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Current Pharmaceutical Biotechnology

Author(s): Jens Allmer*

DOI: 10.2174/1570180819666220520124511

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Noncoding RNA Databases

Page: [825 - 831] Pages: 7

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Abstract

Diseases such as cancer are often defined by dysregulation of gene expression. Noncoding RNAs (ncRNA) such as microRNAs are involved in gene expression and cell-cell communication. Many other ncRNAs exist, such as circular RNAs and small nucleolar RNAs. A wealth of knowledge is available for many ncRNAs, but the information is federated in many databases. A small number of highly complementary ncRNA databases are discussed in this work. Their relevance for cancer research is highlighted, and some of the current problems and limitations are revealed. A central or shared database enforcing community reporting and quality standards is needed in the future.

• RNA-seq

• Noncoding RNAs

• Databases

• Data repositories

Keywords: RNA-seq, noncoding RNAs, databases, data repositories, regulatory RNA, cancer RNAs.

[1]
Soldà, G.; Makunin, I.V.; Sezerman, O.U.; Corradin, A.; Corti, G.; Guffanti, A. An Ariadne’s thread to the identification and annotation of noncoding RNAs in eukaryotes. Brief. Bioinform., 2009, 10(5), 475-489.
[http://dx.doi.org/10.1093/bib/bbp022] [PMID: 19383843]
[2]
Dinger, M.E.; Pang, K.C.; Mercer, T.R.; Mattick, J.S. Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLOS Comput. Biol., 2008, 4(11)e1000176
[http://dx.doi.org/10.1371/journal.pcbi.1000176] [PMID: 19043537]
[3]
Liu, H.; Zhou, X.; Yuan, M.; Zhou, S.; Huang, Y.E.; Hou, F.; Song, X.; Wang, L.; Jiang, W. ncEP: A manually curated database for experimentally validated ncRNA-encoded proteins or peptides. J. Mol. Biol., 2020, 432(11), 3364-3368.
[http://dx.doi.org/10.1016/j.jmb.2020.02.022] [PMID: 32105730]
[4]
Sewer, A.; Paul, N.; Landgraf, P.; Aravin, A.; Pfeffer, S.; Brownstein, M.J.; Tuschl, T.; van Nimwegen, E.; Zavolan, M. Identification of clustered microRNAs using an Ab initio prediction method. BMC Bioinformatics, 2005, 6(1), 267.
[http://dx.doi.org/10.1186/1471-2105-6-267] [PMID: 16274478]
[5]
Griffiths-Jones, S.; Moxon, S.; Marshall, M.; Khanna, A.; Eddy, S.R.; Bateman, A. Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 2005, 33(suppl. 1), D121-D124.
[http://dx.doi.org/10.1093/nar/gki081] [PMID: 15608160]
[6]
Rodriguez, A.; Griffiths-Jones, S.; Ashurst, J.L.; Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res., 2004, 14(10A), 1902-1910.
[http://dx.doi.org/10.1101/gr.2722704] [PMID: 15364901]
[7]
Pfeffer, S.; Zavolan, M.; Grässer, F.A.; Chien, M.; Russo, J.J.; Ju, J.; John, B.; Enright, A.J.; Marks, D.; Sander, C.; Tuschl, T. Identification of virus-encoded microRNAs. Science, 2004, 304(5671), 734-736.
[http://dx.doi.org/10.1126/science.1096781] [PMID: 15118162]
[8]
Jarrous, N. Roles of RNase P and Its Subunits. Trends Genet., 2017, 33(9), 594-603.
[http://dx.doi.org/10.1016/j.tig.2017.06.006] [PMID: 28697848]
[9]
Ergin, K.; Çetinkaya, R. Regulation of MicroRNAs. In: Methods in Molecular Biology; Allmer, J.; Yousef, M., Eds.; Springer US: New York, NY, 2022; 2257, pp. 1-32.
[http://dx.doi.org/10.1007/978-1-0716-1170-8_1]
[10]
Erson-Bensan, A.E. Introduction to MicroRNAs in Biological Systems. In: MicroRNA Biology and Computational Analysis; Yousef, M.; Allmer, J., Eds.; Humana Press: New York, 2014; 1107, pp. 1-14.
[http://dx.doi.org/10.1007/978-1-62703-748-8_1]
[11]
Tocchini-Valentini, G.D.; Fruscoloni, P.; Tocchini-Valentini, G.P. Processing of multiple-intron-containing pretRNA. Proc. Natl. Acad. Sci. USA, 2009, 106(48), 20246-20251.
[http://dx.doi.org/10.1073/pnas.0911658106] [PMID: 19910528]
[12]
Clough, E.; Barrett, T. The gene expression omnibus database. Methods Mol. Biol., 2016, 1418, 93-110.
[http://dx.doi.org/10.1007/978-1-4939-3578-9_5] [PMID: 27008011]
[13]
Leinonen, R.; Sugawara, H.; Shumway, M. The sequence read archive. Nucleic Acids Res., 2011, 39(suppl. 1), D19-D21.
[http://dx.doi.org/10.1093/nar/gkq1019] [PMID: 21062823]
[14]
Hutter, C.; Zenklusen, J.C. The cancer genome atlas: Creating lasting value beyond its data. Cell, 2018, 173(2), 283-285.
[http://dx.doi.org/10.1016/j.cell.2018.03.042] [PMID: 29625045]
[15]
Auton, A.; Brooks, L.D.; Durbin, R.M.; Garrison, E.P.; Kang, H.M.; Korbel, J.O.; Marchini, J.L.; McCarthy, S.; McVean, G.A.; Abecasis, G.R. A global reference for human genetic variation. Nature, 2015, 526(7571), 68-74.
[http://dx.doi.org/10.1038/nature15393] [PMID: 26432245]
[16]
Li, Q.; Zhou, Y.; Jiao, Y.; Zhang, Z.; Bai, L.; Tong, L.; Yang, X.; Sommer, B.; Hofestädt, R.; Chen, M. DaTo: An atlas of biological databases and tools. J. Integr. Bioinform., 2016, 13(4), 297.
[http://dx.doi.org/10.1515/jib-2016-297] [PMID: 28187413]
[17]
Paschoal, A.R.; Maracaja-Coutinho, V.; Setubal, J.C.; Simões, Z.L.P.; Verjovski-Almeida, S.; Durham, A.M. Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA Biol., 2012, 9(3), 274-282.
[http://dx.doi.org/10.4161/rna.19352] [PMID: 22336709]
[18]
Kalvari, I.; Nawrocki, E.P.; Ontiveros-Palacios, N.; Argasinska, J.; Lamkiewicz, K.; Marz, M.; Griffiths-Jones, S.; Toffano-Nioche, C.; Gautheret, D.; Weinberg, Z.; Rivas, E.; Eddy, S.R.; Finn, R.D.; Bateman, A.; Petrov, A.I. Rfam 14: Expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res., 2021, 49(D1), D192-D200.
[http://dx.doi.org/10.1093/nar/gkaa1047] [PMID: 33211869]
[19]
Xie, F.; Liu, S.; Wang, J.; Xuan, J.; Zhang, X.; Qu, L.; Zheng, L.; Yang, J. deepBase v3.0: Expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data. Nucleic Acids Res., 2021, 49(D1), D877-D883.
[http://dx.doi.org/10.1093/nar/gkaa1039] [PMID: 33175131]
[20]
Li, Z.X.; Zhu, Q.N.; Zhang, H.B.; Hu, Y.; Wang, G.; Zhu, Y.S. MALAT1: A potential biomarker in cancer. Cancer Manag. Res., 2018, 10, 6757-6768.
[http://dx.doi.org/10.2147/CMAR.S169406] [PMID: 30584369]
[21]
Zhao, L.; Wang, J.; Li, Y.; Song, T.; Wu, Y.; Fang, S.; Bu, D.; Li, H.; Sun, L.; Pei, D.; Zheng, Y.; Huang, J.; Xu, M.; Chen, R.; Zhao, Y.; He, S. NONCODEV6: An updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res., 2021, 49(D1), D165-D171.
[http://dx.doi.org/10.1093/nar/gkaa1046] [PMID: 33196801]
[22]
The RNAcentral Consortium. RNAcentral: A hub of information for non-coding RNA sequences. Nucleic Acids Res., 2019, 47(D1), D221-D229.
[http://dx.doi.org/10.1093/nar/gky1034] [PMID: 30395267]
[23]
Kozomara, A.; Birgaoanu, M.; Griffiths-Jones, S. miRBase: From microRNA sequences to function. Nucleic Acids Res., 2019, 47(D1), D155-D162.
[http://dx.doi.org/10.1093/nar/gky1141] [PMID: 30423142]
[24]
Belinky, F.; Bahir, I.; Stelzer, G.; Zimmerman, S.; Rosen, N.; Nativ, N.; Dalah, I.; Iny Stein, T.; Rappaport, N.; Mituyama, T.; Safran, M.; Lancet, D. Non-redundant compendium of human ncRNA genes in GeneCards. Bioinformatics, 2013, 29(2), 255-261.
[http://dx.doi.org/10.1093/bioinformatics/bts676] [PMID: 23172862]
[25]
Rappaport, N.; Twik, M.; Plaschkes, I.; Nudel, R.; Iny Stein, T.; Levitt, J.; Gershoni, M.; Morrey, C.P.; Safran, M.; Lancet, D. MalaCards: An amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. Nucleic Acids Res., 2017, 45(D1), D877-D887.
[http://dx.doi.org/10.1093/nar/gkw1012] [PMID: 27899610]
[26]
Li, J.; Xue, Y.; Amin, M.T.; Yang, Y.; Yang, J.; Zhang, W.; Yang, W.; Niu, X.; Zhang, H-Y.; Gong, J. ncRNA-eQTL: A database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types. Nucleic Acids Res., 2020, 48(D1), D956-D963.
[http://dx.doi.org/10.1093/nar/gkz711] [PMID: 31410488]
[27]
Huang, J.L.; Liu, W.; Tian, L.H.; Chai, T.T.; Liu, Y.; Zhang, F.; Fu, H.Y.; Zhou, H.R.; Shen, J.Z. Upregulation of long non-coding RNA MALAT-1 confers poor prognosis and influences cell proliferation and apoptosis in acute monocytic leukemia. Oncol. Rep., 2017, 38(3), 1353-1362.
[http://dx.doi.org/10.3892/or.2017.5802] [PMID: 28713913]
[28]
Li, L.; Wu, P.; Wang, Z.; Meng, X.; Zha, C.; Li, Z.; Qi, T.; Zhang, Y.; Han, B.; Li, S.; Jiang, C.; Zhao, Z.; Cai, J. NoncoRNA: A database of experimentally supported non-coding RNAs and drug targets in cancer. J. Hematol. Oncol., 2020, 13(1), 15.
[http://dx.doi.org/10.1186/s13045-020-00849-7] [PMID: 32111231]
[29]
Zhang, W.; Yao, G.; Wang, J.; Yang, M.; Wang, J.; Zhang, H.; Li, W. ncRPheno: A comprehensive database platform for identification and validation of disease related noncoding RNAs. RNA Biol., 2020, 17(7), 943-955.
[http://dx.doi.org/10.1080/15476286.2020.1737441] [PMID: 32122231]
[30]
Griffiths-Jones, S.; Saini, H.K.; van Dongen, S.; Enright, A.J. miRBase: Tools for microRNA genomics. Nucleic Acids Res., 2008, 36(supple_1), D154-D158.
[http://dx.doi.org/10.1093/nar/gkm952] [PMID: 17991681]
[31]
Hamzeiy, H.; Suluyayla, R.; Brinkrolf, C.; Janowski, S.J.; Hofestaedt, R.; Allmer, J. Visualization and analysis of microRNAs within KEGG pathways using VANESA. J. Integr. Bioinform., 2017, 14(1), jib-2016-0004.
[http://dx.doi.org/10.1515/jib-2016-0004] [PMID: 28609293]
[32]
Saçar Demirci, M.D.; Yousef, M.; Allmer, J. Computational prediction of functional microRNA–MRNA interactions.In Computational Biology of Non-Coding RNA; Humana Press: New York, NY, 2019, pp. 175-196.
[http://dx.doi.org/10.1007/978-1-4939-8982-9_7]
[33]
Karagkouni, D.; Paraskevopoulou, M.D.; Tastsoglou, S.; Skoufos, G.; Karavangeli, A.; Pierros, V.; Zacharopoulou, E.; Hatzigeorgiou, A.G. DIANA-LncBase v3: Indexing experimentally supported miRNA targets on non-coding transcripts. Nucleic Acids Res., 2019.gkz1036
[http://dx.doi.org/10.1093/nar/gkz1036] [PMID: 31732741]
[34]
Twigger, S.; Lu, J.; Shimoyama, M.; Chen, D.; Pasko, D.; Long, H.; Ginster, J.; Chen, C.F.; Nigam, R.; Kwitek, A.; Eppig, J.; Maltais, L.; Maglott, D.; Schuler, G.; Jacob, H.; Tonellato, P.J. Rat Genome Database (RGD): Mapping disease onto the genome. Nucleic Acids Res., 2002, 30(1), 125-128.
[http://dx.doi.org/10.1093/nar/30.1.125] [PMID: 11752273]
[35]
Acar, İ.E.; Saçar Demirci, M.D.; Groß, U.; Allmer, J. The Expressed MicroRNA-mRNA Interactions of Toxoplasma gondii. Front. Microbiol., 2018, 8(JAN), 2630.
[http://dx.doi.org/10.3389/fmicb.2017.02630] [PMID: 29354114]
[36]
Li, S.; Li, Y.; Chen, B.; Zhao, J.; Yu, S.; Tang, Y.; Zheng, Q.; Li, Y.; Wang, P.; He, X.; Huang, S. exoRBase: A database of circRNA, lncRNA and mRNA in human blood exosomes. Nucleic Acids Res., 2018, 46(D1), D106-D112.
[http://dx.doi.org/10.1093/nar/gkx891] [PMID: 30053265]
[37]
Chung, I.F.; Chang, S.J.; Chen, C.Y.; Liu, S.H.; Li, C.Y.; Chan, C.H.; Shih, C.C.; Cheng, W.C. YM500v3: A database for small RNA sequencing in human cancer research. Nucleic Acids Res., 2017, 45(D1), D925-D931.
[http://dx.doi.org/10.1093/nar/gkw1084] [PMID: 27899625]
[38]
Galasso, M.; Sana, M.E.; Volinia, S. Non-coding RNAs: A key to future personalized molecular therapy?Genome Med., 2010, 2(2), 1-0. 12
[http://dx.doi.org/10.1186/gm133] [PMID: 20236487]
[39]
Taylor, C.F.; Paton, N.W.; Lilley, K.S.; Binz, P.A.; Julian, R.K., Jr; Jones, A.R.; Zhu, W.; Apweiler, R.; Aebersold, R.; Deutsch, E.W.; Dunn, M.J.; Heck, A.J.; Leitner, A.; Macht, M.; Mann, M.; Martens, L.; Neubert, T.A.; Patterson, S.D.; Ping, P.; Seymour, S.L.; Souda, P.; Tsugita, A.; Vandekerckhove, J.; Vondriska, T.M.; Whitelegge, J.P.; Wilkins, M.R.; Xenarios, I.; Yates, J.R., III; Hermjakob, H. The Minimum Information about A Proteomics Experiment (MIAPE). Nat. Biotechnol., 2007, 25(8), 887-893.
[http://dx.doi.org/10.1038/nbt1329] [PMID: 17687369]
[40]
Bonifati, A.; Chrysanthis, P.K.; Ouksel, A.M.; Sattler, K.U. Distributed databases and peer-to-peer databases: Past and present. SIGMOD Rec., 2008, 37(1), 5-11.
[http://dx.doi.org/10.1145/1374780.1374781]