Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

Abstract

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.

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

“…The expression of lncRNA has been breed-and tissue-specific. In our study, no lnc-TMEM184C found by Hong et al [62].…”

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

“…Using the RNA-seq technology, previous studies have identified 4404, 2481, 39,907, 8691, 1376, 6543, 2597 and 2056 lncRNAs in breast muscle, spleen, cerebrum, ovarian follicle, trachea, liver, testis and adipose of chickens, respectively [33,[92][93][94][95][96][97][98]. Moreover, Kern et al [99] found 9393 lncRNAs in eight tissue types (adipose, cerebellum, cortex, hypothalamus, liver, lung, skeletal muscle and spleen) of chickens and Hong et al [100] obtained 6900 lncRNAs genes in 20 different tissues (breast, gizzard, liver, pancreas, uterus, heart, bone marrow, kidney, cerebrum, cerebellum, eye, immature egg, mature egg, gall-bladder, comb, shank, skin, lung, spleen and fascia) of an individual Ogye, with c.75% of lncRNAs as tissue-specific. In the present study, 818 candidate lncRNAs were identified in the mid-segments of chicken small intestines.…”

The chicken model organism for epigenomic research

“…By comparing the chicken genes to those of human, investigators found sequence and functional similarities of genes involved in cellular functions such as the immune response, environment adaptation, and reproduction (Dodgson and Romanov 2004a). Scientists have also investigated the non-coding transcriptome of the Gallus gallus genome and reported 9681 long non-coding RNAs according to the non-coding RNA (ncRNA) database NONCODE (Hong et al 2018). Previously considered as junk RNA, ncRNAs are now studied for their possible roles in regulation and conservation among vertebrates.…”