Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

Handle URI:
http://hdl.handle.net/10754/552425
Title:
Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes
Authors:
Cui, Peng; Ding, Feng ( 0000-0001-8237-4062 ) ; Lin, Qiang; Zhang, Lingfang; Li, Ang; Zhang, Zhang; Hu, Songnian; Yu, Jun
Abstract:
Here, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes 2012, 10 (1):4 Genomics, Proteomics & Bioinformatics
Publisher:
Elsevier BV
Journal:
Genomics, Proteomics & Bioinformatics
Issue Date:
23-Mar-2012
DOI:
10.1016/S1672-0229(11)60028-4
Type:
Article
ISSN:
16720229
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S1672022911600284
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorCui, Pengen
dc.contributor.authorDing, Fengen
dc.contributor.authorLin, Qiangen
dc.contributor.authorZhang, Lingfangen
dc.contributor.authorLi, Angen
dc.contributor.authorZhang, Zhangen
dc.contributor.authorHu, Songnianen
dc.contributor.authorYu, Junen
dc.date.accessioned2015-05-07T13:42:42Zen
dc.date.available2015-05-07T13:42:42Zen
dc.date.issued2012-03-23en
dc.identifier.citationDistinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes 2012, 10 (1):4 Genomics, Proteomics & Bioinformaticsen
dc.identifier.issn16720229en
dc.identifier.doi10.1016/S1672-0229(11)60028-4en
dc.identifier.urihttp://hdl.handle.net/10754/552425en
dc.description.abstractHere, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.en
dc.publisherElsevier BVen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S1672022911600284en
dc.rightsArchived with thanks to Genomics, Proteomics & Bioinformatics. http://creativecommons.org/licenses/by-nc-sa/3.0/en
dc.subjectreplicationen
dc.subjecttranscriptionen
dc.subjectmutational pressureen
dc.subjectgenetic variationen
dc.titleDistinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGenomics, Proteomics & Bioinformaticsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, Chinaen
kaust.authorLi, Angen
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