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

Study on the Regulatory Mechanisms of Carapace Marking Formation in Marsupenaeus japonicus

There are two phenotypes in the natural populations of Marsupenaeus japonicus, which is an ideal model for studying the formation of markings and body color in crustaceans. In a previous study, we used comparative transcriptome technology to screen some functional genes related to body color regulation. Here, high-throughput sequencing technology was used to perform microRNA (miRNA) sequencing analysis on the exoskeleton of M. japonicus with two types of carapace markings, and functional studies of related genes were performed. A total of 687 mature miRNAs belonging to 135 miRNA families were identified in this study, and 111 novel miRNAs were found. Through stringent screening conditions, a total of 18 differentially expressed miRNAs were identified, including 14 with upregulated expression and 4 with downregulated expression. Multiple target genes were predicted for almost all of the differentially expressed miRNAs. The expression levels of several target genes, such as those related to cytoplasmic microtubule organization, transmembrane transportation, and signal transduction, were confirmed using qRT-PCR. This study revealed that both the CRCN A2 and CRCN C1 genes were highly expressed in type I individuals, while the expression levels of their related miRNAs in type I individuals were lower than those in type II individuals, which is consistent with the mechanism of miRNAs negatively regulating mRNA expression. Through interference with the CRCN A2 and CRCN C1 genes, a clear regulatory relationship was found between the two genes, and the dendritic xanthophores in the carapace of M. japonicus gradually changed from bright yellow to dark black, with obvious shrinkage. In summary, our studies provide references for the regulatory mechanisms of marking formation in M. japonicus.

Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities

The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a ~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.

Characterization and functional analysis of pl-miR-2188 in melanin synthesis in leopard coral grouper (Plectropomus leopardus)

MicroRNAs (miRNAs) are known to regulate gene expression and play a role in body color formation in fish. However, the molecular mechanisms underlying miRNA involvement in the body color of leopard coral grouper (Plectropomus leopardus) remain largely unexplored. In this study, we investigated the expression levels of miR-2188 in red and black P. leopardus (pl-miR-2188) and found significantly higher expression levels in red fish samples compared to those in black fish samples. Silencing pl-miR-2188 in vivo using a pl-miR-2188 antagomir resulted in increased melanin concentration. Following pl-miR-2188 silencing, the expression levels of melanin-related genes, such as tyrosinase (tyr), TYR-related protein 1 (tyrp1-1 and tyrp1-2) and TYR-related protein 2 (tyrp2), and microphthalmia-associated transcription factor (mitf), were elevated. RNAhybrid predictions and dual-luciferase reporter assays identified sox5 as a target mRNA of pl-miR-2188. Following pl-miR-2188 antagomir injection, sox5 expression was significantly upregulated in the injection group compared to that in control groups (P < 0.05). These results suggest that pl-miR-2188 may regulate melanin synthesis in P. leopardus by targeting sox5. This study provides new insights into the miRNA-mRNA interactions involved in melanin synthesis and body color formation in the leopard coral grouper.

A comprehensive review of current practices, challenges, and future perspectives in Koi fish (Cyprinus carpio var. koi) cultivation

The Koi fish (Cyprinus carpio var. koi) is an ornamental fish with a high selling value because of its attractive colors, color patterns, body shape, and swimming motion. Koi fish is extensively traded in the international fish market because of their popularity among hobbyists from numerous countries worldwide. This review discusses various aspects of Koi fish cultivation, including genetic involvement, selective breeding strategies, and management systems. By examining crucial factors such as water parameters, technological innovations, and evolving cultivation methods, this review explored their influence on the quality of Koi fish. Breakthrough technologies, such as ornamental fish warehousing and recirculation aquaculture systems, enhance breeding efficiency and profitability. Molecular sexing, feed optimization, and color enhancement strategies are central to pursuing superior Koi fish. Reproduction management, disease prevention, and risk reduction during transport underscore ongoing efforts to ensure their survival. Despite notable progress, several challenges remain, including limited genetic studies, gaps in disease research, and unexplored herbal alternatives. The active involvement of hobbyists and breeders in research initiatives is a pivotal force in unlocking the untapped potential. The holistic approaches to enhance production efficiency and improve care standards require further exploration, paving the way for a sustainable future in the evolving management of Koi fish cultivation.

Correlation of skin color and plasma carotenoid-related metabolites of ornamental koi carp under temperature fluctuations

The skin color of koi carp (Cyprinus carpio L.) is one of the traits that most influence their ornamental and economic values. The present study suggested the effects of temperature fluctuation on koi carp in terms of skin color and plasma carotenoids and related-metabolites. The main results were as follows. (1) The vulnerability of koi skin color to acute temperature stress was in the order of white koi> black koi> yellow koi. Both high- (25°C-30°C-25°C) and low-temperature (25°C-20°C-25°C) fluctuations tended to decrease the saturation of white koi. The temperature fluctuation had little effects on the skin color of black and yellow koi. (2) Targeted metabolomics analysis indicated that the effects of cooling stress on oxycarotenoids of all five koi varieties were reversible. The plasma oxycarotenoids in mirror koi with all colors were insensitive to acute heat stress. However, the cooling process from a high temperature (30°C-25°C) still made contributions to the increase of oxycarotenoids. (3) The principal component analysis confirmed the deviation of carotenoid-related metabolites after high temperature fluctuation and the reversibility after low temperature fluctuation. Finally, the correlation analysis revealed that koi skin brightness was negatively correlated with the plasma guanine content and that temperature fluctuations might change koi skin brightness via the L(-)-epinephrine-guanine pathway. The red hue and yellow hue were negatively correlated with the oxycarotenoids in plasma, suggesting that oxycarotenoids were favorable for enhancing koi skin color saturation. Overall, this study revealed the direct action of temperature fluctuations on the skin color and carotenoid-related metabolites of koi.

Involvement of miR-495 in the skin pigmentation of rainbow trout (Oncorhynchus mykiss) through the regulation of mc1r

MicroRNAs (miRNAs) play crucial roles in skin pigmentation in animals. Rainbow trout (Oncorhynchus mykiss) is a key economic fish species worldwide, and skin color directly affects its economic value. However, the functions of miRNAs in rainbow trout skin pigmentation remain largely unknown. Herein, we overexpressed and silenced miR-495 in vitro and in vivo to investigate its functions. The analysis of spatial and temporal expression patterns suggested that miR-495 is a potential regulator during the process of skin pigmentation. In vitro, mc1r was validated as a direct target for miR-495 by dual-luciferase reporter assay, and overexpression of miR-495 significantly inhibited mc1r expression; in contrast, mc1r and its downstream gene mitf levels were markedly upregulated by decreased miR-495. In vivo, overexpressed miR-495 by injecting agomiR-495 led to a substantial decrease in the expression of mc1r and mitf in dorsal skin and liver, while the opposite results were obtained after miR-495 silencing by antagomiR-495. These findings suggested that miR-495 can target mc1r to regulate rainbow trout skin pigmentation, which provide a potential basis for using miRNAs as target drugs to treat pigmentation disorders and melanoma.

Transcriptome analysis reveals candidate miRNAs involved in skin color differentiation of juvenile Plectropomus leopardus in response to different background colors

Red skin color in Plectropomus leopardus is important to its ornamental and economic value. However, the color of P. leopardus can change during the rearing process, darkening and turning black due to the influence of environmental background color. The underlying molecular mechanisms that regulate this phenomenon remain unclear. MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that play important roles in numerous biological processes, such as skin differentiation and color formation in many animals. Therefore, we performed miRNA sequencing of P. leopardus skin before (initial) and after rearing with three different background colors (white, black, and blue) using Illumina sequencing to identify candidate miRNAs that may contribute to skin color differentiation. In total, 154,271,376 clean reads were obtained, with over 92 % of them successfully mapped to the P. leopardus reference genome. The miRNA length distributions of all samples displayed peaks around a typical length of 22 nt. Within these sequences, 243 known and 287 novel miRNAs were identified. A total of 65 significantly differentially expressed miRNAs (DEMs) were identified (P < 0.05), including 40 known DEMs and 25 novel DEMs. These DEMs included novel_561, miR-141-3p, and miR-129-5p, whose target genes were primarily associated with pigmentation related processes, including tyrosine metabolism, melanogenesis, and the Wnt signaling pathway. These findings shed light on the potential roles of miRNAs in the darkening of skin color in P. leopardus, thus enhancing our understanding of the molecular mechanisms involved in skin pigmentation differentiation in this species.

Effects of Natural and Synthetic Astaxanthin on Growth, Body Color, and Transcriptome and Metabolome Profiles in the Leopard Coral Grouper (Plectropomus leopardus)

Natural and synthetic astaxanthin can promote pigmentation in fish. In this study, the effects of dietary astaxanthin on growth and pigmentation were evaluated in leopard coral grouper (Plectropomus leopardus). Fish were assigned to three groups: 0% astaxanthin (C), 0.02% natural astaxanthin (HP), and 0.02% synthetic astaxanthin (AS). Brightness (L*) was not influenced by astaxanthin. However, redness (a*) and yellowness (b*) were significantly higher for fish fed astaxanthin-containing diets than fish fed control diets and were significantly higher in the HP group than in the AS group. In a transcriptome analysis, 466, 33, and 32 differentially expressed genes (DEGs) were identified between C and HP, C and AS, and AS and HP, including various pigmentation-related genes. DEGs were enriched for carotenoid deposition and other pathways related to skin color. A metabolome analysis revealed 377, 249, and 179 differential metabolites (DMs) between C and HP, C and AS, and AS and HP, respectively. In conclusion, natural astaxanthin has a better coloration effect on P. leopardus, which is more suitable as a red colorant in aquaculture. These results improve our understanding of the effects of natural and synthetic astaxanthin on red color formation in fish.

KRS-Net: A Classification Approach Based on Deep Learning for Koi with High Similarity

As the traditional manual classification method has some shortcomings, including high subjectivity, low efficiency, and high misclassification rate, we studied an approach for classifying koi varieties. The main contributions of this study are twofold: (1) a dataset was established for thirteen kinds of koi; (2) a classification problem with high similarity was designed for underwater animals, and a KRS-Net classification network was constructed based on deep learning, which could solve the problem of low accuracy for some varieties that are highly similar. The test experiment of KRS-Net was carried out on the established dataset, and the results were compared with those of five mainstream classification networks (AlexNet, VGG16, GoogLeNet, ResNet101, and DenseNet201). The experimental results showed that the classification test accuracy of KRS-Net reached 97.90% for koi, which is better than those of the comparison networks. The main advantages of the proposed approach include reduced number of parameters and improved accuracy. This study provides an effective approach for the intelligent classification of koi, and it has guiding significance for the classification of other organisms with high similarity among classes. The proposed approach can be applied to some other tasks, such as screening, breeding, and grade sorting.

Cell Junction and Vesicle Trafficking-Mediated Melanosome/Melanin Transfer Are Involved in the Dynamic Transformation of Goldfish Carassius auratus Skin Color

Goldfish are one of the most popular models for studying the genetic diversity of skin color. Transcriptome sequencing (RNA-seq) and whole genome bisulfate sequencing (WGBS) of skin tissues from the third filial (F3) cyan (CN), black (BK), and white (WH) goldfish were conducted to analyze the molecular mechanism of color transformation in fish. The RNA-seq yielded 56 Gb of clean data and 56,627 transcripts from nine skin samples. The DEGs (differentially expressed genes) were enriched in cell junction cellular components and the tight junction pathway. Ninety-five homologs of the claudin family were predicted and 16 claudins were identified in correlation with skin color transformation. WGBS yielded 1079 Gb of clean data from 15 samples. Both the DEGs and the DMRs (differentially methylated regions) in the BK_CN group were found to be enriched in cytoskeleton reorganization and vesicle trafficking. Masson staining and TEM (transmission electron microscopy) confirmed the varied distribution and processes of melanosome/melanin in skin tissues. Our results suggested that cytoskeleton reorganization, cell junction, and the vesicle trafficking system played key roles in the transfer of the melanosome/melanin, and it was the extracellular translocation rather than the biosynthesis or metabolism of the melanin process that resulted in the color transformation of cyan goldfish. The data will facilitate the understanding of the molecular mechanisms underlying dynamic skin color transformation in goldfish.

MiR-382 Functions on the Regulation of Melanogenesis via Targeting dct in Rainbow Trout (Oncorhynchus mykiss)

MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that are involved in a diverse collection of biological processes as important post-transcriptional regulators. However, little is known about the molecular regulatory mechanism of miRNAs in fish skin pigmentation. In this study, we first confirmed that dopachrome tautomerase (dct), a key gene of melanogenesis, is a target of miR-382 in rainbow trout (Oncorhynchus mykiss) using luciferase reporter assay. The analysis of different developmental stages and tissue expression patterns between wild-type and yellow mutant rainbow trout suggested that miR-382 is a potential regulator during the process of skin pigmentation. In vitro, miR-382 mimics in rainbow trout primary liver cells significantly downregulated dct expression and resulted in decreased expression of key melanogenic genes including tyrosine-related protein 1 (tyrp1) and premelanosome protein (pmel), whereas the expression level of dct was markedly increased after transfected with miR-382 inhibitor. In vivo, overexpression of miR-382 by injection of miR-382 agomir significantly depressed the expression of dct in dorsal skin, tail fin, and liver and then reduced the expression levels of tyrp1 and pmel. Furthermore, transfection of miR-382 mimics inhibited cell proliferation and induced apoptosis. Taken together, our results identified a functional role of miR-382 in rainbow trout skin pigmentation through targeting dct, which facilitate understanding the regulatory mechanism of rainbow trout skin color at the post-transcriptional level and provide a theoretical basis for molecular breeding with skin color as the target trait.

UVB irradiation differential regulate miRNAs expression in skin photoaging

Background

UVB irradiation can cause acute damage such as sunburn, or photoaging and melanoma, all of which are major health threats.

Objective

This study was designed to investigate the mechanism of skin photoaging induced by UVB radiation in mice through the analysis of the differential expression of miRNAs.

Methods

A UVB irradiation photoaging model was constructed. HE and Masson special stains were used to examine the modifications in the epidermis and dermis of mice. The miRNA expression profiles of the mouse skin model exposed to UVB radiation and the normal skin of mice were analyzed using miRNA-sequence analysis. GO and Pathway analysis were employed for the prediction of miRNA targets.

Results

A total of 23 miRNAs were evaluated for significantly different expressions in comparison to normal skin. Among them, 7 miRNAs were up-regulated and 16 were down-regulated in the skin with photoaging of mice exposed to UVB irradiation. The differential expression of miRNA is related to a variety of signal transduction pathways, among which mmu-miR-195a-5p and mitogen-activated protein kinase (MAPK) signal pathways are crucial. There was a significant differential expression of miRNA in the skin of normal mice in comparison with the skin with photoaging induced by UVB irradiation.

Study limitations

Due to time and energy constraints, the specific protein level verification, MAPK pathway exploration, and miR-195a-5p downstream molecular mechanism need to be further studied in the future.

Conclusions

UVB-induced skin photoaging can be diagnosed and treated using miRNA.

MicroRNA-183-5p regulates MITF expression in vitiligo skin depigmentation

Microphthalmia-associated transcription factor (MITF) is a master regulatory factor for melanocytes. MITF regulates multiple pigmentary genes for maintaining cellular homeostasis. MicroRNAs (miRNAs) play crucial roles in numerous biological processes however their molecular/cellular mechanisms to regulate pigmentation have not been fully explored. This study was undertaken to investigate the role of miRNAs in skin depigmentation via regulation of MITF gene. Depigmentation in C57BL/6 black mice was induced by an autoimmune response against tyrosinase. Bioinformatics approach was used to detect miRNAs conserved in 3'untraslated region (3'UTR) of MITF mRNA. The iMC23 mouse melanocytes were used for transfection experiments. The data demonstrated that the MITF mRNA/protein was markedly low in lesional skin of depigmented mice (p < 0.05). Targetscan genomic database determined that 3'UTR of mouse MITF constitutes 4819 nucleotide bases and has 23 conserved sites for different miRNAs To validate the pairing of these predicted miRNAs with MITF mRNA, five miRNAs were deregulated in lesional skin (p < 0.05). Among them, mmu-miR-181a-5p and mmu-miR-183-5p were up-regulated, whereas mmu-miR-26a-5p, mmu-miR-26b-5p and mmu-miR-32-5p were down-regulated (p < 0.05). To verify these results, the iMC23 mouse melanocytes were used. Transfection of iMC23 cells with specific miRNAs mimics or inhibitors or with 3'UTR reporter clone of MITF, showed only mmu-miR-183-5p binds to 3'UTR of MITF mRNA and regulates its expression in iMC23 melanocytes. In conclusions, this is the first study shows that miR-183-5p is a direct regulator of MITF in iMC23 melanocytes. Thus, miR-183-5p is an important regulator of melanocytes homeostasis and may be a novel target for autoimmune depigmentation therapy.

Identification and Characterization of miRNAs and Their Predicted mRNAs in the Larval Development of Pearl Oyster Pinctada fucata

As an important economic shellfish, the pearl oyster, Pinctada fucata, and its larvae are an ideal model for studying molecular mechanisms of larval development in invertebrates. Larval development directly affects the quantity and quality of pearl oysters. MicroRNAs (miRNAs) may play important roles in development, but the effects of miRNA expression on P. fucata early development remain unknown. In this study, miRNA and mRNA transcriptomics of seven different P. fucata developmental stages were analyzed using Illumina RNA sequencing. A total of 329 miRNAs, including 87 known miRNAs and 242 novel miRNAs, and 33,550 unigenes, including 26,333 known genes and 7217 predicted new genes, were identified in these stages. A cluster analysis showed that the difference in the numbers of miRNAs was greatest between fertilized eggs and trochophores. In addition, the integrated mRNA transcriptome was used to predict target genes for differentially expressed miRNAs between adjacent developmental stages, and the target genes were subjected to a gene ontology enrichment analysis. Using the gene ontology annotation, 100 different expressed genes and 95 differentially expressed miRNAs were identified as part of larval development regulation. Real-time PCR was used to identify eight mRNAs and three miRNAs related to larval development. The present findings will be helpful for further clarifying the regulatory mechanisms of miRNA in invertebrate larval development.

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

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.

Integrative mRNA-miRNA interaction analysis reveals the molecular mechanism of skin color variation between wild-type and yellow mutant rainbow trout (Oncorhynchus mykiss)

Rainbow trout (Oncorhynchus mykiss) is an important economic fish in China. Skin color affects the economic value of trout. However, the molecular mechanism of the skin color variation between wild-type (WR) and yellow mutant rainbow trout (YR) is unclear. We sequenced mRNAs and miRNAs of dorsal skin to identify key color variation-associated mRNAs and miRNAs between WR and YR. Overall, 2060 out of 3625 differentially expressed genes were upregulated in YR, and 196 out of 275 differentially expressed miRNAs were downregulated in WR. We identified three key YR-upregulated genes related to the formation of xanthophores (GCH1, SLC2A11, and SOX10). Interestingly, several genes related to melanogenesis (TYR, TYRP1, TYRP2, MC1R, MITF, PMEL, SLC45A2, and OCA2) were downregulated in WR. Integrated analysis identified five miRNAs that target at least two skin color-related genes (miR-495-y, miR-543-y, miR-665-z, miR-433-y, and miR-382-x). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of target genes identified noncoding RNA metabolic process as the most significantly enriched GO term, and several metabolic pathways associated with skin color were enriched significantly, such as tyrosine metabolism, histidine metabolism, and vitamin B6 metabolism. Quantitative real-time PCR of selected mRNAs and miRNAs validated the reliability of the integrated analysis. This study provides in-depth insights into the molecular mechanism of skin color variation between WR and YR, which will accelerate the genetic selection and breeding of rainbow trout with consumer-favored traits.

Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas)

Molluscan shell color polymorphism is important in genetic breeding, while the molecular information mechanism for shell coloring is unclear. Here, high-throughput RNA sequencing was used to compare expression profiles of coding and non-coding RNAs (ncRNAs) from Pacific oyster Crassostrea gigas with orange and black shell, which were from an F2 family constructed by crossing an orange shell male with a black shell female. First, 458, 13, and 8 differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, respectively. Functional analysis suggested that the DEGs were significantly enriched in 9 pathways including tyrosine metabolism and oxidative phosphorylation pathways. Several genes related to melanin synthesis and biomineralization expressed higher whereas genes associated with carotenoid pigmentation or metabolism expressed lower in orange shell oyster. Then, based on the ncRNA analysis, 163 and 20 genes were targeted by 13 and 8 differentially expressed lncRNAs (DELs) and miRNAs (DEMs), severally. Potential DELs-DEMs-DEGs interactions were also examined. Seven DEMs-DEGs pairs were detected, in which tyrosinase-like protein 1 was targeted by lgi-miR-133-3p and lgi-miR-252a and cytochrome P450 was targeted by dme-miRNA-1-3p. These results revealed that melanin synthesis-related genes and miRNAs-mRNA interactions functioned on orange shell coloration, which shed light on the molecular regulation of shell coloration in marine shellfish.

MicroRNA-340 is involved in ultraviolet B-induced pigmentation by regulating the MITF/TYRP1 axis

Objective

There is growing evidence that ultraviolet B (UVB) irradiation can change the expression profile of microRNAs (miRNAs) in immortalized human epidermal melanocytes (Pig-1). We aimed to investigate the effect of miR-340 on regulating UVB-induced pigmentation.

Methods

Real-time quantitative PCR (qRT-PCR) was used to evaluate the expression of miR-340 in Pig-1 cells. Immunoblotting analysis, qRT-PCR, and luciferase reporter assays were used to detect the potential target of miR-340. The sodium hydroxide dissolution assay was used to assess the effect of miR-340 on changes in melanin content.

Results

Expression of miR-340 was reduced in human Pig-1 cells after UVB irradiation. We found a negative correlation between miR-340 and melanocyte inducing transcription factor (MITF) in Pig-1 cells after UVB irradiation. Knockdown and overexpression of MITF in Pig-1 cells down- and upregulated melanogenesis, respectively. Overexpression of miR-340 inhibited MITF expression, reduced the amount of melanin, and suppressed expression of multiple key molecules involved in the pigment synthesis pathway, whereas knockdown of miR-340 showed the opposite results.

Conclusions

Our results showed that miR-340 inhibited melanogenesis by regulating the downstream molecules of MITF and its signaling pathways, suggested that miRNA-340 may be a new target for the clinical treatment of UVB-induced pigmentation.

Integrated analysis of microRNA and mRNA expression profiles in Crassostrea gigas to reveal functional miRNA and miRNA-targets regulating shell pigmentation

MicroRNAs (miRNAs) regulate post-transcription gene expression by targeting genes and play crucial roles in diverse biological processes involving body color formation. However, miRNAs and miRNA-targets underlying shell color polymorphism remain largely unknown in mollusca. Using four shell colors full-sib families of the Pacific oyster Crassostrea gigas, we systematically identified miRNAs and miRNA-targets in the mantles, which organ could produce white, golden, black or partially pigmented shell. RNA sequencing and analysis identified a total of 53 known miRNA and 91 novel miRNAs, 47 of which were detected to differentially express among six pairwise groups. By integrating miRNA and mRNA expression profiles, a total of 870 genes were predicted as targets of differentially expressed miRNAs, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of four miRNAs and their target mRNAs were predicted to involve in synthesis of melanin, carotenoid or tetrapyrrole. Of them, lgi-miR-317 and its targets peroxidase and lncRNA TCONS_00951105 are implicated in acting as the competing endogenous RNA to regulate melanogenesis. Our studies revealed the systematic characterization of miRNAs profiles expressed in oyster mantle, which might facilitate understanding the intricate molecular regulation of shell color polymorphism and provide new insights into breeding research in oyster.

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

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.

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

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.

The Mantle Exosome and MicroRNAs of Hyriopsis cumingii Involved in Nacre Color Formation

The nacre color of shells has an effect on the pearl color in Hyriopsis cumingii and is an important indicator for its value. The nacre is part of the shell, and some studies have shown that exosomes of the mantle are involved in the formation of shells. Most of the RNA contained in exosomes are microRNAs (miRNAs); however, little information is available on the roles of exosomes and miRNAs on the formation of nacre color in mussels. In this study, exosomes of mantles were extracted from white and purple mussels. High-throughput Illumina sequencing was performed on the white and purple mussel mantle exosomes, and 7,665,167 and 10,994,115 reads were harvested. Using the standard of |log₂(Fold change)| ≥ 2, and a p value ≤ 0.05, a total of 54 differentially expressed miRNAs were identified. The miRNAs that regulated the target genes (hcApo, HcTyr, HcTyp-1, HcMitf, HcSRCR1, and HcSRCR2) involved in shell color formation were predicted. Moreover, miR-15b negatively regulated hcApo, which plays important roles in the absorption and transport of β-carotene in H. cumingii. These results improve our understanding of the molecular mechanisms of nacre color formation in H. cumingii.