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

- Results: A total of clean reads, 446,614 putative transcripts, 4252 known and 72,907 novel lncRNAs were simultaneously obtained, including 92 significant differentially expressed lncRNAs and 722 mRNAs.
- Additionally, three lncRNAs (Ccr_lnc142711, Ccr_lnc17214525 and Ccr_lnc14830101) and three mRNAs (Asip, Mitf and Tyr) involved in the melanogenesis pathway were investigated in terms of potential functions in embryogenesis and different tissues..
- Conclusions: The findings broaden our understanding of lncRNAs and skin color genetics, and provide new insight into the mechanisms underlying lncRNA-mediated pigmentation and differentiation in Koi carp..
- Non-coding RNAs (ncRNAs), which are not translated into proteins but play vital roles in various biological processes, are receiving increasing attention [1].
- Ren et al.
- Weikard et al.
- In the present study, we conducted a high-throughput sequencing strategy to screen expres- sion of lncRNAs and mRNAs in these three skin colors..
- Putative target mRNAs of lncRNAs in cis and trans were pre- dicted, and we selected candidate lncRNAs and mRNAs that are highly likely affect skin pigmentation to con- struct coding/non-coding gene co-expression diagrams..
- Moreover, we also analyzed the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to excavate the function roles of genes in the determination of skin color.
- Spatial and temporal expression patterns of some lncRNAs and mRNAs involved in the melanogenesis pathway were further analyzed, indicating that these genes have.
- Identification of lncRNAs in koi carp skin.
- Several fil- tering steps were applied to screen lncRNAs in the transcript list by removing protein-coding transcripts, pseudogenes, and other classes of non-coding RNAs in- cluding ribosomal RNA (rRNA), microRNA (miRNA), transfer ribonucleic acid (tRNA).
- Expression profiling of lncRNAs and mRNAs.
- The proportion of significantly DE lncRNAs and mRNAs reflects their specific functions, and detailed lists of all genes are provided in Additional file 4..
- Luo et al.
- Ten lncRNAs and 13 mRNAs (randomly selected from the 85 mRNAs) were chosen for plotting heatmaps.
- Moreover, we identified some differently enriched terms in the three comparisons.
- In the KEGG pathway analysis of DE mRNAs, p-value denotes significance, with lower p-values indicating greater significance (the p-value cut-off determining.
- WS, while tight junction was more highly enriched in the RS_WS comparisons.
- All 206 pathways identified in the three comparisons are presented in Additional file 5..
- Cis and trans role of lncRNAs.
- A total of 41,625 interactions were identified for trans actions between 79 lncRNAs and protein-coding genes (Additional file 7).
- We also identified some key lncRNAs and target mRNAs related to the melanogenesis pathway (Table 3)..
- 2 Differentially expressed genes in the three pairwise comparison groups.
- a Volcano plots of all genes in the three pairwise comparisons..
- miR-196a, miR- 125b, miR-200b and miR-206) that influence pigmen- tation and differentiation in the three main skin colors [23].
- 3 a Venn diagram of differentially expressed lncRNAs in the three pairwise comparison groups.
- b Venn diagram of differentially expressed mRNAs in the three pairwise comparison groups.
- In the current study, 446,614 putative transcripts were obtained, including 4252 known and 72,907 novel lncRNAs, tremendously enriching the pool of lncRNAs correlated with fish skin.
- To gain insight into the expression of skin color-related genes in Koi carp, we determined expression profiles, and identified 92 DE lncRNAs and 722 DE mRNAs through pairwise com- parison.
- 4 Relative expression levels of genes measured using quantitative real-time PCR (qRT-PCR) and Illumina sequencing (RNA-seq) in the three comparative groups.
- Verification by qRT-PCR con- firmed the reliability of the RNA-seq data and the lncRNAs and mRNAs identified.
- Notably, Mitf and Wnt3a, both members of the Wnt family, were found to be regulated by lncRNAs both in cis (Ccr_lnc17821911) and in trans (Ccr_lnc125640361, Ccr_lnc1485701 and others) in the melanogenesis pathway.
- To gain insight into the functions of some lncRNAs and mRNAs in physiological processes, we further an- alyzed their temporal and spatial expression patterns..
- LncRNAs expressed during blastula and gastrula stages might play important roles in cell fate decisions, Table 2 The top ten KEGG pathways related to differentially expressed mRNAs in the three comparative groups.
- 6 Networks analysis of putative interactions between five selected lncRNAs and trans-regulated mRNAs related to the pigmentation process..
- Square and circular nodes represent lncRNAs and protein-coding genes, respectively.
- Table 3 LncRNAs and their potential target genes involved in melanogenesis Protein-coding.
- By comparing RNA-seq data from three pairwise groups, we identified significant DE lncRNAs and mRNAs, and explored potential cis and trans targets of lncRNAs.
- Functional enrichment and lncRNA-mRNA regulatory network analyses revealed novel lncRNAs and mRNAs associated with pigmenta- tion and differences in skin color.
- Additionally, temporal and spatial expression patterns of lncRNAs and mRNAs revealed tissue specificity.
- The numerous lncRNAs and mRNAs identi- fied, and the accompanying de novo transcriptome data, provide valuable resources for future transcriptome studies investigating functions associated with skin color in fish..
- Fish in the three experimental groups (black, white and red spots in one fish synchronous.
- Identification of differentially expressed lncRNAs and mRNAs.
- Differential cluster analysis of genes and volcano plotting of differentially expressed lncRNAs and mRNAs were performed using the E Charts platform (http://.
- To explore the functions of significant differentially expressed lncRNAs and mRNAs, and the corresponding target genes of differentially expressed lncRNAs, GO term and KEGG pathway enrichment analysis were con- ducted using the DAVID program v6.8 (https://david..
- expression levels of differentially expressed lncRNAs and mRNAs were normalized against glyceraldehydes-3- phosphate dehydrogenase (GAPDH) and β-actin using the 2 -△△Ct method [35].
- Photograph showing the three different skin color types in Koi carp.
- Primers used for analysis of differentially expressed genes related to skin color in Koi carp.
- Pipeline for analysis of skin color-related lncRNAs by Illumina sequencing..
- Additional file 4: Differentially expressed lncRNAs and mRNAs identified in the three different skin color groups.
- Additional file 5: GO term and KEGG pathway enrichment analysis of significant differentially expressed mRNAs in the three skin color groups..
- Additional file 8: Expression profiles of three lncRNAs (A) and three mRNAs (B) involved in the melanogenesis pathway in different tissues of Koi carp.
- All raw transcriptome data reported in this article have been deposited in the NCBI and Sequence Read Archive (SRA) databases (https://www.ncbi.nlm..
- Shi XF, Sun M, Yao Y, et al.
- Long non-coding RNAs: a new frontier in the study of human diseases.
- Volders PJ, Verheggen K, Menschaert G, et al.
- Gopalakrishnan K, Kumarasamy S, Mell B, et al.
- Tarifeno Saldivia E, Valenzuela Miranda D, Gallardo Escarate C, et al.
- In the shadow: the emerging role of long non-coding RNAs in the immune response of Atlantic salmon.
- Kaushik K, Leonard VE, Shamsudheen KV, et al.
- Ren HX, Wang GF, Zhou P, et al.
- Bar I, Kaddar E, Velan A, et al.
- Melanocortin receptor 1 and black pigmentation in the Japanese ornamental carp (Cyprinus carpio var.
- Liu JH, Wen S, Xiao YM, et al.
- Involvement of the Mitfa gene in the development of pigment cell in Japanese ornamental (koi) carp (Cyprinus carpio L.
- Manas KM, Deepjyoti B, Nandeesha TL, et al.
- Xu P, Zhang X, Sun XW, et al.
- Luo MK, Wang LM, Dong ZJ, et al.
- Identification and characterization of skin color microRNAs in koi carp (Cyprinus carpio L.) by Illumina sequencing..
- Kimmel CB, Ballard WW, Kimmel SR, et al.
- Haas BJ, Papanicolaou A, Yassour M, et al.
- Fu LM, Niu BF, Zhu ZW, et al.
- Sun L, Zhang Z, Bailey TL, et al.
- Finn RD, Tate J, Mistry J, et al.
- Shannon P, Markiel A, Ozier O, et al.
- Cieslak M, Reissmann M, Hofreiter M, et al.
- Li XM, Song YN, Xiao GB, et al.
- Li XZ, Zeng J, Zhang HT, et al.
- Cabili MN, Trapnell C, Goff LA, et al.
- Li L, Eichten SR, Shimizu R, et al.
- Derrien T, Johnson R, Bussotti G, et al.
- Differential expression patterns of Wnt genes in the murine female reproductive tract during development and the estrous cycle.
- Berson JF, Harper DC, Tenza D, et al.
- Zhu W, Wang L, Dong Z, et al.
- Hodgkinson CA, Moore KJ, Nakayama A, et al.
- Nagel D, Vincendeau M, Eitehuber AC, et al.
- Young RM, Shaffer A, Phelan JD, et al.
- Oetting W, Stine OC, Townsend D, et al.
- Englaro W, Rezzonico R, Durand M, et al.
- Grichnik JM, Burch JA, Burchette J, et al.
- The SCF/KIT pathway plays a critical role in the control of normal human melanocyte homeostasis.
- Squarzoni P, Parveen F, Zanetti L, et al.
- Zhang P, Liu W, Yuan XY, et al.
- Chiang HM, Chien YC, Wu CH, et al.
- Guttman M, Amit I, Garber M, et al.
- Hung T, Wang Y, Lin MF, et al.
- Guttman M, Donaghey J, Carey BW, et al.
- LincRNAs act in the circuitry controlling pluripotency and differentiation.
- Manceau M, Domingues VS, Mallarino R, et al

Xem thử không khả dụng, vui lòng xem tại trang nguồn
hoặc xem Tóm tắt