Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Desert Agriculture Initiative
Online Publication Date2012-03-23
Print Publication Date2012-02
Permanent link to this recordhttp://hdl.handle.net/10754/552425
MetadataShow full item record
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.
CitationDistinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes 2012, 10 (1):4 Genomics, Proteomics & Bioinformatics
- Partitioning the human transcriptome using HKera, a novel classifier of housekeeping and tissue-specific genes.
- Authors: Chiang AW, Shaw GT, Hwang MJ
- Issue date: 2013
- DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes.
- Authors: Liu L, De S, Michor F
- Issue date: 2013
- DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.
- Authors: Thomas D, Finan C, Newport MJ, Jones S
- Issue date: 2015 Oct
- DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes.
- Authors: Woo YH, Li WH
- Issue date: 2012
- Replication-associated mutational asymmetry in the human genome.
- Authors: Chen CL, Duquenne L, Audit B, Guilbaud G, Rappailles A, Baker A, Huvet M, d'Aubenton-Carafa Y, Hyrien O, Arneodo A, Thermes C
- Issue date: 2011 Aug