Comprehensive analysis of lncRNAs modified by m6A methylation in sheep skin
Comprehensive analysis of lncRNAs modified by m6 A methylation in sheep skin
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초록
Objective: N6-methyladenosine (m<sup>6</sup>A) is the most prevalent methylation of mRNA and plays crucial roles in various physiological processes, including pigmentation. Yet, the regulatory mechanisms, including long noncoding RNAs (lncRNAs) m<sup>6</sup>A methylation contributing to pigmentation in sheep skin remains unclear. The purpose of this study was to identify potential lncRNAs and the m<sup>6</sup>A methylation of lncRNAs associated with pigmentation.Methods: RNA-seq and MeRIP-seq were performed to study the expression of lncRNAs and the m<sup>6</sup>A methylation of lncRNAs in black and white sheep skin. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the consistency with the RNA-seq and MeRIP-seq data.Results: We identified 168 differentially expressed lncRNAs between the two sheep skin colors. The differentially expressed lncRNAs enriched in the pathway of ECM-receptor interaction, Rap1 signaling pathway, and Non-homologous end-joining may play essential roles in pigmentation. We identified 577 m<sup>6</sup>A peaks and 617 m<sup>6</sup>A peaks in black and white sheep skin, respectively, among which 20 m<sup>6</sup>A peaks showed significant differences. The enriched motif in sheep skin was “GGACU”, which aligned with the consensus motif “RRACH” (R = A or G, H = A, C or U). Differently methylated lncRNAs enriched in PI3K-Akt signaling pathway and Wnt signaling pathway might participate in skin pigmentation. ENSOARG00020015168 was the unique lncRNA with high expression and methylation (Hyper-Up) in black sheep shin. A lncRNA-mRNA network was constructed, with pigmentation-related genes, such as <i>PSEN2</i>, <i>CCND3</i>, <i>COL2A1</i>, and <i>ERCC3</i>.Conclusion: The m<sup>6</sup>A modifications of lncRNAs in black and white colored sheep skin were analyzed comprehensively, providing new candidates for the regulation of pigmentation.
Abstract
Objective: N6-methyladenosine (m6 A) is the most prevalent methylation of mRNA and plays crucial roles in various physiological processes, including pigmentation. Yet, the regulatory mechanisms, including long noncoding RNAs (lncRNAs) m6 A methylation contributing to pigmentation in sheep skin remains unclear. The purpose of this study was to identify potential lncRNAs and the m6 A methylation of lncRNAs associated with pigmentation. Methods: RNA-seq and MeRIP-seq were performed to study the expression of lncRNAs and the m6 A methylation of lncRNAs in black and white sheep skin. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the consistency with the RNA-seq and MeRIP-seq data. Results: We identified 168 differentially expressed lncRNAs between the two sheep skin colors. The differentially expressed lncRNAs enriched in the pathway of ECM-receptor interaction, Rap1 signaling pathway, and Non-homologous end-joining may play essential roles in pigmentation. We identified 577 m6 A peaks and 617 m6 A peaks in black and white sheep skin, respectively, among which 20 m6 A peaks showed significant differences. The enriched motif in sheep skin was “GGACU”, which aligned with the consensus motif “RRACH” (R = A or G, H = A, C or U). Differently methylated lncRNAs enriched in PI3K-Akt signaling pathway and Wnt signaling pathway might participate in skin pigmentation. ENSOARG00020015168 was the unique lncRNA with high expression and methylation (Hyper-Up) in black sheep shin. A lncRNA-mRNA network was constructed, with pigmentation-related genes, such as PSEN2, CCND3, COL2A1, and ERCC3. Conclusion: The m6 A modifications of lncRNAs in black and white colored sheep skin were analyzed comprehensively, providing new candidates for the regulation of pigmentation.
참고문헌 (47)
- Bhat B, "Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat", Sci Rep, 9, pp.6361~ (2019)[DOI]
- Kuzumaki T, "Eumelanin biosynthesis is regulated by coordinate expression of tyrosinase and tyrosinase-related protein-1 genes", Exp Cell Res, 20, pp.33~40 (1993)[DOI]
- Gelmi MC, "Mitf in normal melanocytes, cutaneous and uveal melanoma : a delicate balance", Int J Mol Sci, 23, pp.6001~ (2022)[DOI]
- Archambault M, "Keratinocytes and fibroblasts in a human skin equivalent model enhance melanocyte survival and melanin synthesis after ultraviolet irradiation", J Invest Dermatol, 104, pp.859~867 (1995)[DOI]
- Wang Y, "Precise role of dermal fibroblasts on melanocyte pigmentation", J Dermatol Sci, 88, pp.159~166 (2017)[DOI]
- Fu C, "Roles of inflammation factors in melanogenesis", Mol Med Rep, 21, pp.1421~1430 (2020)[DOI]
- Zhou S, "Epigenetic regulation of melanogenesis", Ageing Res Rev, 69, pp.101349~ (2021)[DOI]
- Kopp F, "Functional classification and experimental dissection of long noncoding RNAs", Cell, 172, pp.393~407 (2018)[DOI]
- Ji K, "Long non-coding RNA expression profile in Cdk5-knockdown mouse skin", Gene, 672, pp.195~201 (2018)[DOI]
- Ji K, "ifferential expression of lncRNAs and predicted target genes in normal mouse melanocytes and B16 cells", Exp Dermatol, 27, pp.1230~1236 (2018)[DOI]
- Ji KY, "A genomewide integrated analysis of lncRNA-mRNA in melanocytes from white and brown skin hair boer goats(Capra aegagrus hircus)", Front Vet Sci, 9, pp.1009174~ (2022)[DOI]
- Zhao B, "Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep", BMC Biol, 19, pp.197~ (2021)[DOI]
- Jin L, "Transcriptional differences of coding and non-coding genes related to the absence of melanocyte in skins of bama pig", Genes(Basel), 11, pp.47~ (2019)[DOI]
- Pei S, "UVB-inhibited H19 activates melanogenesis by paracrine effects", Exp Dermatol, 27, pp.1120~1125 (2018)[DOI]
- Kim NH, "Reduced MiR-675 in exosome in H19 RNA-related melanogenesis via MITF as a direct target", J Invest Dermatol, 134, pp.1075~1082 (2014)[DOI]
- Zhao W, "The long noncoding RNA SPRIGHTLY regulates cell proliferation in primary human melanocytes", J Invest Dermatol, 136, pp.819~828 (2016)[DOI]
- Jiang L, "Identification of the ceRNA networks in α-MSH-induced melanogenesis of melanocytes", Aging(Albany NY), 13, pp.2700~2726 (2021)[DOI]
- Pei S, "The long noncoding RNA UCA1negatively regulates melanogenesis in melanocytes", J Invest Dermatol, 140, pp.152~163 (2020)[DOI]
- Fu C, "Downregulation of TUG1 promotes melanogenesis and UVB-induced melanogenesis", Exp Dermatol, 28, pp.730~733 (2019)[DOI]
- Ho JC, "Targeting steroid receptor RNA activator(SRA), a long non-coding RNA, enhances melanogenesis through activation of TRP1 and inhibition of p38 phosphorylation", PLoS One, 15, pp.e0237577~ (2020)[DOI]
- Zeng Q, "Analysis of lncRNAs expression in UVB-induced stress responses of melanocytes", J Dermatol Sci, 81, pp.53~60 (2016)[DOI]
- Deng X, "Widespread occurrence of N 6-methyladenosine in bacterial mRNA", Nucleic Acids Res, 43, pp.6557~6567 (2015)[DOI]
- Lence T, "A fly view on the roles and mechanisms of the m6A mRNA modification and its players", RNA Biol, 14, pp.1232~1240 (2017)[DOI]
- Zhao BS, "Post-transcriptional gene regulation by mRNA modifications", Nat Rev Mol Cell Biol, 18, pp.31~42 (2017)[DOI]
- Yue H, "N6-methyladenosine regulatory machinery in plants : composition, function and evolution", Plant Biotechnol J, 17, pp.1194~1208 (2019)[DOI]
- Oerum S, "A comprehensive review of m6A", m6A mRNA methyltransferase structures, 2021, pp.49, 7239~7255
- Zhang J, "Comprehensive analysis of transcriptome-wide m(6)A methylome upon clostridium perfringens beta2 toxin exposure in porcine intestinal epithelial cells by m(6)A sequencing", Front Genet, 12, pp.689748~ (2021)[DOI]
- Lu Z, "m(6)A mRNA methylation analysis provides novel insights into heat stress responses in the liver tissue of sheep", Genomics, 113, pp.484~492 (2021)[DOI]
- Dahal U, "RNA m6A methyltransferase METTL3 regulates invasiveness of melanoma cells by matrix metallopeptidase 2", Melanoma Res, 29, pp.382~389 (2019)[DOI]
- Wang ZY, "Construction of a single-molecule biosensor for antibody-free detection of locus-specific N 6-methyladenosine in cancer cells and tissues", Anal Chem, 95, pp.5454~5462 (2023)[DOI]
- Zhao Y, "m6A mRNA methylation analysis provides novel insights into pigmentation in sheep skin", Epigenetics, 18, pp.2230662~ (2023)[DOI]
- Wang S, "Comprehensive analysis of long noncoding RNA modified by m6A methylation in oxidative and glycolytic skeletal muscles", Int J Mol Sci, 23, pp.4600~ (2022)[DOI]
- Huang C, "Transcriptome-wide study of mRNAs and lncRNAs modified by m6A RNA methylation in the longissimus dorsi muscle development of cattle-yak", Cells, 11, pp.3654~ (2022)[DOI]
- Yang J, "N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in IPEC-J2 cells treated with clostridium perfringens beta2toxin", Front Immunol, 12, pp.769204~ (2021)[DOI]
- He S, "mRNA N6-methyladenosine methylation of postnatal liver development in pig", PLoS One, 12, pp.e0173421~ (2017)[DOI]
- Qin Z, "Transcriptome-wide m(6)A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation", BMC Genomics, 22, pp.588~ (2021)[DOI]
- Melzer ME, "Rapid determination of RNA modifications in consensus motifs by nuclease protection with ion-tagged oligonucleotide probes and matrixassisted laser desorption ionization mass spectrometry", Genes(Basel), 13, pp.1008~ (2022)[DOI]
- Zuo X, "M6A-mediated upregulation of LINC00958 increases lipogenesis and acts as a nanotherapeutic target in hepatocellular carcinoma", J Hematol Oncol, 13, pp.5~ (2020)[DOI]
- Yang J, "METTL3-mediated LncRNA EN_42575 m6A modification alleviates CPB2 toxin-induced damage in IPEC-J2 cells", Int J Mol Sci, 24, pp.5725~ (2023)[DOI]
- Zhu T, "Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine", Cell Res, 24, pp.1493~1496 (2014)[DOI]
- Zhu S, "An oncopeptide regulates m(6)A recognition by the m(6)A reader IGF2BP1 and tumorigenesis", Nat Commun, 11, pp.1685~ (2020)[DOI]
- Hong L, "Analysis and screening of reproductive long non-coding RNAs through genome-wide analyses of goat endometrium during the pre-attachment phase", Front Genet, 11, pp.568017~ (2020)[DOI]
- Nornes S, "Independent and cooperative action of Psen2with Psen1 in zebrafish embryos", Exp Cell Res, 315, pp.2791~2801 (2009)[DOI]
- Jiang H, "The zebrafish orthologue of familial Alzheimer's disease gene PRESENILIN 2 is required for normal adult melanotic skin pigmentation", PLoS One, 13, pp.e0206155~ (2018)[DOI]
- Spofford LS, "Cyclin D3 expression in melanoma cells is regulated by adhesiondependent phosphatidylinositol 3-kinase signaling and contributes to G1-S progression", J Biol Chem, 281, pp.25644~25651 (2006)[DOI]
- Li MY, "UV-induced reduction in Polycomb repression promotes epidermal pigmentation", Dev Cell, 56, pp.2547~2561 (2021)[DOI]
- Yu M, "Deficiency in nucleotide excision repair family gene activity, especially ERCC3, is associated with non-pigmented hair fiber growth", PLoS One, 7, pp.e34185~ (2012)[DOI]
