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

doi:10.11843/j.issn.0366-6964.2017.08.006

Abstract

Abstract:

This study aimed to predict the transcription factor, protein and miRNA interacting with HOTAIR by bioinformatics, provide research direction for understanding the molecular mechanism of melanoma pathogenesis, and provide a target for designing new drugs and a theoretical basis for treating the melanoma. In this study, we downloaded HOTAIR sequences of 8 species from UCSC database, established phylogenetic tree by MEGA4.0. We used lncRNAtor and other databases to analyze the upstream regulatory factors, miRNA interacting with HOTAIR and related proteins. The expression patterns of HOTAIR in various tissues and the diseases associated with HOTAIR were analyzed via NONCODE and lncDisease databases. Some of the target miRNAs related to melanoma were predicted by TargetScan software. The molecular regulatory network of miRNA-HOTAIR-melanoma-associated genes was drew using Cytoscape3.2.0 software. The results showed that HOTAIR was located on human 12q13.13 chromosome between HOXC11 and HOXC12 genes at 54 356 092-54 368 740 nt. The HOTAIR was conservative among different species. HOTAIR was regulated by 27 regulatory factors in 18 different cells. HOTAIR was expressed in various tissues, and the expression in testis was higher than that in other tissues, but the expression in lung and ovary was lower than that in other tissues. GO analysis showed that the target genes of HOTAIR involved in cell apoptosis, DNA replication, transcription and other biological processes, which showed that HOTAIR played important roles in the process of pathology and physiology of cancer and some human diseases. The interaction analysis showed that there were interaction sites in miR-217, miR-203 and miR-194 with HOTAIR. In melanoma, HOTAIR may compete with MITF and NKX3-1 to miR-217, miR-203 and miR-194. GO function analysis and KEGG pathway analysis show that the expression level of HOTAIR was closely related to tumor metastasis, recurrence and prognosis, combined with the regulation of transcription factors to HOTAIR, which provide a theoretical basis for treatment of tumors.

CLC Number:

S813.1

LI Yuan, LIU Wen-yan, CAI Yong-qiang, ZHANG Li-huan, LI Hong, ZHU Zhi-wei. Analysis of Long Non-coding RNA HOTAIR and Prediction of Its Interaction Molecules in Melanoma Pathogenesis[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(8): 1424-1435.

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References

[1] MAO Y S, SUNWOO H, ZHANG B, et al. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs[J]. Nat Cell Biol, 2010, 13(1):95-101.
[2] Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs[J]. Nature, 2009, 457(7232):1028-1032.
[3] MERCER T R, DINGER M E, MATTICK J S. Long non-coding RNAs:insights into functions[J]. Nat Rev Genet, 2009, 10(3):155-159.
[4] SAXENA A, CARNINCI P. Long non-coding RNA modifies chromatin:epigenetic silencing by long non-coding RNAs[J]. Bioessays, 2011, 33(11):830-839.
[5] 贺小云, 狄冉, 胡文萍, 等. 动物繁殖相关lncRNA的研究新进展[J]. 畜牧兽医学报, 2016, 47(9):1749-1756.
HE X Y, DI R, HU W P, et al. New research progress in animal reproduction-related long noncoding RNAs[J]. Acta Veterinaria et Zootechnica Sinica, 2016, 47(9):1749-1756. (in Chinese)
[6] GUTTMAN, M, RINN J L. Modular regulatory principles of large non-coding RNAs[J]. Nature, 2012, 482(7385):339-346.
[7] RINN J L, KERTESZ M, WANG J K, et al. Functional demarcation of active and Silent chromatin domains in human HOX loci by noncoding RNAs[J]. Cell, 2007, 129(7):1311-1323.
[8] GRIER D G, THOMPSON A, KWASNIEWSKA A, et al. The pathophysiology of HOX genes and their role in cancer[J]. J Pathol, 2005, 205(2):154-171.
[9] TSAI M C, MANOR O, WAN Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes[J]. Science, 2010, 329(5992):689-693.
[10] TANG L H, ZHANG W, SU B, et al. Long noncoding RNA HOTAIR is associated with motility, invasion, and metastatic potential of metastatic melanoma[J]. BioMed Res Int, 2013, 2013:251098.
[11] YANG Z, ZHOU L, WU L M, et al. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation[J]. Ann Surg Oncol, 2011, 18(5):1243-1250.
[12] KIM K, JUTOORU I, CHADALAPAKA G, et al. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer[J]. Oncogene, 2013, 32(13):1616-1625.
[13] NⅡNUMA T, SUZUKI H, NOJIMA M, et al. Upregulation of miR-196a and HOTAIR drive malignant character in gastrointestinal stromal tumors[J]. Cancer Res, 2012, 72(5):1126-1136.
[14] LI D D, FENG J P, WU T Y, et al. Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma[J]. Am J Pathol, 2013, 182(1):64-70.
[15] NIE Y, LIU X, QU S H, et al. Long non-coding RNA HOTAIR is an independent prognostic marker for nasopharyngeal carcinoma progression and survival[J]. Cancer Sci, 2013, 104(4):458-464.
[16] GUPTA R A, SHAH N, WANG K C, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis[J]. Nature, 2010, 464(7291):1071-1076.
[17] PARK C, YU N, CHOI I, et al. lncRNAtor:a comprehensive resource for functional investigation of long non-coding RNAs[J]. Bioinformatics, 2014, 30(17):2480-2485.
[18] TAMURA K, DUDLEY J, NEI M, et al. MEGA4:Molecular evolutionary genetics analysis (MEGA) software version 4.0[J]. Mol Biol Evol, 2007, 24(8):1596-1599.
[19] CHEN G, WANG Z Y, WANG D Q, et al. LncRNADisease:a database for long-non-coding RNA-associated diseases[J]. Nucleic Acids Res, 2013, 41(D1):D983-D986.
[20] LIU C N, BAI B Y, SKOGERBØ G, et al. NONCODE:an integrated knowledge database of non-coding RNAs[J]. Nucleic Acids Res, 2005, 33(D1):D112-D115.
[21] HOU M, TANG X, TIAN F, et al. AnnoLnc:a web server for systematically annotating novel human lncRNAs[J]. BMC Genomics, 2016, 17(1):931.
[22] LI J H, LIU S, ZHOU H, et al. starBase v2.0:decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data[J]. Nucleic Acids Res, 2014, 42(D1):D92-D97.
[23] ZHAO Z, BAI J, WU A W, et al. Co-LncRNA:investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data[J]. Database, 2015, 2015:bav082.
[24] KACZKOWSKI B, TANAKA Y, KAWAJI H, et al. Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers[J]. Cancer Res, 2016, 76(2):216-226.
[25] ALPHONSE P Jr, HOOD N, LYN S, et al. MP-4.09:TargetScan®:a novel approach for outpatient prostate biopsy with the potential for use as an aid to focal prostate therapy[J]. Urology, 2008, 72(5S):S86-S87.
[26] BIRNEY E, STAMATOYANNOPOULOS J A, DUTTA A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project[J]. Nature, 2007, 447(7146):799-816.
[27] KAPRANOV P, CHENG J, DIKE S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription[J]. Science, 2007, 316(5830):1484-1488.
[28] GAO J Z, LI J, DU J L, et al. Long non-coding RNA HOTAIR is a marker for hepatocellular carcinoma progression and tumor recurrence[J]. Oncol Lett, 2016, 11(3):1791-1798.
[29] FANG S, GAO H Y, TONG Y, et al. Long noncoding RNA-HOTAIR affects chemoresistance by regulating HOXA1 methylation in small cell lung cancer cells[J]. Lab Invest, 2016, 96(1):60-68.
[30] AFTAB M N, DINGER M E, PERERA R J. The role of microRNAs and long non-coding RNAs in the pathology, diagnosis, and management of melanoma[J]. Arch Biochem Biophys, 2014, 563:60-70.
[31] DONG L J, HU L N. HOTAIR promotes proliferation, migration, and invasion of ovarian cancer SKOV3 cells through regulating PIK3R3[J]. Med Sci Monit, 2016, 22:325-331.
[32] WAN L D, KONG J L, TANG J L, et al. HOTAIRM1 as a potential biomarker for diagnosis of colorectal cancer functions the role in the tumour suppressor[J]. J Cell Mol Med, 2016, 20(11):2036-2044.
[33] YAN J, DANG Y N, LIU S Y, et al. LncRNA HOTAIR promotes cisplatin resistance in gastric cancer by targeting miR-126 to activate the PI3K/AKT/MRP1 genes[J]. Tumor Biol, 2016, 37(12):16345-16355.
[34] NEAGU M, CONSTANTIN C, MANDA G, et al. Biomarkers of metastatic melanoma[J]. Biomark Med, 2009, 3(1):71-89.

Analysis of Long Non-coding RNA HOTAIR and Prediction of Its Interaction Molecules in Melanoma Pathogenesis

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