAs during the development of muscle in chicken, we performed RNA-seq with linear RNA depletion for chicken breast muscle in 12 (E 12) and17 (E 17) day embryos, and 1 (D 1), 14 (D 14), 56 (D 56), and 98 (D 98) days post-hatch. Results We identified 5755 differentially expressed (DE)-circRNAs during muscle development. We profiled the expression of DE-circRNAs and mRNAs (identified in our previous study) at up to six time points during chicken muscle development and uncovered a significant profile (profile 16) for circRNA upregulation during aging in muscle tissues. To investigate competing endogenous RNA (ceRNA) regulation in muscle and identify muscle-related circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network using the circRNAs and mRNAs from profile 16 and miRNAs identified in our previous study, which included 361 miRNAs, 68 circRNAs, 599 mRNAs, and 31,063 interacting pairs. Functional annotation showed that upregulated circRNAs might contribute to glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, carbon metabolism, glycogen and sucrose metabolism through the ceRNA network, and thus affected postnatal muscle development by regulating muscle protein deposition. Of them, circRNA225 and circRNA226 from the same host gene might be key circRNAs that could regulate muscle development by interacting with seven common miRNAs and 207 mRNAs. Our experiments also demonstrated that there were interactions among circRNA225, gga-miR-1306-5p, and heat shock protein alpha 8 (HSPA8). Conclusions Our results suggest that adequate supply of nutrients such as energy and protein after hatching may be a key factor in ensuring chicken yield, and provide several candidate circRNAs for future studies concerning ceRNA regulation during chicken muscle development.

RNA sequencing reveals CircRNA expression profiles in chicken embryo fibroblasts infected with velogenic Newcastle disease virus

“…CircRNAs are characterized by abundant expression, stable structure, and evolutionary conservation. In this study, circRNAs from CEFs mainly originated from chromosomes 1, 2, and 3, consistent with the study by Lei et al on chicken muscle ( 22 ), Wang et al on hen granulosa cells ( 23 ), and Zhang et al on CEF and HD-11 cells ( 24 ). Our results showed that circRNAs from CEFs were mainly located in exons (80.8%), consistent with the findings of Wang et al and Chen et al, who studied circRNAs from hen granulosa and DF1 cells ( 13 , 23 ).…”

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress

“…According to the main roles of lncRNA in the regulation of RNA at the epigenetic level, including the regulation of DNA methylation 56 , histone modification 57 and chromatin remodeling 58 , and at the transcriptional level, including the interaction with transcription factors 59 – 62 , proteins in the nucleus 63 and proteins in the cytoplasm 64 , and interaction with miRNAs 22 , 65 – 69 . Several studies have shown that the expression of some genes under AHS is modified 36 , 70 – 72 , possibly through the interaction with small or long noncoding RNAs 20 – 24 . Therefore, the identification of key coding genes and their corresponding regulatory elements (i.e., lncRNA and miRNA) is critically important to reveal the causative factors associated with AHS in liver of chickens, as liver is extremely vulnerable under the influence of heat stress 73 , 74 .…”

“…Recently, numerous researches have reported multiple small and long non-coding RNAs that are crucially important for the resistance of chicken to HS via altering or regulating the expression levels of the protein coding genes 20 – 24 . lncRNAs are non-coding RNAs longer than 200 nucleotides, which can be divided into four categories including; intronic, intergenic, sense, and antisense lncRNAs 25 .…”

Analysis of circRNA-miRNA-mRNA regulatory network of embryonic gonadal development in Mulard duck

“…As a result, they collectively regulate the expression levels of mRNA. The circRNA-miRNA-mRNA regulatory network is closely associated with various growth and development processes ( Lei et al, 2022 ; Xiao et al, 2022 ; Zou et al, 2020 ). circRNAs can act as ceRNAs ( Hansen et al, 2013 ) to regulate gene expression and thus control traits.…”