Research Progress of the Human Long Non-coding RNA Related SNP Identification and Function Prediction

doi:10.13560/j.cnki.biotech.bull.1985.2015.11.002

Abstract

Abstract: Long non-coding RNA(lncRNA)is a class of RNA, whose length is greater than 200 nucleotides and it does not show any protein-coding potential. The latest research shows that lncRNA plays function widely in the development of plants and animals, as well as in various diseases. There have been a series of reports on the discovery, prediction method, function study of lncRNA. Here, we reviewed the study of lncRNA related SNPs, including their identification and functional prediction. A comprehensive review of the bioinformatics methods and databases about the lncRNA related SNP was provided. These reviews may help to provide a new point of view for lncRNA research and a hint for the prediction, diagnosis and treatment of complex diseases based on lncRNA.

Key words: long non-coding RNA, bioinformatics, single nucleotide polymorphism, database

Gong Jing, Liu Chunjie, Miao Xiaoping, Guo Anyuan. Research Progress of the Human Long Non-coding RNA Related SNP Identification and Function Prediction[J]. Biotechnology Bulletin, 2015, 31(11): 27-34.

References

[1] Qi P, Du X. The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine[J].Modern Pathology: an Official Journal of the United States and Canadian Academy of Pathology, Inc, 2013, 26(2): 155-165.
[2] Birney E, Stamatoyannopoulos JA, 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.
[3] Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insig-hts into functions[J].Nature Genetics, 2009, 10(3): 155-159.
[4] Wutz A, Rasmussen TP, Jaenisch R. Chromosomal silencing and localization are mediated by different domains of Xist RNA[J].Nature Genetics, 2002, 30(2): 167-174.
[5] Gong C, Maquat LE. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements[J].Nature, 2011, 470(7333): 284-288.
[6] Carpenter S, Aiello D, Atianand MK, et al. A long noncoding RNA mediates both activation and repression of immune response genes[J].Science, 2013, 341(6147): 789-792.
[7] Han BW, Chen YQ. Potential pathological and functional links between long noncoding RNAs and hematopoiesis[J].Science Signaling, 2013, 6(289): re5.
[8] Clemson CM, Hutchinson JN, Sara SA, et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles[J].Molecular Cell, 2009, 33(6): 717-726.
[9] Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis[J].Nature, 2010, 464(7291): 1071-1076.
[10] Tsai MC, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes[J].Science, 2010, 329(5992): 689-693.
[11] Carlson CS, Eberle MA, Kruglyak L, et al. Mapping complex disease loci in whole-genome association studies[J].Nature, 2004, 429(6990): 446-452.
[12] Abecasis GR, Altshuler D, Auton A, et al. A map of human genome variation from population-scale sequencing[J].Nature, 2010, 467(7319): 1061-1073.
[13] Abecasis GR, Auton A, Brooks LD, et al. An integrated map of genetic variation from 1, 092 human genomes[J].Nature, 2012, 491(7422): 56-65.
[14] Hovhannisyan Z, Weiss A, Martin A, et al. The role of HLA-DQ8 beta57 polymorphism in the anti-gluten T-cell response in coeliac disease[J].Nature, 2008, 456(7221): 534-538.
[15] Hruska KS, LaMarca ME, Scott CR, et al. Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene(GBA)[J].Human Mutation, 2008, 29(5): 567-583.
[16] Garvin MR, Saitoh K, Gharrett AJ. Application of single nucleotide polymorphisms to non-model species: a technical review[J].Molecular Ecology Resources, 2010, 10(6): 915-934.
[17] Welter D, MacArthur J, Morales J, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations[J].Nucleic Acids Research, 2014, 42(Database issue): D1001-1006.
[18] Todesco M, Balasubramanian S, Hu TT, et al. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana[J].Nature, 2010, 465(7298): 632-636.
[19] Bochukova EG, Huang N, Keogh J, et al. Large, rare chromosomal deletions associated with severe early-onset obesity[J].Nature, 2010, 463(7281): 666-670.
[20] Petukhova L, Duvic M, Hordinsky M, et al. Genome-wide association study in alopecia areata implicates both innate and adaptive immunity[J].Nature, 2010, 466(7302): 113-117.
[21] Lango Allen H, Estrada K, Lettre G, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height[J].Nature, 2010, 467(7317): 832-838.
[22] Ramirez-Gonzalez RH, Bonnal R, Caccamo M, et al. Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments[J].Source Code for Biology and Medicine, 2012, 7(1): 6.
[23] McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Research, 2010, 20(9): 1297-1303.
[24] Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data[J].Nucleic Acids Research, 2010, 38(16): e164.
[25] Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm[J].Nature Protocols, 2009, 4(7): 1073-1081.
[26] Xu Z, Taylor JA. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies[J].Nucleic Acids Research, 2009, 37(Web Server issue): W600-605.
[27] Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses[J].American Journal of Human Genetics, 2007, 81(3): 559-575.
[28] Gong J, Tong Y, Zhang HM, et al. Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis[J].Human Mutation, 2012, 33(1): 254-263.
[29] Bhattacharya A, Ziebarth JD, Cui Y. PolymiRTS Database 3. 0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways[J].Nucleic Acids Research, 2014, 42(Database issue): D86-91.
[30] Petry CJ, Ong KK, Barratt BJ, et al. Common polymorphism in H19 associated with birthweight and cord blood IGF-II levels in humans[J].BMC Genetics, 2005, 6: 22.
[31] Verhaegh GW, Verkleij L, Vermeulen SH, et al. Polymorphisms in the H19 gene and the risk of bladder cancer[J].European Urology, 2008, 54(5): 1118-1126.
[32] Bayram S, Sumbul AT, Batmaci CY, et al. Effect of HOTAIR rs920778 polymorphism on breast cancer susceptibility and clinicopathologic features in a Turkish population[J].Tumour Biology: the journal of the International Society for Oncodevelopmental Biology and Medicine, 2015, 36(5): DOI: 10.1007/s13277-014-3028-0.
[33] Zhang X, Zhou L, Fu G, et al. The identification of an ESCC susceptibility SNP rs920778 that regulates the expression of lncRNA HOTAIR via a novel intronic enhancer[J].Carcinogenesis, 2014, 35(9): 2062-2067.
[34] Pan W, Liu L, Wei J, et al. A functional lncRNA HOTAIR genetic variant contributes to gastric cancer susceptibility[J].Molecular Carcinogenesis, 2015: DOI: 10.1002/mc.22261.
[35] Pang KC, Stephen S, Engstrom PG, et al. RNAdb--a comprehensive mammalian noncoding RNA database[J].Nucleic Acids Research, 2005, 33(Database issue): D125-130.
[36] Quek XC, Thomson DW, Maag JL, et al. lncRNAdb v2. 0: expanding the reference database for functional long noncoding RNAs[J].Nucleic Acids Research, 2015, 43(Database issue): D168-173.
[37] Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression[J].Genome Research, 2012, 22(9): 1775-1789.
[38] Volders PJ, Helsens K, Wang X, et al. LNCipedia: a database for annotated human lncRNA transcript sequences and structures[J].Nucleic Acids Research, 2013, 41(Database issue): D246-251.
[39] Bu D, Yu K, Sun S, et al. NONCODE v3. 0: integrative annotation of long noncoding RNAs[J].Nucleic Acids Research, 2012, 40(Database issue): D210-215.
[40] Xie C, Yuan J, Li H, et al. NONCODEv4: exploring the world of long non-coding RNA genes[J].Nucleic Acids Research, 2014, 42(Database issue): D98-103.
[41] Chan WL, Huang HD, Chang JG. lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome[J].Computational Biology and Chemistry, 2014, 50: 41-49.
[42] Bhartiya D, Pal K, Ghosh S, et al. lncRNome: a comprehensive knowledgebase of human long noncoding RNAs[J].Database: the Journal of Biological Databases and Curation, 2013, 2013: bat034.
[43] Niazi F, Valadkhan S. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3’ UTRs[J].RNA, 2012, 18(4): 825-843.
[44] Li JH, 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 Research, 2014, 42(Database issue): D92-97.
[45] Dinger ME, Pang KC, Mercer TR, et al. NRED: a database of long noncoding RNA expression[J].Nucleic Acids Research, 2009, 37(Database issue): D122-126.
[46] Gong J, Liu W, Zhang J, et al. lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse[J].Nucleic Acids Research, 2015, 43(Database issue): D181-186.
[47] Ding J, Lu Q, Ouyang Y, et al. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice[J].Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(7): 2654-2659.
[48] Denman RB. Using RNAFOLD to predict the activity of small catalytic RNAs[J].BioTechniques, 1993, 15(6): 1090-1095.
[49] Andronescu M, Aguirre-Hernandez R, Condon A, et al. RNAsoft: A suite of RNA secondary structure prediction and design software tools[J].Nucleic Acids Research, 2003, 31(13): 3416-3422.
[50] Zuker M. Mfold web server for nucleic acid folding and hybridization prediction[J].Nucleic Acids Research, 2003, 31(13): 3406-3415.
[51] Doench JG, Sharp PA. Specificity of microRNA target selection in translational repression[J].Genes & Development, 2004, 18(5): 504-511.
[52] Barenboim M, Zoltick BJ, Guo Y, et al. MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets[J].Human Mutation, 2010, 31(11): 1223-1232.
[53] Sabarinathan R, Tafer H, Seemann SE, et al. The RNAsnp web server: predicting SNP effects on local RNA secondary structure[J].Nucleic Acids Research, 2013, 41(Web Server issue): W475-479.
[54] Bruno AE, Li L, Kalabus JL, et al. miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3’UTRs of human genes[J].BMC Genomics, 2012, 13: 44.
[55] Liu C, Zhang F, Li T, et al. MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs[J].BMC Genomics, 2012, 13: 661.
[56] Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets[J].Cell, 2005, 120(1): 15-20.
[57] Paraskevopoulou MD, Georgakilas G, Kostoulas N, et al. DIANA-microT web server v5. 0: service integration into miRNA functional analysis workflows[J].Nucleic Acids Research, 2013, 41(Web Server issue): W169-173.
[58] Krek A, Grun D, Poy MN, et al. Combinatorial microRNA target predictions[J].Nature Genetics, 2005, 37(5): 495-500.
[59] Rusinov V, Baev V, Minkov IN, et al. MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence[J].Nucleic Acids Research, 2005, 33(Web Server issue): W696-700.
[60] Gong J, Wu Y, Zhang X, et al. Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing[J].RNA Biology, 2014, 11(11): 1375-1385.
[61] Jin G, Sun J, Isaacs SD, et al. Human polymorphisms at long non-coding RNAs(lncRNAs)and association with prostate cancer risk[J].Carcinogenesis, 2011, 32(11): 1655-1659.
[62] Ning S, Zhao Z, Ye J, et al. LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs[J].BMC Bioinformatics, 2014, 15: 152.