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Identification and evolutionary analysis of long non-coding RNAs in zebra finch
Chih-Kuan Chen1,2, Chun-Ping Yu2, Sung-Chou Li3
1Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.
BMC Genomics
|February 2, 2017
Summary
This study identifies 1,081 long non-coding RNAs (lncRNAs) during zebra finch embryonic development, revealing conserved lncRNAs potentially involved in feather and down development. These findings expand our understanding of avian lncRNA biology.
Area of Science:
- Genomics
- Developmental Biology
- Evolutionary Biology
Background:
- Long non-coding RNAs (lncRNAs) play crucial roles in biological processes, yet their study in avian species is limited.
- Feather development is a complex process influenced by gene regulation, with lncRNAs potentially playing a significant role.
- Understanding avian lncRNAs is essential for comprehending avian development and evolution.
Purpose of the Study:
- To systematically identify and characterize long non-coding RNAs (lncRNAs) expressed during embryonic feather development in the zebra finch (Taeniopygia guttata).
- To analyze the evolutionary conservation of identified avian lncRNAs across different bird species and amniotes.
- To predict the potential functions of these lncRNAs, particularly their association with feather and down development.
Main Methods:
- Single-stranded RNA sequencing (ssRNA-seq) was performed on embryonic zebra finch dorsal tissues (anterior and posterior).
- A novel pipeline was utilized to identify and classify lncRNAs, including intergenic, intronic, and antisense lncRNAs.
- Published transcriptomic data were used for evolutionary conservation analysis, and quantitative PCR (qPCR) was employed for validation.
Main Results:
- A total of 1,081 lncRNAs were identified, comprising 965 lincRNAs, 59 intronic lncRNAs, and 57 lncNATs.
- Avian lncRNAs exhibit distinct characteristics compared to mammalian lncRNAs, including shorter length, fewer exons, lower expression, and less conservation.
- Three highly conserved lncRNAs potentially associated with natal down development were identified and validated in zebra finch and chicken.
Conclusions:
- This study presents the first systematic identification of avian lncRNAs using ssRNA-seq, providing a valuable resource for avian developmental biology.
- The identified lncRNAs offer insights into the regulatory mechanisms of feather and down development in birds.
- The findings highlight the conserved roles of specific lncRNAs in avian development and evolution.
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