title: Preferential regulation of miRNA targets by environmental chemicals in the human genome.
abstract: BACKGROUND
  microRNAs (miRNAs) represent a class of small (typically 22 nucleotides in length) non-coding RNAs that can degrade their target mRNAs or block their translation. Recent disease research showed the exposure to some environmental chemicals (ECs) can regulate the expression patterns of miRNAs, which raises the intriguing question of how miRNAs and their targets cope with the exposure to ECs throughout the genome.
  
  
  RESULTS
  In this study, we comprehensively analyzed the properties of genes regulated by ECs (EC-genes) and found miRNA targets were significantly enriched among the EC-genes. Compared with the non-miRNA-targets, miRNA targets were roughly twice as likely to be EC-genes. By investigating the collection methods and other properties of the EC-genes, we demonstrated that the enrichment of miRNA targets was not attributed to either the potential collection bias of EC-genes, the presence of paralogs, longer 3'UTRs or more conserved 3'UTRs. Finally, we identified 1,842 significant concurrent interactions between 407 miRNAs and 497 ECs. This association network of miRNAs-ECs was highly modular and could be separated into 14 interconnected modules. In each module, miRNAs and ECs were closely connected, providing a good method to design accurate miRNA markers for ECs in toxicology research.
  
  
  CONCLUSIONS
  Our analyses indicated that miRNAs and their targets played important roles in cellular responses to ECs. Association analyses of miRNAs and ECs will help to broaden the understanding of the pathogenesis of such chemical components.
authors: Key laboratory of Photosynthesis and Environmental Molecular Physiology, the Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. xudong33@yahoo.com.cn
authors: Xudong
authors: X
authors: Wu
authors: Yijiang
authors: Y
authors: Song
references: Genes Dev. 2006 Oct 15;20(20):2769-72
references: 17043305
references: BMC Genomics. 2010 Oct 28;11:609
references: 21029445
references: Nat Rev Genet. 2004 Feb;5(2):101-13
references: 14735121
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92
references: 18782832
references: PLoS Comput Biol. 2010 May 20;6(5):e1000788
references: 20502671
references: BMC Genomics. 2009 Sep 14;10:431
references: 19751524
references: Nature. 2005 Jun 9;435(7043):839-43
references: 15944709
references: BMC Genomics. 2009 Jan 14;10:22
references: 19144180
references: Genome Biol. 2010 Jan 20;11(1):R6
references: 20089154
references: BMC Genomics. 2010 Dec 01;11 Suppl 3:S5
references: 21143787
references: Nat Genet. 2005 May;37(5):495-500
references: 15806104
references: BMC Bioinformatics. 2009 Oct 08;10:326
references: 19814812
references: Nature. 2005 Feb 17;433(7027):769-73
references: 15685193
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73
references: 16381958
references: J Environ Sci Health C Environ Carcinog Ecotoxicol Rev. 2010 Apr;28(2):89-124
references: 20552498
references: Bioinformatics. 2010 Sep 15;26(18):2347-8
references: 20656902
references: Epigenetics. 2011 Feb;6(2):134-40
references: 20962593
references: Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7821-6
references: 12060727
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: Annu Rev Pharmacol Toxicol. 2011;51:25-43
references: 20809797
references: BMC Med Genomics. 2010 May 06;3:17
references: 20459635
references: Cien Saude Colet. 2008 Jan-Feb;13(1):269-81
references: 18813540
references: Nat Genet. 2007 Oct;39(10):1278-84
references: 17893677
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D98-104
references: 18927107
references: Environ Health Perspect. 2009 Feb;117(2):231-40
references: 19270793
references: Nat Genet. 2006 Dec;38(12):1452-6
references: 17072316
references: Environ Health Perspect. 2010 Jul;118(7):943-8
references: 20211803
references: Nat Genet. 2006 Jun;38 Suppl:S20-4
references: 16736020
references: Environ Health Perspect. 2009 Nov;117(11):1745-51
references: 20049127
references: Cancer Res. 2010 Sep 15;70(18):7027-30
references: 20807816
references: BMC Syst Biol. 2009 May 05;3:46
references: 19416532
references: Genes Dev. 2006 Oct 15;20(20):2793-805
references: 17015424
references: Biochim Biophys Acta. 2010 Oct-Dec;1799(10-12):760-7
references: 20493978
references: Nat Rev Genet. 2004 Jul;5(7):522-31
references: 15211354
references: EMBO J. 2009 Feb 4;28(3):213-22
references: 19131968
references: Comput Appl Biosci. 1997 Oct;13(5):555-6
references: 9367129
references: PLoS Comput Biol. 2007 Jul;3(7):e131
references: 17630826
references: Cell. 2005 Jan 14;120(1):15-20
references: 15652477
references: Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.3
references: 18792934
references: Science. 2006 Apr 7;312(5770):75-9
references: 16484454
references: Genome Biol. 2008;9(8):R132
references: 18727826
references: PLoS One. 2008;3(10):e3420
references: 18923704
references: Biochem Biophys Res Commun. 2007 Jan 19;352(3):733-8
references: 17141185
references: Epigenomics. 2009 Dec;1(2):281-90
references: 22122703
references: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references: 12883005
references: BMC Genomics. 2007 Mar 06;8:66
references: 17341314
references: Nucleic Acids Res. 2007;35(1):152-64
references: 17158157
references: BMC Evol Biol. 2010 May 18;10:145
references: 20478072
references: Genome Res. 2009 May;19(5):734-43
references: 19411598
references: Cell. 2004 Jan 23;116(2):281-97
references: 14744438
references: Cell. 2005 Aug 26;122(4):553-63
references: 16122423
references: Nature. 2008 Sep 4;455(7209):64-71
references: 18668037
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8
references: 18084021
references: Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13122-7
references: 17664417