title: Integrated Analysis of Long Non-coding RNAs (LncRNAs) and mRNA Expression Profiles Reveals the Potential Role of LncRNAs in Skeletal Muscle Development of the Chicken.
abstract: Long non-coding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation. However, little is currently known about the mechanisms by which they regulate skeletal muscle development in the chicken. In this study, we used RNA sequencing to profile the leg muscle transcriptome (lncRNA and mRNA) at three stages of skeletal muscle development in the chicken: embryonic day 11 (E11), embryonic day 16 (E16), and 1 day after hatching (D1). In total, 129, 132, and 45 differentially expressed lncRNAs, and 1798, 3072, and 1211 differentially expressed mRNAs were identified in comparisons of E11 vs. E16, E11 vs. D1, and E16 vs. D1, respectively. Moreover, we identified thecis- andtrans-regulatory target genes of differentially expressed lncRNAs, and constructed lncRNA-gene interaction networks. In total, 126 and 200cis-targets, and two and threetrans-targets were involved in lncRNA-gene interaction networks that were constructed based on the E11 vs. E16, and E11 vs. D1 comparisons, respectively. The comparison of the E16 vs. D1 lncRNA-gene network comprised 25cis-targets. We determined that lncRNA target genes are potentially involved in cellular development, and cellular growth and proliferation using Ingenuity Pathway Analysis. The gene networks identified for the E11 vs. D1 comparison were involved in embryonic development, organismal development and tissue development. The present study provides an RNA sequencing based evaluation of lncRNA function during skeletal muscle development in the chicken. Comprehensive analysis facilitated the identification of lncRNAs and target genes that might contribute to the regulation of different stages of skeletal muscle development.
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Zhenhui
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Hongjia
authors.initials: H
authors.lastname: Ouyang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Zheng
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Bolin
authors.initials: B
authors.lastname: Cai
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Peigong
authors.initials: P
authors.lastname: Han
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Bahareldin A
authors.initials: BA
authors.lastname: Abdalla
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Nie
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.
authors.forename: Xiquan
authors.initials: X
authors.lastname: Zhang
keywords: chicken; cis-acting; long non-coding RNA; skeletal muscle development; trans-acting