Systematic screening of long intergenic noncoding RNAs expressed during chicken embryogenesis

Junxiao Ren, Quanlin Li, Qinghe Zhang, Michael Clinton, Congjiao Sun, Ning Yang

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes, including embryogenesis and development. To provide a systematic analysis of lncRNAs expressed during chicken embryogenesis, we used Iso-Seq and RNA-Seq to identify potential lncRNAs at embryonic stages from d 1 to d 8 of incubation: sequential stages covering gastrulation, somitogenesis, and organogenesis. The data characterized an expanded landscape of lncRNAs, yielding 45,410 distinct lncRNAs (31,282 genes). Amongst these, a set of 13,141 filtered intergenic lncRNAs (lincRNAs) transcribed from 9803 lincRNA gene loci, of which, 66.5% were novel, were further analyzed. These lincRNAs were found to share many characteristics with mammalian lincRNAs, including relatively short lengths, fewer exons, lower expression levels, and stage-specific expression patterns. Functional studies motivated by "guilt-by-association" associated individual lincRNAs with specific GO functions, providing an important resource for future studies of lincRNA function. Most importantly, a weighted gene co-expression network analysis suggested that genes of the brown module were specifically associated with the day 2 stage. LincRNAs within this module were co-expressed with proteins involved in hematopoiesis and lipid metabolism. This study presents the systematic identification of lincRNAs in developing chicken embryos and will serve as a powerful resource for the study of lincRNA functions.

Original languageEnglish
Article number101160
JournalPoultry Science
Volume100
Issue number7
Early online date26 Mar 2021
DOIs
Publication statusE-pub ahead of print - 26 Mar 2021

Keywords / Materials (for Non-textual outputs)

  • lincRNA
  • RNA-Seq
  • Iso-Seq
  • embryonic development
  • chicken

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