title: Cis-Natural Antisense Transcripts Are Mainly Co-expressed with Their Sense Transcripts and Primarily Related to Energy Metabolic Pathways during Muscle Development.
abstract: Cis-natural antisense transcripts (cis-NATs) are a new class of RNAs identified in various species. However, the biological functions of cis-NATs are largely unknown. In this study, we investigated the transcriptional characteristics and functions of cis-NATs in the muscle tissue of lean Landrace and indigenous fatty Lantang pigs. In total, 3,306 cis-NATs of 2,469 annotated genes were identified in the muscle tissue of pigs. More than 1,300 cis-NATs correlated with their sense genes at the transcriptional level, and approximately 80% of them were co-expressed in the two breeds. Furthermore, over 1,200 differentially expressed cis-NATs were identified during muscle development. Function annotation showed that the cis-NATs participated in muscle development mainly by co-expressing with genes involved in energy metabolic pathways, including citrate cycle (TCA cycle), glycolysis or gluconeogenesis, mitochondrial activation and so on. Moreover, these cis-NATs and their sense genes abruptly increased at the transition from the late fetal stages to the early postnatal stages and then decreased along with muscle development. In conclusion, the cis-NATs in the muscle tissue of pigs were identified and determined to be mainly co-expressed with their sense genes. The co-expressed cis-NATs and their sense gene were primarily related to energy metabolic pathways during muscle development in pigs. Our results offered novel evidence on the roles of cis-NATs during the muscle development of pigs.
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Yunxia
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Hou
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Changzhi
authors.initials: C
authors.lastname: Zhao
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Luan
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Lu
authors.initials: L
authors.lastname: Jing
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Xinyun
authors.initials: X
authors.lastname: Li
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Mengjin
authors.initials: M
authors.lastname: Zhu
authors.affiliation: 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China.
authors.forename: Shuhong
authors.initials: S
authors.lastname: Zhao
mesh_terms: D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D005091:Exons / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology*; D024510:Muscle Development / Q000235:genetics / Q000502:physiology*; D016372:RNA, Antisense / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D013552:Swine; D014158:Transcription, Genetic / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D016372:RNA, Antisense; D034741:RNA, Small Interfering
keywords: Cis-natural antisense transcript; energy metabolic pathway; muscle; pig