Abstract：Long noncoding RNA (LncRNA) was widely transcribed in the mammalian genome. LncRNA can play biological functions through the corresponding micRNA and target genes. By combining bioinformatics prediction and experimental verification, the LncRNA target genes can be rapidly and efficiently obtained and screened. To further explore the expression characteristics and predict its interaction molecules in melanoma pathogenesis of LncRNA XLOC_15448, the tissue expression profile LncRNA XLOC_15448 was detected using qRT-PCR method in different tissues of Youzhou dark goat (Capra hircus) and Youzhou blank goat (Capra hircus), as well as the LncRNA XLOC_15448 expression characteristics were detected in B16 cells at different developmental stages. The target genes were also predicted using miRBase, TargetScan7.2, miRTarBase, RNA22 version 2.0, and RNAhybrid2.2, and finally the lncRNA-miRNA-mRNA regulatory network was constructed in Capra hircus. The results demonstrated that LncRNA XLOC_15448 was widely expressed in different tissues of the goat, especially with the highest expression in the heart and lowest level in spleen, and it was also widely expressed in muscle, brain, skin, liver, kidney, lung and spleen. Comparison analysis illustrated that the skin LncRNA XLOC_15448 was expressed significantly higher in Youzhou dark goat than that of Youzhou blank white goat, and that the expression pattern of the lncRNA was increasing during the B16 cell proliferation. Bio-information analysis indicated that LncRNA XLOC_15448 might regulate gene expression of MITF (microphthalmia-associated transcription factor) by targeting to miR-182-5p. It was speculated that there may be a lncRNA-miRNA-mRNA network which modulate the dermal melanogenesis and melanin deposition in Youzhou dark goat, which would provide the basic data for further research on the regulatory mechanisms of lncRNAs related to goat skin pigmentation.
付琳, 任航行, 王高富, 蒋婧, 李杰, 孙晓燕, 刘良佳, 周鹏, 张丽. 酉州乌羊LncRNA XLOC_15448的组织表达及其在黑色素沉积过程中互作分子的预测[J]. 农业生物技术学报, 2020, 28(8): 1441-1449.
FU Lin, REN Hang-Xing, WANG Gao-Fu, JIANG Jing, LI Jie, SUN Xiao-Yan, LIU Liang-Jia, ZHOU Peng, ZHANG Li. Tissue Expression of LncRNA XLOC_15448 in Youzhou Dark Goat (Capra hircus) and Prediction of Its Interaction Molecules in Melanoma Pathogenesis. 农业生物技术学报, 2020, 28(8): 1441-1449.
[1] 李园,刘文艳,蔡永强,等.2017.长链非编码RNA HOTAIR的分析及在黑色素瘤致病过程中互作分子的预测[J].畜牧兽医学报,08:1424-1435.
(Li Y,Liu W Y,Cai Y Q,et al.2017.Analysis of long non-coding RNA HOTAIR and prediction of its interaction molecules in melanoma pathogenesis[J].Acta Veterinaria et Zootechnica Sinica,48(8):1424-1435.)
[2] 王伟,黄晓宇,闫尊强,等.2019.猪miR-339-3p靶基因预测分析及部分靶基因验证[J].农业生物技术学报,27(05):885-896.
(Wang W,Huang X Y,Yan Z Q,et al.2018.Target gene prediction analysis and partial target gene verification of pig (Sus scrofa) miR-339-3p[J].Journal of Agricultural Biotechnology,27(05):885-896.)
[3] 张彬彬,殷媛,黄朝晖.2014.长链非编码RNA在肿瘤中的研究进展[J].肿瘤防治研究,41(6):669-673.
(Zhang B B,Yin Y,Huang C H.2014.New research of long noncoding rna in tumor[J].Cancer?Research?Prevention?Treat,41(6):669-673.)
[4] Billerey C,Boussaha M,Esquerré D,et al.2014.Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing[J].BMC Genomics,15:499.
[5] Brunner A L,Beck A H,Edris B,et al.2012.Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel ofarchived human cancer[J].Genome Biology,13(8):R75.
[6] Carrieri C,Cimatti L,Biagioli M,et al.2012.Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat[J].Nature,491(7424):454-457.
[7] Derrien T,Johnson R,Bussotti G,et al.2012.The GENCODE v7 catalog of human long noncoding RNAs:Analysis of their gene structure,evolution,and expression[J].Genome Research,22(9):1775-1789.
[8] Fan Q,Huang L Z,Zhu X J,et al.2014.Identification of proteins that interact with alpha A-crystallin using a human proteome microarray[J].Molecular Vision,20:117-24.
[9] Geisler S,Coller J.2013.RNA in unexpected places:Long non-coding RNA functions in diverse cellular contexts[J].Nature Reviews Molecular Cell Biology,14(11):699-712.
[10] Gong C,Maquat L E.2011.lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements[J].Nature,470(7333):284-288.
[11] Huang W,Long N,Khatib H.2012.Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data[J].Animal Genetics,43(6):674-682.
[12] Kinslechner K,Schütz B,Pistek M,et al.2019.Loss of SR-BI down-regulates MITF and suppresses extracellular vesicle release in human melanoma[J].Science,20(5):1063-1075.
[13] Kretz M,Siprashvili Z,Chu C,et al.2013.Control of somatic tissue differentiation by the long non-coding RNA TINCR[J].Nature,493(7431):231-235.
[14] Liao Z,Zhao J,Yang Y.2018.Downregulation of lncRNA H19 inhibits the migration and invasion of melanoma cells by inactivating the NFkappaB and PI3K/Akt signaling pathways[J].Molecular Medicine Reports,17(5):7313-7318.
[15] Mercer T R,Dinger M E,Mattick J S.2009.Long non-coding RNAs:Insights into functions[J].Nature Reviews Genetics,10(3):155-159.
[16] Ørom U A,Shiekhattar R.2013.Long noncoding RNAs usher in a new era in the biology of enhancers[J].Cell,154(6):1190-1193.
[17] Quek X C,Thomson D W,Maag J L,et al.2015.lncRNAdb v2.0:Expanding the reference database for functional long noncoding RNAs[J].Nucleic Acids Research,43:168-173.
[18] Ren H,Wang G,Chen L,et al.2016.Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus)[J].BMC Genomics,17:67.
[19] Ross C L,Kaushik S,Valdes-Rodriguez R,et al.2018.MicroRNAs in cutaneous melanoma:Role as diagnostic and prognostic biomarkers[J].Journal of Cellular Physiology,233(7):5133-5141.
[20] Schmidt K,Joyce C E,Buquicchio F,et al.2016.The lncRNA SLNCR1 mediates melanoma invasion through a conserved SRA1-like region[J].Cell Reports,15(9):2025-2037.
[21] Schmitt A M,Chang H Y.2016.Long noncoding RNAs in cancer pathways[J].Cancer Cell,29(4):452-463.
[22] Seok W L,Jae H K,Hyerim S,et al.2019.Luteolin 7-sulfate attenuates melanin synthesis through inhibition of CREB- and MITF-mediated tyrosinase expression[J].Antioxidants (Basel),8(4):·pii:E87.
[23] Volders P J,Verheggen K,Menschaert G,et al.2015.An update on LNCipedia:A database for annotated human lncRNA sequences[J].Nucleic Acids Research,43:174-180.
[24] Wu J,Hann S S.2018.Emerging functional and mechanistic paradigms of mammalian long noncoding RNAs[J].Cell Physiol Biochem,45(3):1191-1204
[25] Xing Y,Wen X,Ding X,et al.2017.CANT1 lncRNa triggers efficient therapeutic efficacy by correcting aberrant lncing cascade in malignant uveal melanoma[J].Molecular Therapy,25(5):1209-1221.
[26] Xu H,Gong J,Liu H.2017.High expression of lncRNA PVT1 independently predicts poor overall survival in patients with primary uveal melanoma[J].PLoS One,12(12):e0189675.
[27] Xu S,Wang H,Pan H,et al.2016.ANRIL lncRNA triggers efficient therapeutic efficacy by reprogramming the aberrant INK4-hub in melanoma[J].Cancer Letters,381(1):41-48.
[28] Zhang H,Bai M,Zeng A,et al.2017.LncRNA HOXD-AS1 promotes melanoma cell proliferation and invasion by suppressing RUNX3 expression[J].American Journal of Cancer Research,7(12):2526-2535.
[29] Zhang Y,Qian W,Feng F,et al.2019.Upregulated lncRNA CASC2 may inhibit malignant melanoma development through regulating miR-18a-5p/RUNX1[J].Oncology Research,27(3):371-377.
[30] Zhao W,Mu Y,Ma L,et al.2015.Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development[J].Science Reports,5:8957.
[31] Zhou Z Y,Li A M,Adeola A C,et al.2014.Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs[J].Genome Biology and Evolution,6(6):1387-1392.
