Hyosun Hong: Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea. yohae25@gmail.com.
Han-Ha Chai: Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea. hanha@korea.kr.
Kyoungwoo Nam: Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea. nkw0228@gmail.com.
Dajeong Lim: Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea. lim.dj@korea.kr.
Kyung-Tai Lee: Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea. leekt@korea.kr.
Yoon Jung Do: Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea. clonea@korea.kr. ORCID
Chang-Yeon Cho: Animal Genetic Resource Research Center of National Institute of Animal Science, RDA, Namwon 55717, Korea. bloodtype@korea.kr.
Jin-Wu Nam: Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea. jwnam@hanyang.ac.kr. ORCID
Yeonsan Ogye is a rare Korean domestic chicken breed whose entire body, including 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 widely investigated. Thus, we evaluated coding and non-coding transcriptome expression and identified long non-coding RNAs functionally linked to protein-coding genes in Ogye. High-throughput RNA sequencing and DNA methylation sequencing were performed to profile the expression of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes and detect DNA methylation in 20 different tissues of an individual Ogye. Approximately 75% of Ogye lncRNAs and 45% of protein-coding genes showed tissue-specific expression. For some genes, tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. Approximately 39% of tissue-specific lncRNAs displayed functional associations with proximal or distal protein-coding genes. Heat shock transcription factor 2-associated lncRNAs appeared to be functionally linked to protein-coding genes specifically expressed in black skin tissues, more syntenically conserved in mammals, and differentially expressed in black relative to in white tissues. Pending experimental validation, our findings increase the understanding of how the non-coding genome regulates unique phenotypes and can be used for future genomic breeding of chickens.
