A schematic workflow for collecting information about the interaction between copy number variants and MicroRNAs using existing resources

Methods in Molecular Biology

Volumn 1182, Issue , 2014, Pages 307-320

  Dweep, Harsh ^a   Gretz, Norbert ^a   Felekkis, Kyriakos ^b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF NICOSIA   (Cyprus)

Author keywords

3' UTR; CNV miRNA interaction predictions; Copy number variant; MicroRNA; miRWalk

Indexed keywords

MICRORNA;

ALGORITHM; ARTICLE; BINDING SITE; COPY NUMBER VARIATION; DATA BASE; HUMAN; HUMAN GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; RNA BINDING; ANIMAL; BIOLOGY; GENETIC DATABASE; GENETICS; PROCEDURES; WORKFLOW;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; HUMANS; MICRORNAS; WORKFLOW;

EID: 84925883658     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1062-5_26     Document Type: Article

References (26)

1. Hastings PJ, Ira G, Lupski JR (2009) A microhomology- mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5: e1000327
2. Zaman MS, Shahryari V, Deng G et al (2012) Up-regulation of microRNA-21 correlates with lower kidney cancer survival. PLoS One 7: e31060
3. Rovelet-Lecrux A, Hannequin D, Raux G et al (2006) APP locus duplication causes autosomal dominant early-onset alzheimer disease with cerebral amyloid angiopathy. Nat Genet 38: 24-26
4. Cheng C, Li W, Zhang Z et al (2013) MicroRNA-144 is regulated by activator protein- 1 (AP-1) and decreases expression of Alzheimer disease-related a disintegrin and metalloprotease 10 (ADAM10). J Biol Chem 288: 13748-13761
5. Le Marechal C, Masson E, Chen JM et al (2006) Hereditary pancreatitis caused by triplication of the trypsinogen locus. Nat Genet 38: 1372-1374
6. Li A, Yu J, Kim H et al (2013) MicroRNA array analysis fi nds elevated serum miR-1290 accurately distinguishes patients with low-stage pancreatic cancer from healthy and disease controls. Clin Cancer Res 19: 3600-3610
7. Townson JR, Barcellos LF, Nibbs RJ (2002) Gene copy number regulates the production of the human chemokine CCL3-L1. Eur J Immunol 32: 3016-3026
8. Narayanan A, Iordanskiy S, Das R et al (2013) Exosomes derived from HIV-1-infected cells contain trans-Activation response element RNA. J Biol Chem 288: 20014-20033
9. Aitman TJ, Dong R, Vyse TJ et al (2006) Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439: 851-855
10. Papagregoriou G, Erguler K, Dweep H et al (2012) A miR-1207-5p binding site polymorphism abolishes regulation of HBEGF and is associated with disease severity in CFHR5 nephropathy. PLoS One 7: e31021
11. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
12. Kim DH, Saetrom P, Snove O Jr et al (2008) MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A 105: 16230-16235
13. Lai EC (2002) Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-Transcriptional regulation. Nat Genet 30: 363-364
14. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157
15. Conrad DF, Pinto D, Redon R et al (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712
16. Iafrate AJ, Feuk L, Rivera MN et al (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951
17. Dear PH (2009) Copy-number variation: the end of the human genome? Trends Biotechnol 27: 448-454
18. Henrichsen CN, Chaignat E, Reymond A (2009) Copy number variants, diseases and gene expression. Hum Mol Genet 18: R1-8
19. Nozawa M, Kawahara Y, Nei M (2007) Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci U S A 104: 20421-20426
20. Schuster-Bockler B, Conrad D, Bateman A (2010) Dosage sensitivity shapes the evolution of copy-number varied regions. PLoS One 5: e9474
21. Felekkis K, Voskarides K, Dweep H et al (2011) Increased number of microRNA target sites in genes encoded in CNV regions. Evidence for an evolutionary genomic interaction. Mol Biol Evol 28: 2421-2424
22. Woodwark C, Bateman A (2011) The characterisation of three types of genes that overlie copy number variable regions. PLoS One 6: e14814
23. Dweep H, Sticht C, Pandey P et al (2011) miRWalk - database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 44: 839-837
24. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often fl anked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20
25. Dweep H, Sticht C, Gretz N (2013) In-silico algorithms for the screening of possible microRNA binding sites and their interactions. Curr Genomics 14: 127-136
26. Dweep H, Sticht C, Kharkar A et al (2013) Parallel analysis of mRNA and microRNA microarray profi les to explore functional regulatory patterns in polycystic kidney disease: using PKD/Mhm rat model. PLoS One 8: e53780