Dataset Information

IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING

ABSTRACT: Skin color patterns are ubiquitous in nature, evolve rapidly, and impact social behavior, predator avoidance, and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal-containing cells called iridophores that reflect light. It was suggested that the zebrafish’s alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores, however, we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro-environment. RNA-sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment, while cryogenic scanning electron microscopy and micro-X-ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine, all indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model, pattern phenotype depends not only on interactions among pigment cells that affect their arrangements, but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles.

ORGANISM(S): Danio rerio

PROVIDER: GSE144734 | GEO | 2020/10/27

REPOSITORIES: GEO

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Project description:Purpose:In order to elucidate the molecular mechanism of the stripe patterns in B. superciliaris skin.These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors. Methods:In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns were observed in 5 mRNAs and mir-217 by qRT-PCR. Results:Based on the zebrafish genome, a total of 44,206,176 and 46,941,318 high-quality transcriptome reads were generated, which resulted in 134,586 unigenes that were used as reference sequences. A total of 24,113 genes exhibited significantly different expression patterns (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05), including 15,117 up-regulated genes and 8,996 down-regulated genes associated with black and yellow stripes.These genes were enriched in 65 GO terms and 7 KEGG pathways (q ≤ 0.05), which included melanogenesis, and contained 32 up-regulated genes and 12 down-regulated genes. High-throughput miRNA sequencing identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs that contained 50 up-regulated and 37 down-regulated miRNAs were identified in different color skin Conclusions:This study provides novel insight into the mechanism that produces different color stripes in B. superciliaris by combining RNA-seq with small RNA-seq. 5 genes and 1 miRNAs were selected arbitrarily for verification . Compared with previous fish studies, revealed that these DE mRNAs and miRNAs are likely involved in melanin synthesis, and the quantitative mRNA/miRNA data and pathway information presented here provide a strong basis for elucidation of the detailed functions of mRNAs and miRNAs associated with black and yellow stripe formation in aquarium fish.

Project description: Purpose:In order to elucidate the molecular mechanism of the stripe patterns in B. superciliaris skin.These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors. Methods:In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns were observed in 5 mRNAs and mir-217 by qRT-PCR. Results:Based on the zebrafish genome, a total of 44,206,176 and 46,941,318 high-quality transcriptome reads were generated, which resulted in 134,586 unigenes that were used as reference sequences. A total of 24,113 genes exhibited significantly different expression patterns (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05), including 15,117 up-regulated genes and 8,996 down-regulated genes associated with black and yellow stripes.These genes were enriched in 65 GO terms and 7 KEGG pathways (q ≤ 0.05), which included melanogenesis, and contained 32 up-regulated genes and 12 down-regulated genes. High-throughput miRNA sequencing identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs that contained 50 up-regulated and 37 down-regulated miRNAs were identified in different color skin Conclusions:This study provides novel insight into the mechanism that produces different color stripes in B. superciliaris by combining RNA-seq with small RNA-seq. 5 genes and 1 miRNAs were selected arbitrarily for verification . Compared with previous fish studies, revealed that these DE mRNAs and miRNAs are likely involved in melanin synthesis, and the quantitative mRNA/miRNA data and pathway information presented here provide a strong basis for elucidation of the detailed functions of mRNAs and miRNAs associated with black and yellow stripe formation in aquarium fish.

Dataset Information

IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING

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