title: Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat.
abstract: Long non-coding RNAs (lncRNAs) have been studied extensively over the past few years. Large numbers of lncRNAs have been identified in mouse, rat, and human, and some of them have been shown to play important roles in muscle development and myogenesis. However, there are few reports on the characterization of lncRNAs covering all the development stages of skeletal muscle in livestock.
  
  
  
  RNA libraries constructed from developing longissimus dorsi muscle of fetal (45, 60, and 105 days of gestation) and postnatal (3 days after birth) goat (Capra hircus) were sequenced. A total of 1,034,049,894 clean reads were generated. Among them, 3981 lncRNA transcripts corresponding to 2739 lncRNA genes were identified, including 3515 intergenic lncRNAs and 466 anti-sense lncRNAs. Notably, in pairwise comparisons between the libraries of skeletal muscle at the different development stages, a total of 577 transcripts were differentially expressed (P < 0.05) which were validated by qPCR using randomly selected six lncRNA genes. The identified goat lncRNAs shared some characteristics, such as fewer exons and shorter length, with the lncRNAs in other mammals. We also found 1153 lncRNAs genes were neighbored 1455 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in transcriptional regulation and development-related processes, indicating they may be in cis-regulatory relationships. Additionally, Pearson's correlation coefficients of co-expression levels suggested 1737 lncRNAs and 19,422 mRNAs were possibly in trans-regulatory relationships (r > 0.95 or r < -0.95). These co-expressed mRNAs were enriched in development-related biological processes such as muscle system processes, regulation of cell growth, muscle cell development, regulation of transcription, and embryonic morphogenesis.
  
  
  
  This study provides a catalog of goat muscle-related lncRNAs, and will contribute to a fuller understanding of the molecular mechanism underpinning muscle development in mammals.
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Siyuan
authors.initials: S
authors.lastname: Zhan
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhao
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Jiazhong
authors.initials: J
authors.lastname: Guo
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhong
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Linjie
authors.initials: L
authors.lastname: Wang
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China. lilyzh002@sohu.com.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China. zhp@sicau.edu.cn.
authors.forename: Hongping
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D055106:Genome-Wide Association Study; D006041:Goats / Q000196:embryology / Q000235:genetics* / Q000254:growth & development; D059014:High-Throughput Nucleotide Sequencing; D024510:Muscle Development / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding
keywords: Differential expression; Goat; LncRNA; Muscle development; Transcriptome; cis-acting; trans-acting