Transcriptional Differences of Coding and Non-Coding Genes Related to the Absence of Melanocyte in Skins of Bama Pig

Abstract

Skin is the body’s largest organ, and the main function of skin is to protect underlying organs from possible external damage. Melanocytes play an important role in skin pigmentation. The Bama pig has a “two-end-black” phenotype with different coat colors across skin regions, e.g., white skin (without melanocytes) and black skin (with melanocytes), which could be a model to investigate skin-related disorders, specifically loss of melanocytes. Here, we generated expression profiles of mRNAs and long noncoding RNAs in Bama pig skins with different coat colors. In total, 14,900 mRNAs and 7549 lncRNAs were expressed. Overall, 2338 mRNAs/113 lncRNAs with FDR-adjusted p-value ≤ 0.05 were considered to be differentially expressed (DE) mRNAs/lncRNAs, with 1305 down-regulated mRNAs and 1033 up-regulated mRNAs in white skin with|log2(fold change)| > 1. The genes down-regulated in white skin were associated with pigmentation, melanocyte–keratinocyte interaction, and keratin, while up-regulated ones were mainly associated with cellular energy metabolisms. Furthermore, those DE lncRNAs were predicted to be implicated in pigmentation, keratin synthesis and cellular energy metabolism. In general, this study provides insight into the transcriptional difference involved in melanocyte-loss-induced keratinocyte changes and promotes the Bama pig as a biomedical model in skin research.

Comprehensive analysis of LncRNAs modified by m6A methylation in sheep skin

“…This result broadens the annotation of the sheep lncRNAs. At the same time, the transcript length, exon number and expression of novel lncRNAs consisted with previously known lncRNAs but differed from the mRNAs, which was similar to pigs and goats [13,32]. We identified 168 DE lncRNAs (110 down-regulated and 58 up-regulated) between black and white sheep skin, which might be key candidate lncRNAs related to pigmentation.…”

“…LncRNAs are noncoding transcripts that are transcribed by RNA polymerase II, >200 bp in length, and possess widely functions by cis-or trans-action, including melanogenesis [7,8]. The lncRNA expression profiles of mouse skin [9], mouse melanocytes [10], goat skin and melanocytes [1,11], sheep skin [12], and pig skin [13] have been obtained. Some pigment-related lncRNAs have also been validated.…”

Commensal microbiota modulates phenotypic characteristics and gene expression in piglet Peyer’s patches

“…Conjoint cis / tans analyses were performed to indirectly predict lncRNA functions ( Jin et al, 2019 ). Briefly, the protein-coding genes within 100 kb of the DE lncRNAs were collected, and those among the DE mRNAs were filtered ( cis analysis).…”

Transcriptome profiling analysis of uterus during chicken laying periods

“…The rapid development of RNA sequencing (RNAseq) has provided a powerful tool for the study of the transcriptome [22,23]. RNA-seq has been widely used in the study of various species and traits in recent years [24][25][26][27][28][29]. There have been many studies on poultry uterus over the years [3,[30][31][32].…”