title: Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development.
abstract: Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species. By weighted co-expression network analysis, we identified 5 developmental stages specific co-expression modules. Gene ontology enrichment analysis of these specific co-expression modules suggested that many lincRNAs are associated with cell cycle regulation, transcription and metabolism to regulate the process of zygotic genome activation. Futhermore, we identified hub lincRNAs in each co-expression modules, and found two lincRNAs TCONS_00166370 and TCONS_00020255 may play a vital role in porcine PED. This study systematically analyze lincRNAs in pig and provides the first catalog of lincRNAs that might function as gene regulatory factors of porcine PED.
authors.affiliation: College of Life Science, North-east Agricultural University, Harbin, 150030, China.|Chong Qing Reproductive and Genetics Institute, Chongqing Obstetrics and Gynecology Hospital, 64 Jing Tang ST, Yu Zhong District, Chongqing, 400013, China.
authors.forename: Jingyu
authors.initials: J
authors.lastname: Li
authors.affiliation: College of Life Science, North-east Agricultural University, Harbin, 150030, China.
authors.forename: Zhengling
authors.initials: Z
authors.lastname: Gao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China.
authors.forename: Xingyu
authors.initials: X
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Life Science, North-east Agricultural University, Harbin, 150030, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D002453:Cell Cycle / Q000235:genetics; D047108:Embryonic Development / Q000235:genetics*; D005091:Exons; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D016678:Genome; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013552:Swine / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome; D015053:Zygote
chemical_list: D062085:RNA, Long Noncoding