Circular RNAs in cattle muscle: developmental stage-dependent changes. Bos taurus

Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of circRNAs across cattle muscle development has never been investigated. Here, we examine the expression of circRNA in cattle skeletal muscle at embryonic stage and adult stage, exhibiting the first report of circRNA in the cattle muscle development of a large animal. 12,981 circRNAs are identified and annotated in Qinchuan cattle muscle tissues, including 530 circular intronic RNAs (ciRNAs). We discovered that one parental gene could generate multiple circRNA isoforms with only one or two circRNA isoforms being expressed at higher levels, and several host genes produced different alternative circularization numbers between different muscle development stages. The most circRNA candidates contained two to seven exons, and the genomic distance of the back-splicing site was generally no more than 50 kb. The flanking intron length of most circRNAs was not more than 105 nt and the mean length of upstream or downstream flanking intron was about 11,000 nt. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these circRNAs, including several highly abundant circRNAs, and a subset of differently expressed circRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results display that an abundant circRNAs are dynamically expressed in a spatio-temporal manner in cattle muscle, indicating important and diverse functions during mammalian muscle development. Overall design: Six longissimus muscle samples from Qinchuan cattles of two developmental states (embryonic, 90 d; and adult, 24 M old) were collected from Yiming abattoir, a local slaughterhouse of Xi’An, P.R. China.