MicroPIR2: a Comprehensive Database for Human-mouse Comparative Study of MicroRNA-promoter Interactions

Overview

Journal Database (Oxford)

Specialty Biology

Date 2014 Nov 27

PMID 25425035

Citations 8

Authors

Jittima Piriyapongsa

Chaiwat Bootchai

Chumpol Ngamphiw

Sissades Tongsima

Affiliations

Soon will be listed here.

Abstract

microRNA (miRNA)-promoter interaction resource (microPIR) is a public database containing over 15 million predicted miRNA target sites located within human promoter sequences. These predicted targets are presented along with their related genomic and experimental data, making the microPIR database the most comprehensive repository of miRNA promoter target sites. Here, we describe major updates of the microPIR database including new target predictions in the mouse genome and revised human target predictions. The updated database (microPIR2) now provides ∼80 million human and 40 million mouse predicted target sites. In addition to being a reference database, microPIR2 is a tool for comparative analysis of target sites on the promoters of human-mouse orthologous genes. In particular, this new feature was designed to identify potential miRNA-promoter interactions conserved between species that could be stronger candidates for further experimental validation. We also incorporated additional supporting information to microPIR2 such as nuclear and cytoplasmic localization of miRNAs and miRNA-disease association. Extra search features were also implemented to enable various investigations of targets of interest. Database URL: http://www4a.biotec.or.th/micropir2

Citing Articles

Noncanonical functions of microRNAs in the nucleus.

Gu J, Li Y, Tian Y, Zhang Y, Cheng Y, Tang Y Acta Biochim Biophys Sin (Shanghai). 2024; 56(2):151-161.

PMID: 38167929 PMC: 10984876. DOI: 10.3724/abbs.2023268.

miRNA therapeutics in precision oncology: a natural premium to nurture.

Jain C, Srivastava P, Pandey A, Singh N, Kumar R Explor Target Antitumor Ther. 2022; 3(4):511-532.

PMID: 36071981 PMC: 9446160. DOI: 10.37349/etat.2022.00098.

MIREyA: a computational approach to detect miRNA-directed gene activation.

Elizarova A, Ozturk M, Guler R, Medvedeva Y F1000Res. 2021; 10:249.

PMID: 34527215 PMC: 8411277. DOI: 10.12688/f1000research.28142.2.

MicroRNA 195-5p Targets Promoter Region to Regulate Its Expression in Granulosa Cells.

Bai Y, Pan B, Zhan X, Silver H, Li J Int J Mol Sci. 2021; 22(13).

PMID: 34201585 PMC: 8267755. DOI: 10.3390/ijms22136721.

MicroRNAs: Key Regulators to Understand Osteoclast Differentiation?.

Lozano C, Duroux-Richard I, Firat H, Schordan E, Apparailly F Front Immunol. 2019; 10:375.

PMID: 30899258 PMC: 6416164. DOI: 10.3389/fimmu.2019.00375.

References

Blanco E, Messeguer X, Smith T, Guigo R . Transcription factor map alignment of promoter regions. PLoS Comput Biol. 2006; 2(5):e49. PMC: 1464811. DOI: 10.1371/journal.pcbi.0020049. View

Guo A, Sun J, Jia P, Zhao Z . A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst Biol. 2010; 4:10. PMC: 2834616. DOI: 10.1186/1752-0509-4-10. View

Yang J, Li J, Shao P, Zhou H, Chen Y, Qu L . starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res. 2010; 39(Database issue):D202-9. PMC: 3013664. DOI: 10.1093/nar/gkq1056. View

Huang E, Reichardt L . Neurotrophins: roles in neuronal development and function. Annu Rev Neurosci. 2001; 24:677-736. PMC: 2758233. DOI: 10.1146/annurev.neuro.24.1.677. View

Carrington J, Ambros V . Role of microRNAs in plant and animal development. Science. 2003; 301(5631):336-8. DOI: 10.1126/science.1085242. View

Huang V, Zheng J, Qi Z, Wang J, Place R, Yu J . Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet. 2013; 9(9):e1003821. PMC: 3784563. DOI: 10.1371/journal.pgen.1003821. View

Kocerha J, Faghihi M, Lopez-Toledano M, Huang J, Ramsey A, Caron M . MicroRNA-219 modulates NMDA receptor-mediated neurobehavioral dysfunction. Proc Natl Acad Sci U S A. 2009; 106(9):3507-12. PMC: 2651305. DOI: 10.1073/pnas.0805854106. View

Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury M . A navigator for human genome epidemiology. Nat Genet. 2008; 40(2):124-5. DOI: 10.1038/ng0208-124. View

Zuccato C, Ciammola A, Rigamonti D, Leavitt B, Goffredo D, Conti L . Loss of huntingtin-mediated BDNF gene transcription in Huntington's disease. Science. 2001; 293(5529):493-8. DOI: 10.1126/science.1059581. View

10.

Hong C, Liu H, Liu T, Lin C, Cheng C, Tsai S . Brain-derived neurotrophic factor (BDNF) Val66Met polymorphisms in Parkinson's disease and age of onset. Neurosci Lett. 2003; 353(1):75-7. DOI: 10.1016/j.neulet.2003.09.009. View

11.

Nakata K, Ujike H, Sakai A, Uchida N, Nomura A, Imamura T . Association study of the brain-derived neurotrophic factor (BDNF) gene with bipolar disorder. Neurosci Lett. 2003; 337(1):17-20. DOI: 10.1016/s0304-3940(02)01292-2. View

12.

Sklar P, Gabriel S, McInnis M, Bennett P, Tsan G, Schaffner S . Family-based association study of 76 candidate genes in bipolar disorder: BDNF is a potential risk locus. Brain-derived neutrophic factor. Mol Psychiatry. 2002; 7(6):579-93. DOI: 10.1038/sj.mp.4001058. View

13.

Wassink T, Nelson J, Crowe R, Andreasen N . Heritability of BDNF alleles and their effect on brain morphology in schizophrenia. Am J Med Genet. 1999; 88(6):724-8. DOI: 10.1002/(sici)1096-8628(19991215)88:6<724::aid-ajmg25>3.0.co;2-7. View

14.

Ambros V . The functions of animal microRNAs. Nature. 2004; 431(7006):350-5. DOI: 10.1038/nature02871. View

15.

. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004; 432(7018):695-716. DOI: 10.1038/nature03154. View

16.

Filipowicz W, Bhattacharyya S, Sonenberg N . Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet. 2008; 9(2):102-14. DOI: 10.1038/nrg2290. View

17.

Majid S, Dar A, Saini S, Yamamura S, Hirata H, Tanaka Y . MicroRNA-205-directed transcriptional activation of tumor suppressor genes in prostate cancer. Cancer. 2010; 116(24):5637-49. PMC: 3940365. DOI: 10.1002/cncr.25488. View

18.

Piriyapongsa J, Bootchai C, Ngamphiw C, Tongsima S . microPIR: an integrated database of microRNA target sites within human promoter sequences. PLoS One. 2012; 7(3):e33888. PMC: 3306312. DOI: 10.1371/journal.pone.0033888. View

19.

Kim D, Saetrom P, Snove Jr O, Rossi J . MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A. 2008; 105(42):16230-5. PMC: 2571020. DOI: 10.1073/pnas.0808830105. View

20.

Toda T, Momose Y, Murata M, Tamiya G, Yamamoto M, Hattori N . Toward identification of susceptibility genes for sporadic Parkinson's disease. J Neurol. 2003; 250 Suppl 3:III40-3. DOI: 10.1007/s00415-003-1307-6. View