PT  - JOURNAL ARTICLE
AU  - Hyosun Hong
AU  - Han-Ha Chai
AU  - Kyoungwoo Nam
AU  - Dajeong Lim
AU  - Kyung-Tai Lee
AU  - Yoon Jung Do
AU  - Chang-Yeon Cho
AU  - Jin-Wu Nam
TI  - Non-coding Transcriptome Maps Across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye
AID  - 10.1101/223644
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 223644
4099  - http://biorxiv.org/content/early/2017/11/23/223644.short
4100  - http://biorxiv.org/content/early/2017/11/23/223644.full
AB  - The Yeonsan Ogye (Ogye) is a rare chicken breed that populates the Korean peninsula. The entire body of this bird, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS) were performed to construct whole non-coding transcriptome maps across twenty different Ogye tissues. The resulting maps included 6900 long non-coding RNA (lncRNA) genes comprising 1290 known and 5610 novel lncRNA genes. Compared to lncRNAs previously annotated in the Galllus gallus red junglefowl, a considerable number were either fragments of protein-coding genes or not expressed in Ogye tissues. Newly annotated Ogye lncRNA genes showed tissue-specific expression and simple gene structures containing 2 or 3 exons. Systematic analyses of sequencing data and other genomic data demonstrated that about 39% of the tissue-specific lncRNAs displayed evidence of function. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our findings and resulting maps provide not only a comprehensive catalogue of lncRNAs but also a set of functional lncRNAs that will facilitate understanding how the non-coding genome regulates unique phenotypes. Furthermore, our results should be of use for future genomic breeding of chickens.