title: Properties of untranslated regions of the S. cerevisiae genome.
abstract: BACKGROUND
  During evolution selection forces such as changing environments shape the architecture of genomes. The distribution of genes along chromosomes and the length of intragenic regions are basic genomic features known to play a major role in the regulation of gene transcription and translation.
  
  
  RESULTS
  In this work we perform the first large scale analysis of the length distribution of untranslated regions (promoters, 5' and 3' untranslated regions, terminators) in the genome of the yeast Saccharomyces cerevisiae. Our analysis shows that the length of each open reading frame (ORF) and that of its associated regulatory and untranslated regions significantly correlate with each other. Moreover, significant correlations with other features related to gene expression and evolution (number of regulating transcription factors, mRNA and protein abundance, evolutionary rate, etc) were observed. Furthermore, the function of genes seems to have an important role in the evolution of these lengths. Notably, genes that are related to RNA metabolism tend to have shorter untranslated regions and thus tend to be closer to their neighbouring genes while genes coding for cell wall proteins tend to be isolated in the genome.
  
  
  CONCLUSIONS
  These results indicate that genome architecture has a significant role in regulating gene expression, and in shaping the characteristics and functionality of proteins.
authors.affiliation: School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel. tamirtul@post.tau.ac.il
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
authors.forename: Eytan
authors.initials: E
authors.lastname: Ruppin
authors.forename: Martin
authors.initials: M
authors.lastname: Kupiec
mesh_terms: D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016681:Genome, Fungal; D016366:Open Reading Frames; D012331:RNA, Fungal / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020506:Untranslated Regions
chemical_list: D012331:RNA, Fungal; D020506:Untranslated Regions
references.citation: Mol Biol Evol. 2006 Sep;23(9):1715-23
references.pmid: 16757654
references.citation: Nat Genet. 2005 Jul;37(7):777-82
references.pmid: 15951822
references.citation: Yeast. 2006 Jul 15;23(9):689-99
references.pmid: 16845687
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8796-801
references.pmid: 12077310
references.citation: EMBO J. 1999 Jun 1;18(11):3139-52
references.pmid: 10357825
references.citation: Curr Microbiol. 1999 Dec;39(6):369-0373
references.pmid: 10525844
references.citation: Nature. 2006 Jun 15;441(7095):840-6
references.pmid: 16699522
references.citation: Trends Genet. 1996 Jul;12(7):263-70
references.pmid: 8763498
references.citation: Nature. 2006 Aug 17;442(7104):772-8
references.pmid: 16862119
references.citation: Nat Genet. 2003 Mar;33(3):392-5
references.pmid: 12577060
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8
references.pmid: 15800036
references.citation: Nucleic Acids Res. 2000 Feb 15;28(4):1000-10
references.pmid: 10648794
references.citation: Genome Res. 2003 Sep;13(9):1998-2004
references.pmid: 12915492
references.citation: Genetics. 2004 Aug;167(4):2121-5
references.pmid: 15342545
references.citation: PLoS Biol. 2008 Oct 28;6(10):e255
references.pmid: 18959479
references.citation: Nat Genet. 2000 Oct;26(2):183-6
references.pmid: 11017073
references.citation: Nat Genet. 2007 Mar;39(3):303-9
references.pmid: 17325681
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13004-9
references.pmid: 16916930
references.citation: Nucleic Acids Res. 2005 May 19;33(9):2838-51
references.pmid: 15905473
references.citation: Nat Rev Genet. 2004 Apr;5(4):299-310
references.pmid: 15131653
references.citation: Genome Biol. 2002;3(3):REVIEWS0004
references.pmid: 11897027
references.citation: PLoS Comput Biol. 2005 Dec;1(7):e72
references.pmid: 16355254
references.citation: Trends Genet. 2008 May;24(5):216-9
references.pmid: 18378035
references.citation: Biochem Biophys Res Commun. 1999 Sep 24;263(2):265-9
references.pmid: 10491282
references.citation: Nat Genet. 2002 Jun;31(2):180-3
references.pmid: 11992122
references.citation: BMC Genomics. 2008 Apr 25;9:189
references.pmid: 18439287
references.citation: Bioinformatics. 2007 May 1;23(9):1053-60
references.pmid: 17237058
references.citation: Genome Biol. 2007;8(11):R233
references.pmid: 17983469
references.citation: Nature. 2003 Oct 16;425(6959):737-41
references.pmid: 14562106
references.citation: Hum Mol Genet. 2003 Oct 1;12(19):2411-5
references.pmid: 12915446
references.citation: Trends Genet. 2006 Aug;22(8):420-3
references.pmid: 16806566
references.citation: Genome Biol. 2003;5(1):R2
references.pmid: 14709174
references.citation: PLoS Biol. 2007 May;5(5):e127; author reply e128
references.pmid: 17503963
references.citation: Trends Genet. 2006 Oct;22(10):528-32
references.pmid: 16934358
references.citation: Cell Mol Life Sci. 2008 Mar;65(5):798-813
references.pmid: 18043867
references.citation: BMC Genomics. 2008 Nov 29;9:574
references.pmid: 19040753
references.citation: Proc Natl Acad Sci U S A. 1984 Aug;81(16):5096-100
references.pmid: 6433345
references.citation: Biochem Biophys Res Commun. 2007 Aug 31;360(3):586-92
references.pmid: 17610841
references.citation: Mol Cell Biol. 2000 Nov;20(21):7881-92
references.pmid: 11027259
references.citation: Trends Biochem Sci. 2003 Apr;28(4):182-8
references.pmid: 12713901
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Biol Chem Hoppe Seyler. 1994 Nov;375(11):721-9
references.pmid: 7695834
references.citation: Nat Rev Genet. 2005 Oct;6(10):775-81
references.pmid: 16160692
references.citation: Mol Syst Biol. 2008;4:223
references.pmid: 18854817
references.citation: Genes Dev. 2004 Jun 15;18(12):1371-84
references.pmid: 15198979
references.citation: Genetics. 2004 Sep;168(1):373-81
references.pmid: 15454550
references.citation: Science. 2004 Feb 6;303(5659):808-13
references.pmid: 14764870
references.citation: Mol Biol Evol. 2005 Mar;22(3):767-75
references.pmid: 15574806
references.citation: Mol Biol Cell. 2000 Dec;11(12):4241-57
references.pmid: 11102521
references.citation: Genome Res. 2003 May;13(5):875-82
references.pmid: 12695325
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5860-5
references.pmid: 11972065
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
references.pmid: 16569694
references.citation: Genome Biol. 2005;6(10):R86
references.pmid: 16207357
references.citation: Biochem Biophys Res Commun. 2001 Oct 26;288(2):291-5
references.pmid: 11606041
references.citation: Curr Biol. 2004 Jul 27;14(14):1284-90
references.pmid: 15268860
references.citation: Science. 2001 Feb 16;291(5507):1289-92
references.pmid: 11181992
references.citation: Bioinformatics. 2005 Aug 15;21(16):3439-40
references.pmid: 16082012
references.citation: J Comput Biol. 2009 Feb;16(2):303-16
references.pmid: 19193148
references.citation: Nature. 2004 Sep 2;431(7004):99-104
references.pmid: 15343339
references.citation: Microbiol Mol Biol Rev. 1998 Dec;62(4):1492-553
references.pmid: 9841679