Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

Luo, Ming; Wang, Lanmei; Yin, Hao; Zhu, Wenbin; Fu, Jianjun; Dong, Zaijie

doi:10.1186/s12864-019-5894-8

Cited by 42 publications

(30 citation statements)

References 73 publications

(69 reference statements)

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“…LncRNAs function by targeting protein-coding genes. There is growing evidence suggesting that lncRNAs are critical factors in controlling and regulating gene expression via cis and trans -acting mechanisms [ 16 ]. Therefore, to identify lncRNA cis -target genes, we employed window function in BEDTools.v2.1.2 software to search for cis -target genes located within 100 kb upstream and downstream of differentially expressed lncRNAs.…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Augustino

Liu

et al. 2020

BMC Genomics

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Background Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that are associated with Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets. To address this, we used RNA sequencing to profile lncRNAs and mRNAs of small intestine epithelial cells in Large White piglets differing in their ETEC-F4 adhesion phenotypes and ITGB5 genotypes. Eight male piglets were used in this study and were divided into two groups on the basis of their adhesion phenotype and ITGB5 genotypes, a candidate gene for F4ac receptor. Non-adhesive group (n = 4) with CC genotype and adhesive group (n = 4) with TT genotype. Results In total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC| > 1, P < 0.05) were identified in the comparison of non-adhesive vs. adhesive small intestine epithelial cells. Furthermore, cis- and trans-regulatory target genes of DE-lncRNAs were identified, then interaction networks of lncRNAs and their cis- and trans-target differentially expressed genes (DEGs) were constructed separately. A total of 194 cis-targets were involved in the lncRNAs-cis genes interaction network and 61 trans-targets, were involved in lncRNA-trans gene interaction network that we constructed. We determined that cis-target genes were involved in alcoholism, systemic lupus erythematosus, viral carcinogenesis and malaria. Whereas trans-target DEGs were engaged in three important pathways related to the ETEC-F4 adhesion phenotype namely cGMP-PKG signaling pathway, focal adhesion, and adherens junction. The trans-target DEGs which directly involved in these pathways are KCNMB1 in cGMP-PKG signaling pathway, GRB2 in focal adhesion pathway and ACTN4 in focal adhesion and adherens junction pathways. Conclusion The findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of lncRNAs on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets’ diarrhea susceptibility/resistance.

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Section: Discussionmentioning

confidence: 99%

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Augustino

Liu

et al. 2020

BMC Genomics

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“…Other genes, such as tyrosinase-related protein-1 (Tyrp1) and dopachrome tautomerase (Dct or Tyrp2), primarily regulate the eumelanin pathway (Braasch et al, 2009). Interestingly, we also identified some important miRNAs and mRNAs on black, white, and red skin of koi carp, which involved in the cAMP signaling, melanogenesis, and tyrosine metabolism pathway through Illumina sequencing (Luo et al, 2018;Luo et al, 2019). Therefore, it is necessary to further excavate the specific relationship between the coding and non-coding RNAs, e.g.…”

Section: Introductionmentioning

confidence: 88%

MicroRNA-206 Regulation of Skin Pigmentation in Koi Carp (Cyprinus carpio L.)

et al. 2020

Self Cite

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MicroRNAs (miRNAs) are~22 nucleotide non-coding RNA molecules that act as crucial roles in plenty of biological processes. However, the molecular and cellular mechanisms of miRNAs to regulate skin color differentiation and pigmentation in fish have not been fully understood. Herein, we revealed that miR-206, a skin-enriched miRNA, regulates melanocortin 1 receptor (Mc1r, a key regulator of melanogenesis) expression by binding to its 3'-untranslated (UTR) region through bioinformatics and luciferase reporter assay in koi carp (Cyprinus carpio L.). The analysis of spatial and temporal expression patterns suggested that miR-206 is a potential regulator in the skin pigmentation process. Then, we silenced it in vivo with an antagomir method. The result showed a substantial increase of Mc1r mRNA expression and protein level, and also its downstream genes: tyrosinase (Tyr) and dopachrome tautomerase (Dct) that encoding key enzymes involved in melanin synthesis. Moreover, we constructed the miRNA-206 sponge lentivirus vector to transfect koi carp melanocytes in vitro, further checked the functions of melanocytes using Cck-8 and Transwell assays. As a result, inhibition of miR-206 significantly up-regulated Mc1r mRNA expression and protein level and accelerated the melanocyte proliferation and migration ability compared with the scrambled-sequence negative control group (miR-NC). Overall, these findings provide the evidence that miR-206 plays a regulatory role in the skin color pigmentation through targeting the Mc1r gene and would facilitate understanding the molecular regulatory mechanisms underlying miRNA-mediated skin color pigmentation in koi carp.

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“…S4). LncRNAs might be important in fish colour patterning (Luo et al, 2019), but will be not considered further. Overall 89.86% (200 out of 223) of the genes in close vicinity of the CPLs detected in this study have been mentioned in the literature dealing with colour, or affecting integument patterning, differentiation or structure.…”

Section: Resultsmentioning

confidence: 99%

Spotting genome-wide pigmentation variation in a brown trout admixture context

Valette¹,

Leitwein

Lascaux³

et al. 2020

Preprint

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Colour and pigmentation variation attracted fish biologists for a while, but high-throughput genomic studies investigating the molecular basis of body pigmentation remain still limited to few species and conservation biology issues ignored. Using 75,684 SNPs, we investigated the genomic basis of pigmentation pattern variation among individuals of the Atlantic and Mediterranean clades of the brown trout (Salmo trutta), a polytypic species in which Atlantic hatchery individuals are commonly used to supplement local wild populations. Using redundancy analyses and genome-wide association studies, a set of 384 “colour patterning loci” (CPL) significantly correlated with pigmentation traits such as the number of red and black spots on flanks, but also the presence of a large black stain on the opercular bone was identified. CPLs map onto 35 out of 40 brown trout linkage groups indicating a polygenic basis to pigmentation patterns. They are mostly located in coding regions (43.4%) of 223 candidate genes, and correspond to GO-terms known to be involved in pigmentation (e.g. calcium and ion-binding, cell adhesion). Annotated genes especially include 24 candidates with known pigmentation effects (e.g. SOX10, PEML, SLC45A2), but also the Gap-junction Δ2 (GJD2) gene that was previously showed be differentially expressed in trout skin. Patterns of admixture were found significantly distinct when using either the full SNP data set or the set of CPLs, indicating that pigmentation patterns accessible to practitioners are not a reliable proxy of genome-wide admixture. Consequences for management are discussed.

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Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

Cited by 42 publications

References 73 publications

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

MicroRNA-206 Regulation of Skin Pigmentation in Koi Carp (Cyprinus carpio L.)

Spotting genome-wide pigmentation variation in a brown trout admixture context

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