Genomic evidence for elevated mutation rates in highly expressed genes
dc.contributor.author | Park, Chungoo | en_US |
dc.contributor.author | Qian, Wenfeng | en_US |
dc.contributor.author | Zhang, Jianzhi | en_US |
dc.date.accessioned | 2014-01-08T20:34:24Z | |
dc.date.available | 2014-01-08T20:34:24Z | |
dc.date.issued | 2012-12 | en_US |
dc.identifier.citation | Park, Chungoo; Qian, Wenfeng; Zhang, Jianzhi (2012). "Genomic evidence for elevated mutation rates in highly expressed genes." EMBO reports 13(12): 1123-1129. <http://hdl.handle.net/2027.42/102069> | en_US |
dc.identifier.issn | 1469-221X | en_US |
dc.identifier.issn | 1469-3178 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/102069 | |
dc.publisher | John Wiley & Sons, Ltd | en_US |
dc.subject.other | Yeast | en_US |
dc.subject.other | Human | en_US |
dc.subject.other | Transcription | en_US |
dc.subject.other | Gene Expression | en_US |
dc.subject.other | Mutation Rate | en_US |
dc.title | Genomic evidence for elevated mutation rates in highly expressed genes | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Molecular, Cellular and Developmental Biology | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.identifier.pmid | 23146897 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/102069/1/embr2012165.reviewer_comments.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/102069/2/embr2012165-sup-0001.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/102069/3/embr2012165.pdf | |
dc.identifier.doi | 10.1038/embor.2012.165 | en_US |
dc.identifier.source | EMBO reports | en_US |
dc.identifier.citedreference | Pleasance ED et al ( 2010 ) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191 – 196 | en_US |
dc.identifier.citedreference | Hoede C, Denamur E, Tenaillon O ( 2006 ) Selection acts on DNA secondary structures to decrease transcriptional mutagenesis. PLoS Genet 2: e176 | en_US |
dc.identifier.citedreference | Bartel DP ( 2004 ) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281 – 297 | en_US |
dc.identifier.citedreference | Filipowicz W, Bhattacharyya SN, Sonenberg N ( 2008 ) Mechanisms of post‐transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9: 102 – 114 | en_US |
dc.identifier.citedreference | Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, Bartel DP ( 2009 ) RNAi in budding yeast. Science 326: 544 – 550 | en_US |
dc.identifier.citedreference | Lee W et al ( 2010 ) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465: 473 – 477 | en_US |
dc.identifier.citedreference | Pleasance ED et al ( 2010 ) A small‐cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184 – 190 | en_US |
dc.identifier.citedreference | Araten DJ, Golde DW, Zhang RH, Thaler HT, Gargiulo L, Notaro R, Luzzatto L ( 2005 ) A quantitative measurement of the human somatic mutation rate. Cancer Res 65: 8111 – 8117 | en_US |
dc.identifier.citedreference | Zhang J, He X ( 2005 ) Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol Biol Evol 22: 1147 – 1155 | en_US |
dc.identifier.citedreference | Kimura M ( 1967 ) On the evolutionary adjustment of spontaneous mutation rates. Genet Res 9: 23 – 34 | en_US |
dc.identifier.citedreference | Zhang J ( 2000 ) Protein‐length distributions for the three domains of life. Trends Genet 16: 107 – 109 | en_US |
dc.identifier.citedreference | Wagner A ( 2005 ) Energy constraints on the evolution of gene expression. Mol Biol Evol 22: 1365 – 1374 | en_US |
dc.identifier.citedreference | Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB ( 2004 ) Noise minimization in eukaryotic gene expression. PLoS Biol 2: e137 | en_US |
dc.identifier.citedreference | Wang Z, Zhang J ( 2011 ) Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci USA 108: E67 – E76 | en_US |
dc.identifier.citedreference | Yang JR, Zhuang SM, Zhang J ( 2010 ) Impact of translational error‐induced and error‐free misfolding on the rate of protein evolution. Mol Syst Biol 6: 421 | en_US |
dc.identifier.citedreference | Cherry JL ( 2010 ) Expression level, evolutionary rate, and the cost of expression. Genome Biol Evol 2: 757 – 769 | en_US |
dc.identifier.citedreference | Gout JF, Kahn D, Duret L ( 2010 ) The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet 6: e1000944 | en_US |
dc.identifier.citedreference | Martincorena I, Seshasayee AS, Luscombe NM ( 2012 ) Evidence of non‐random mutation rates suggests an evolutionary risk management strategy. Nature 485: 95 – 98 | en_US |
dc.identifier.citedreference | Yang Z ( 2007 ) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586 – 1591 | en_US |
dc.identifier.citedreference | Kimura M ( 1980 ) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111 – 120 | en_US |
dc.identifier.citedreference | Hodgkinson A, Eyre‐Walker A ( 2011 ) Variation in the mutation rate across mammalian genomes. Nat Rev Genet 12: 756 – 766 | en_US |
dc.identifier.citedreference | Lang GI, Murray AW ( 2011 ) Mutation rates across budding yeast chromosome VI are correlated with replication timing. Genome Biol Evol 3: 799 – 811 | en_US |
dc.identifier.citedreference | Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR ( 2009 ) Human mutation rate associated with DNA replication timing. Nat Genet 41: 393 – 395 | en_US |
dc.identifier.citedreference | Chen X, Chen Z, Chen H, Su Z, Yang J, Lin F, Shi S, He X ( 2012 ) Nucleosomes suppress spontaneous mutations base‐specifically in eukaryotes. Science 335: 1235 – 1238 | en_US |
dc.identifier.citedreference | Kim N, Jinks‐Robertson S ( 2012 ) Transcription as a source of genome instability. Nat Rev Genet 13: 204 – 214 | en_US |
dc.identifier.citedreference | Aguilera A ( 2002 ) The connection between transcription and genomic instability. EMBO J 21: 195 – 201 | en_US |
dc.identifier.citedreference | Svejstrup JQ ( 2002 ) Mechanisms of transcription‐coupled DNA repair. Nat Rev Mol Cell Biol 3: 21 – 29 | en_US |
dc.identifier.citedreference | Hanawalt PC, Spivak G ( 2008 ) Transcription‐coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol 9: 958 – 970 | en_US |
dc.identifier.citedreference | Savic DJ, Kanazir DT ( 1972 ) The effect of a histidine operator‐constitutive mutation on UV‐induced mutability within the histidine operon of Salmonella typhimurium. Mol Gen Genet 118: 45 – 50 | en_US |
dc.identifier.citedreference | Herman RK, Dworkin NB ( 1971 ) Effect of gene induction on the rate of mutagenesis by ICR‐191 in Escherichia coli. J Bacteriol 106: 543 – 550 | en_US |
dc.identifier.citedreference | Beletskii A, Bhagwat AS ( 1996 ) Transcription‐induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci USA 93: 13919 – 13924 | en_US |
dc.identifier.citedreference | Takahashi T, Burguiere‐Slezak G, Van der Kemp PA, Boiteux S ( 2011 ) Topoisomerase 1 provokes the formation of short deletions in repeated sequences upon high transcription in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 108: 692 – 697 | en_US |
dc.identifier.citedreference | Datta A, Jinks‐Robertson S ( 1995 ) Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 268: 1616 – 1619 | en_US |
dc.identifier.citedreference | Kim N, Jinks‐Robertson S ( 2009 ) dUTP incorporation into genomic DNA is linked to transcription in yeast. Nature 459: 1150 – 1153 | en_US |
dc.identifier.citedreference | Lippert MJ, Kim N, Cho JE, Larson RP, Schoenly NE, O‧Shea SH, Jinks‐Robertson S ( 2011 ) Role for topoisomerase 1 in transcription‐associated mutagenesis in yeast. Proc Natl Acad Sci USA 108: 698 – 703 | en_US |
dc.identifier.citedreference | Hendriks G, Calleja F, Besaratinia A, Vrieling H, Pfeifer GP, Mullenders LH, Jansen JG, de Wind N ( 2010 ) Transcription‐dependent cytosine deamination is a novel mechanism in ultraviolet light‐induced mutagenesis. Curr Biol 20: 170 – 175 | en_US |
dc.identifier.citedreference | Lynch M et al ( 2008 ) A genome‐wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci USA 105: 9272 – 9277 | en_US |
dc.identifier.citedreference | Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M ( 2008 ) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344 – 1349 | en_US |
dc.identifier.citedreference | Gojobori T, Li WH, Graur D ( 1982 ) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18: 360 – 369 | en_US |
dc.identifier.citedreference | Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES ( 2003 ) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241 – 254 | en_US |
dc.identifier.citedreference | Qian W, Yang JR, Pearson NM, Maclean C, Zhang J ( 2012 ) Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet 8: e1002603 | en_US |
dc.identifier.citedreference | Hershberg R, Petrov DA ( 2008 ) Selection on codon bias. Annu Rev Genet 42: 287 – 299 | en_US |
dc.identifier.citedreference | Drummond DA, Wilke CO ( 2008 ) Mistranslation‐induced protein misfolding as a dominant constraint on coding‐sequence evolution. Cell 134: 341 – 352 | en_US |
dc.identifier.citedreference | Pal C, Papp B, Hurst LD ( 2001 ) Highly expressed genes in yeast evolve slowly. Genetics 158: 927 – 931 | en_US |
dc.identifier.citedreference | Yang JR, Liao BY, Zhuang SM, Zhang J ( 2012 ) Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci USA 109: E831 – E840 | en_US |
dc.identifier.citedreference | Parenteau J, Durand M, Morin G, Gagnon J, Lucier JF, Wellinger RJ, Chabot B, Elela SA ( 2011 ) Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 147: 320 – 331 | en_US |
dc.identifier.citedreference | Juneau K, Miranda M, Hillenmeyer ME, Nislow C, Davis RW ( 2006 ) Introns regulate RNA and protein abundance in yeast. Genetics 174: 511 – 518 | en_US |
dc.identifier.citedreference | Hwang DG, Green P ( 2004 ) Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA 101: 13994 – 14001 | en_US |
dc.identifier.citedreference | Washietl S, Machne R, Goldman N ( 2008 ) Evolutionary footprints of nucleosome positions in yeast. Trends Genet 24: 583 – 587 | en_US |
dc.identifier.citedreference | Mugal CF, von Grunberg HH, Peifer M ( 2009 ) Transcription‐induced mutational strand bias and its effect on substitution rates in human genes. Mol Biol Evol 26: 131 – 142 | en_US |
dc.identifier.citedreference | Fujita PA et al ( 2011 ) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39: D876 – D882 | en_US |
dc.identifier.citedreference | Xiong Y, Chen X, Chen Z, Wang X, Shi S, Wang X, Zhang J, He X ( 2010 ) RNA sequencing shows no dosage compensation of the active X‐chromosome. Nat Genet 42: 1043 – 1047 | en_US |
dc.identifier.citedreference | Brawand D et al ( 2011 ) The evolution of gene expression levels in mammalian organs. Nature 478: 343 – 348 | en_US |
dc.identifier.citedreference | Polak P, Arndt PF ( 2008 ) Transcription induces strand‐specific mutations at the 5' end of human genes. Genome Res 18: 1216 – 1223 | en_US |
dc.identifier.citedreference | Green P, Ewing B, Miller W, Thomas PJ, Green ED ( 2003 ) Transcription‐associated mutational asymmetry in mammalian evolution. Nat Genet 33: 514 – 517 | en_US |
dc.identifier.citedreference | Cho RJ et al ( 1998 ) A genome‐wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2: 65 – 73 | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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