Dynamic regulation of mRNA and miRNA associated with the developmental stages of skin pigmentation in Japanese ornamental carp

Xue, Tian; Pang, Xiaolei; Wang, Liangyan; Li, Mengrong; Dong, Chuanju; Ma, Xiao; Wang, Lei; Song, Dongying; Feng, Jianxin; Xu, Peng; Li, Xuejun

doi:10.1016/j.gene.2018.04.054

Cited by 29 publications

(16 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Coloration is determined mainly by diverse pigments synthesized by pigment cells that are developed and differentiated from neural crest cells during embryonic development 3 . Unlike mammals, in which only melanophores (black or brown) are present, and amphibians and reptiles which possess xanthophores (yellow), erythrophores (red or orange), and iridophores (reflecting), six types of pigment cells, namely melanophores, xanthophores, erythrophores, iridophores, leucophores (white), and cyanophores (blue), have been identified in teleosts based on their hue, implying great plasticity in skin coloration 4 . Owing to the diversity of pigment cells in fish, skin color has become an essential phenotypic characteristic that assists the breeding of high yield and superior quality, and helps increase economic value 5 .…”

Section: Introductionmentioning

confidence: 99%

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Huang

et al. 2022

Sci Rep

View full text Add to dashboard Cite

Yellow mutant rainbow trout (YR), an economically important aquaculture species, is popular among consumers due to its excellent meat quality and attractive appearance. Skin color is a key economic trait for YR, but little is known about the molecular mechanism of skin color development. In this study, YR skin transcriptomes were analyzed to explore temporal expression patterns of pigmentation-related genes in three different stages of skin color development. In total, 16,590, 16,682, and 5619 genes were differentially expressed between fish at 1 day post-hatching (YR1d) and YR45d, YR1d and YR90d, and YR45d and YR90d. Numerous differentially expressed genes (DEGs) associated with pigmentation were identified, and almost all of them involved in pteridine and carotenoid synthesis were significantly upregulated in YR45d and YR90d compared to YR1d, including GCH1, PTS, QDPR, CSFIR1, SLC2A11, SCARB1, DGAT2, PNPLA2, APOD, and BCO2. Interestingly, many DEGs enriched in melanin synthesis pathways were also significantly upregulated, including melanogenesis (MITF, MC1R, SLC45A2, OCA2, and GPR143), tyrosine metabolism (TYR, TYRP1, and DCT), and MAPK signaling (KITA) pathways. Using short time-series expression miner, we identified eight differential gene expression pattern profiles, and DEGs in profile 7 were associated with skin pigmentation. Protein–protein interaction network analysis showed that two modules were related to xanthophores and melanophores. In addition, 1,812,329 simple sequence repeats and 2,011,334 single-nucleotide polymorphisms were discovered. The results enhance our understanding of the molecular mechanism underlying skin pigmentation in YR, and could accelerate the molecular breeding of fish species with valuable skin color traits and will likely be highly informative for developing new therapeutic approaches to treat pigmentation disorders and melanoma.

show abstract

Section: Introductionmentioning

confidence: 99%

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Huang

et al. 2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…For example, BCO2 encodes a carotenoid-cleavage enzyme which is associated with yellow/white skin and plumage color polymorphism in birds [18,19]; CYP2J19 encodes a ketolase that catalyzes the metabolic conversion of dietary yellow carotenoids into red ketocarotenoids in birds and turtles [20][21][22]; SCARB1 encodes a high-density lipoprotein receptor that mediates the cellular uptake of carotenoids and was found to be responsible for the presence/absence of carotenoid plumage coloration in canary breeds [23]. Comparative transcriptomic analyses revealed correlations between carotenoidbased skin color differences and the expression levels of some of the known carotenoid color genes, and identified novel candidate genes which might be involved in carotenoid-based coloration (e.g., [24][25][26][27][28]). In the present study, we used RNA sequencing (RNA-Seq) to test for differential gene expression associated with the presence/absence of carotenoid-based coloration in a cichlid fish.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish

et al. 2020

View full text Add to dashboard Cite

Background Carotenoids contribute significantly to animal body coloration, including the spectacular color pattern diversity among fishes. Fish, as other animals, derive carotenoids from their diet. Following uptake, transport and metabolic conversion, carotenoids allocated to body coloration are deposited in the chromatophore cells of the integument. The genes involved in these processes are largely unknown. Using RNA-Sequencing, we tested for differential gene expression between carotenoid-colored and white skin regions of a cichlid fish, Tropheus duboisi “Maswa”, to identify genes associated with carotenoid-based integumentary coloration. To control for positional gene expression differences that were independent of the presence/absence of carotenoid coloration, we conducted the same analyses in a closely related population, in which both body regions are white. Results A larger number of genes (n = 50) showed higher expression in the yellow compared to the white skin tissue than vice versa (n = 9). Of particular interest was the elevated expression level of bco2a in the white skin samples, as the enzyme encoded by this gene catalyzes the cleavage of carotenoids into colorless derivatives. The set of genes with higher expression levels in the yellow region included genes involved in xanthophore formation (e.g., pax7 and sox10), intracellular pigment mobilization (e.g., tubb, vim, kif5b), as well as uptake (e.g., scarb1) and storage (e.g., plin6) of carotenoids, and metabolic conversion of lipids and retinoids (e.g., dgat2, pnpla2, akr1b1, dhrs). Triglyceride concentrations were similar in the yellow and white skin regions. Extracts of integumentary carotenoids contained zeaxanthin, lutein and beta-cryptoxanthin as well as unidentified carotenoid structures. Conclusion Our results suggest a role of carotenoid cleavage by Bco2 in fish integumentary coloration, analogous to previous findings in birds. The elevated expression of genes in carotenoid-rich skin regions with functions in retinol and lipid metabolism supports hypotheses concerning analogies and shared mechanisms between these metabolic pathways. Overlaps in the sets of differentially expressed genes (including dgat2, bscl2, faxdc2 and retsatl) between the present study and previous, comparable studies in other fish species provide useful hints to potential carotenoid color candidate genes.

show abstract

“…Recent studies demonstrated that the expression profiles of miRNA showed tissue-specific expression patterns in the epidermis hair follicles, stage-specific expression in the periodic development of hair follicles as well as pigmentation [26][27][28]. miRNAs in different cell types form a comprehensive, multi-level network system through interactions with signal pathway and regulation factors [29,30].…”

Section: Discussionmentioning

confidence: 99%

The comprehensive detection of miRNA, lncRNA, and circRNA in regulation of mouse melanocyte and skin development

Zhu

et al. 2020

Biol Res

View full text Add to dashboard Cite

Background: 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. 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. Results:We 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. Conclusions:The 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.

show abstract

Dynamic regulation of mRNA and miRNA associated with the developmental stages of skin pigmentation in Japanese ornamental carp

Cited by 29 publications

References 42 publications

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish

The comprehensive detection of miRNA, lncRNA, and circRNA in regulation of mouse melanocyte and skin development

Contact Info

Product

Resources

About