Properties of untranslated regions of the S. cerevisiae genome.
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.
Tuller
Tamir
T
School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel. tamirtul@post.tau.ac.il
Ruppin
Eytan
E
Kupiec
Martin
M
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
D012331:RNA, Fungal; D020506:Untranslated Regions
Mol Biol Evol. 2006 Sep;23(9):1715-23
16757654
Nat Genet. 2005 Jul;37(7):777-82
15951822
Yeast. 2006 Jul 15;23(9):689-99
16845687
Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8796-801
12077310
EMBO J. 1999 Jun 1;18(11):3139-52
10357825
Curr Microbiol. 1999 Dec;39(6):369-0373
10525844
Nature. 2006 Jun 15;441(7095):840-6
16699522
Trends Genet. 1996 Jul;12(7):263-70
8763498
Nature. 2006 Aug 17;442(7104):772-8
16862119
Nat Genet. 2003 Mar;33(3):392-5
12577060
Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8
15800036
Nucleic Acids Res. 2000 Feb 15;28(4):1000-10
10648794
Genome Res. 2003 Sep;13(9):1998-2004
12915492
Genetics. 2004 Aug;167(4):2121-5
15342545
PLoS Biol. 2008 Oct 28;6(10):e255
18959479
Nat Genet. 2000 Oct;26(2):183-6
11017073
Nat Genet. 2007 Mar;39(3):303-9
17325681
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13004-9
16916930
Nucleic Acids Res. 2005 May 19;33(9):2838-51
15905473
Nat Rev Genet. 2004 Apr;5(4):299-310
15131653
Genome Biol. 2002;3(3):REVIEWS0004
11897027
PLoS Comput Biol. 2005 Dec;1(7):e72
16355254
Trends Genet. 2008 May;24(5):216-9
18378035
Biochem Biophys Res Commun. 1999 Sep 24;263(2):265-9
10491282
Nat Genet. 2002 Jun;31(2):180-3
11992122
BMC Genomics. 2008 Apr 25;9:189
18439287
Bioinformatics. 2007 May 1;23(9):1053-60
17237058
Genome Biol. 2007;8(11):R233
17983469
Nature. 2003 Oct 16;425(6959):737-41
14562106
Hum Mol Genet. 2003 Oct 1;12(19):2411-5
12915446
Trends Genet. 2006 Aug;22(8):420-3
16806566
Genome Biol. 2003;5(1):R2
14709174
PLoS Biol. 2007 May;5(5):e127; author reply e128
17503963
Trends Genet. 2006 Oct;22(10):528-32
16934358
Cell Mol Life Sci. 2008 Mar;65(5):798-813
18043867
BMC Genomics. 2008 Nov 29;9:574
19040753
Proc Natl Acad Sci U S A. 1984 Aug;81(16):5096-100
6433345
Biochem Biophys Res Commun. 2007 Aug 31;360(3):586-92
17610841
Mol Cell Biol. 2000 Nov;20(21):7881-92
11027259
Trends Biochem Sci. 2003 Apr;28(4):182-8
12713901
Science. 2008 Jun 6;320(5881):1344-9
18451266
Biol Chem Hoppe Seyler. 1994 Nov;375(11):721-9
7695834
Nat Rev Genet. 2005 Oct;6(10):775-81
16160692
Mol Syst Biol. 2008;4:223
18854817
Genes Dev. 2004 Jun 15;18(12):1371-84
15198979
Genetics. 2004 Sep;168(1):373-81
15454550
Science. 2004 Feb 6;303(5659):808-13
14764870
Mol Biol Evol. 2005 Mar;22(3):767-75
15574806
Mol Biol Cell. 2000 Dec;11(12):4241-57
11102521
Genome Res. 2003 May;13(5):875-82
12695325
Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5860-5
11972065
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
16569694
Genome Biol. 2005;6(10):R86
16207357
Biochem Biophys Res Commun. 2001 Oct 26;288(2):291-5
11606041
Curr Biol. 2004 Jul 27;14(14):1284-90
15268860
Science. 2001 Feb 16;291(5507):1289-92
11181992
Bioinformatics. 2005 Aug 15;21(16):3439-40
16082012
J Comput Biol. 2009 Feb;16(2):303-16
19193148
Nature. 2004 Sep 2;431(7004):99-104
15343339
Microbiol Mol Biol Rev. 1998 Dec;62(4):1492-553
9841679