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Current Bioinformatics

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ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

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Research Article

piRSNP: A Database of piRNA- related SNPs and their Effects on Cancerrelated piRNA Functions

Author(s): Yajun Liu*, Aimin Li, Yingda Zhu, Xinchao Pang, Xinhong Hei, Guo Xie and Fang-Xiang Wu

Volume 18, Issue 6, 2023

Published on: 04 May, 2023

Page: [509 - 516] Pages: 8

DOI: 10.2174/1574893618666230320144630

Price: $65

Abstract

Background: PIWI-interacting RNAs (piRNAs) are a kind of small non-coding RNAs which interact with PIWI proteins and play a vital role in safeguarding genome. Single nucleotide polymorphisms (SNPs) are widely distributed variations which are associated with diseases and have rich information. Up to now, various studies have proved that SNPs on piRNA were related to diseases.

Objective: In order to create a comprehensive source about piRNA-related SNPs, we developed a publicly available online database piRSNP.

Methods: We systematically identified SNPs on human and mouse piRNAs. piRSNP contains 42,967,522 SNPs on 10,773,081 human piRNAs and 29,262,185 SNPs on 16,957,706 mouse piRNAs.

Results: 7,446 SNPs on 519 cancer-related piRNAs and their flanks are investigated. Impacts of 2,512 variations of cancer-related piRNAs on piRNA-mRNA interactions are analyzed.

Conclusion: All these useful data and piRNA expression profiles of 12 cancer types in both tumor and pericarcinomatous tissues are compiled into piRSNP. piRSNP characterizes human and mouse piRNArelated SNPs comprehensively and could be beneficial for researchers to investigate subsequent piRNA functions. Database URL is http://www.ibiomedical.net/piRSNP/.

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[1]
Kim VN. Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 2006; 20(15): 1993-7.
[http://dx.doi.org/10.1101/gad.1456106] [PMID: 16882976]
[2]
Morceau F, Chateauvieux S, Gaigneaux A, Dicato M, Diederich M. Long and short non-coding RNAs as regulators of hematopoietic differentiation. Int J Mol Sci 2013; 14(7): 14744-70.
[http://dx.doi.org/10.3390/ijms140714744] [PMID: 23860209]
[3]
Grivna ST, Beyret E, Wang Z, Lin H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 2006; 20(13): 1709-14.
[http://dx.doi.org/10.1101/gad.1434406] [PMID: 16766680]
[4]
Yan Z, Hu HY, Jiang X, et al. Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Res 2011; 39(15): 6596-607.
[http://dx.doi.org/10.1093/nar/gkr298] [PMID: 21546553]
[5]
Martinez VD, Vucic EA, Thu KL, et al. Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology. Sci Rep 2015; 5(1): 10423.
[http://dx.doi.org/10.1038/srep10423] [PMID: 26013764]
[6]
Houwing S, Kamminga LM, Berezikov E, et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell 2007; 129(1): 69-82.
[http://dx.doi.org/10.1016/j.cell.2007.03.026] [PMID: 17418787]
[7]
Ku HY, Gangaraju VK, Qi H, Liu N, Lin H. Tudor-SN interacts with piwi antagonistically in regulating spermatogenesis but synergistically in silencing transposons in drosophila. PLoS Genet 2016; 12(1): e1005813.
[http://dx.doi.org/10.1371/journal.pgen.1005813] [PMID: 26808625]
[8]
Kiuchi T, Koga H, Kawamoto M, et al. A single female-specific piRNA is the primary determiner of sex in the silkworm. Nature 2014; 509(7502): 633-6.
[http://dx.doi.org/10.1038/nature13315] [PMID: 24828047]
[9]
Watanabe T, Cheng E, Zhong M, Lin H. Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res 2015; 25(3): 368-80.
[http://dx.doi.org/10.1101/gr.180802.114] [PMID: 25480952]
[10]
Zhang D, Tu S, Stubna M, et al. The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science 2018; 359(6375): 587-92.
[http://dx.doi.org/10.1126/science.aao2840] [PMID: 29420292]
[11]
Liu CJ, Fu X, Xia M, Zhang Q, Gu Z, Guo AY. miRNASNP-v3: A comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. Nucleic Acids Res 2021; 49(D1): D1276-81.
[http://dx.doi.org/10.1093/nar/gkaa783] [PMID: 32990748]
[12]
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. BMC Genomics 2012; 13(1): 661.
[http://dx.doi.org/10.1186/1471-2164-13-661] [PMID: 23173617]
[13]
Bruno AE, Li L, Kalabus JL, Pan Y, Yu A, Hu Z. miRdSNP: A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics 2012; 13(1): 44.
[http://dx.doi.org/10.1186/1471-2164-13-44] [PMID: 22276777]
[14]
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. Hum Mutat 2012; 33(1): 254-63.
[http://dx.doi.org/10.1002/humu.21641] [PMID: 22045659]
[15]
Gong J, Liu CJ, Liu W, et al. An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools. Database 2015; 2015: bav029.
[http://dx.doi.org/10.1093/database/bav029]
[16]
Chen X, Hao Y, Cui Y, Fan Z, Chen R. LncVar: Deciphering genetic variations associated with long noncoding genes. Methods Mol Biol 2019; 1870: 189-98.
[http://dx.doi.org/10.1007/978-1-4939-8808-2_14] [PMID: 30539556]
[17]
Gong J, Liu W, Zhang J, Miao X, Guo AY. lncRNASNP: A database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 2015; 43(D1): D181-6.
[http://dx.doi.org/10.1093/nar/gku1000] [PMID: 25332392]
[18]
Ning S, Yue M, Wang P, et al. LincSNP 2.0: An updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs. Nucleic Acids Res 2017; 45(D1): D74-8.
[http://dx.doi.org/10.1093/nar/gkw945] [PMID: 27924020]
[19]
Gao Y, Li X, Shang S, et al. LincSNP 3.0: aArcular RNAs and their regulatory elements. Nucleic Acids Res 2021; 49(D1): D1244-50.
[http://dx.doi.org/10.1093/nar/gkaa1037] [PMID: 33219661]
[20]
Miao YR, Liu W, Zhang Q, Guo AY. lncRNASNP2: An updated database of functional SNPs and mutations in human and mouse lncRNAs. Nucleic Acids Res 2018; 46(D1): D276-80.
[http://dx.doi.org/10.1093/nar/gkx1004] [PMID: 29077939]
[21]
Xin J, Du M, Jiang X, et al. Systematic evaluation of the effects of genetic variants on PIWI-interacting RNA expression across 33 cancer types. Nucleic Acids Res 2021; 49(1): 90-7.
[http://dx.doi.org/10.1093/nar/gkaa1190] [PMID: 33330918]
[22]
Chen X, Hao Y, Cui Y, et al. LncVar: A database of genetic variation associated with long non-coding genes. Bioinformatics 2017; 33(1): 112-8.
[http://dx.doi.org/10.1093/bioinformatics/btw581] [PMID: 27605101]
[23]
Chu H, Xia L, Qiu X, et al. Genetic variants in noncoding PIWI-interacting RNA and colorectal cancer risk. Cancer 2015; 121(12): 2044-52.
[http://dx.doi.org/10.1002/cncr.29314] [PMID: 25740697]
[24]
Fu A, Jacobs DI, Hoffman AE, Zheng T, Zhu Y. PIWI-interacting RNA 021285 is involved in breast tumorigenesis possibly by remodeling the cancer epigenome. Carcinogenesis 2015; 36(10): 1094-102.
[http://dx.doi.org/10.1093/carcin/bgv105] [PMID: 26210741]
[25]
Jacobs DI, Qin Q, Lerro MC, et al. PIWI-Interacting RNAs in gliomagenesis: Evidence from Post-GWAS and functional analyses. Cancer Epidemiol Biomarkers Prev 2016; 25(7): 1073-80.
[http://dx.doi.org/10.1158/1055-9965.EPI-16-0047] [PMID: 27197292]
[26]
Wang J, Zhang P, Lu Y, et al. piRBase: A comprehensive database of piRNA sequences. Nucleic Acids Res 2019; 47(D1): D175-80.
[http://dx.doi.org/10.1093/nar/gky1043] [PMID: 30371818]
[27]
Liu Y, Zhang J, Li A, et al. Prediction of cancer-associated piRNA–mRNA and piRNA–lncRNA interactions by integrated analysis of expression and sequence data. Tsinghua Sci Technol 2018; 23(2): 115-25.
[http://dx.doi.org/10.26599/TST.2018.9010056]
[28]
Hao Z, Lv D, Ge Y, Shi J, Chen J. RIdeogram: Drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput Sci 2019; 6: e251.
[http://dx.doi.org/10.7287/peerj.preprints.27928v1]
[29]
Sai Lakshmi S, Agrawal S. piRNABank: A web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res 2008; 36(S1): D173-7.
[http://dx.doi.org/10.1093/nar/gkm696] [PMID: 17881367]
[30]
Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006; 442(7099): 199-202.
[http://dx.doi.org/10.1038/nature04917] [PMID: 16751776]
[31]
Izumi N, Shoji K, Suzuki Y, Katsuma S, Tomari Y. Zucchini consensus motifs determine the mechanism of pre-piRNA production. Nature 2020; 578(7794): 311-6.
[http://dx.doi.org/10.1038/s41586-020-1966-9] [PMID: 31996847]
[32]
Gou LT, Dai P, Yang JH, et al. Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell Res 2014; 24(6): 680-700.
[http://dx.doi.org/10.1038/cr.2014.41] [PMID: 24787618]
[33]
Zhang P, Kang JY, Gou LT, et al. MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes. Cell Res 2015; 25(2): 193-207.
[http://dx.doi.org/10.1038/cr.2015.4] [PMID: 25582079]
[34]
Goh WSS, Falciatori I, Tam OH, et al. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev 2015; 29(10): 1032-44.
[http://dx.doi.org/10.1101/gad.260455.115] [PMID: 25995188]
[35]
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004; 2(11): e363.
[http://dx.doi.org/10.1371/journal.pbio.0020363] [PMID: 15502875]
[36]
Wang Y, Zhou Y, Ali MA, et al. Comparative analysis of piRNA profiles helps to elucidate cryoinjury between giant panda and boar sperm during cryopreservation. Front Vet Sci 2021; 8: 635013.
[http://dx.doi.org/10.3389/fvets.2021.635013] [PMID: 33969033]
[37]
Shang J, Wang X, Wu X, et al. A review of ant colony optimization based methods for detecting epistatic interactions. IEEE Access 2019; 7: 13497-509.
[http://dx.doi.org/10.1109/ACCESS.2019.2894676]
[38]
Yuan X, Yu J, Xi J, et al. CNV_IFTV: An isolation forest and total variation-based detection of cnvs from short-read sequencing data. IEEE/ACM Trans Comput Biol Bioinformat 2021; 18(2): 539-49.
[http://dx.doi.org/10.1109/TCBB.2019.2920889] [PMID: 31180897]

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