Abstract
BackgroundPigmentation development, is a complex process regulated by many transcription factors during development. With the development of the RNA sequencing (RNA-seq), non-coding RNAs, such as miRNAs, lncRNAs, and circRNAs, are found to play an important role in the function detection of related regulation factors. In this study, we provided the expression profiles and development of ncRNAs related to melanocyte and skin development in mice with black coat color skin and mice with white coat color skin during embryonic day 15 (E15) and postnatal day 7 (P7). The expression profiles of different ncRNAs were detected via RNA-seq and also confirmed by the quantitative real-time PCR (qRT-PCR) method. GO and KEGG used to analyze the function the related target genes.ResultsWe identified an extensive catalogue of 206 and 183 differently expressed miRNAs, 600 and 800 differently expressed lncRNAs, and 50 and 54 differently expressed circRNAs, respectively. GO terms and pathway analysis showed the target genes of differentially expressed miRNA and lncRNA. The host genes of circRNA were mainly enriched in cellular process, single organism process. The target genes of miRNAs were mainly enriched in chromatin binding and calcium ion binding in the nucleus. The function of genes related to lncRNAs are post translation modification. The competing endogenous RNA (ceRNA) network of lncRNAs and circRNAs displays a complex interaction between ncRNA and mRNA related to skin development, such as Tcf4, Gnas, and Gpnms related to melanocyte development.ConclusionsThe ceRNA network of lncRNA and circRNA displays a complex interaction between ncRNA and mRNA related to skin development and melanocyte development. The embryonic and postnatal development of skin provide a reference for further studies on the development mechanisms of ncRNA during pigmentation.
Highlights
Pigmentation development, is a complex process regulated by many transcription factors during development
A comparison of the gene expression profile of miRNA in the embryo and postnatal showed that 206 miRNAs were differently expressed in black coat color skin and 183 were differently expressed in white coat color skin (Fig. 2a, b). miRNAs such as miR-233, miR-217 and miR-211 were chosen based on the significant difference and raw signal intensity of their expressions. miR-233, miR-217 and miR-211 were not significant difference in BP compared with BE (P > 0.05), but were significant
According to the Gene ontology (GO) database, we found that the term enriched by two groups of miRNAs had a high degree of overlap, which indicated that these terms played key roles in embryonic development, including cytoplasm, transcription factor complex and nucleus were in cellular components; chromatin binding, transcription factor binding in black coat color skin
Summary
Pigmentation development, is a complex process regulated by many transcription factors during development. With the development of the RNA sequencing (RNA-seq), non-coding RNAs, such as miRNAs, lncRNAs, and circRNAs, are found to play an important role in the function detection of related regulation factors. More and more attention has been paid to research on skin and embryo development, and its differentiation and regulation-related factors, which has. People have been paying more and more attention to the role of non-coding RNA (ncRNA) as a regulators of post-transcriptional gene expression [6]. Recent studies have shown that they control many functions, including epigenetic modifications [8,9,10], transcriptional and translational regulation, and RNA and protein scaffolds, which represent a new regulatory approach [11, 12]
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