Abstract:
BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. RESULTS:We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. CONCLUSIONS:Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Tomkova M,Tomek J,Kriaucionis S,Schuster-Böckler Bdoi
10.1186/s13059-018-1509-ysubject
Has Abstractpub_date
2018-09-10 00:00:00pages
129issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-018-1509-yjournal_volume
19pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-12-r122
更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:Acute myeloid leukemia (AML) comprises a group of diseases characterized by the abnormal development of malignant myeloid cells. Recent studies have demonstrated an important role for aberrant transcriptional regulation in AML pathophysiology. Although several transcription factors (TFs) involved in myeloid ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-2-r38
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-3-r20
更新日期:2012-01-01 00:00:00
abstract::Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a ma...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1437-x
更新日期:2018-06-01 00:00:00
abstract::How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approa...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-10-reviews1029
更新日期:2002-09-19 00:00:00
abstract::The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-7-r61
更新日期:2005-01-01 00:00:00
abstract::ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing infor...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-4-r29
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0677-2
更新日期:2015-05-30 00:00:00
abstract::High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-2-207
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensiv...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-1-r6
更新日期:2014-01-07 00:00:00
abstract:BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02190-1
更新日期:2020-11-25 00:00:00
abstract:BACKGROUND:The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial s...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r103
更新日期:2007-01-01 00:00:00
abstract::The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-2-205
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-8-r75
更新日期:2012-08-28 00:00:00
abstract::The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasingly reliable sequence-derived dates, and it may become possible ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2001-3-1-reviews0001
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1744-x
更新日期:2019-07-12 00:00:00
abstract:BACKGROUND:To understand the heterogeneous behaviors of individual cancer cells, it is essential to investigate gene expression levels as well as their divergence between different individual cells. Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analy...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0636-y
更新日期:2015-04-03 00:00:00
abstract::Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0680-7
更新日期:2015-05-28 00:00:00
abstract::Next-generation massively parallel sequencing technology provides a powerful new means of assessing rates and regulation of translation across an entire transcriptome. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2009-10-4-215
更新日期:2009-01-01 00:00:00
abstract::We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae: single deletion mutants, double mutants conferring 'synthetic' lethality and the 'TRIPLES' collection of mutants obtained by random transposon insertion. Over 100 experimental conditions have been tested and mo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2004-5-7-229
更新日期:2004-01-01 00:00:00
abstract::PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-020-02221-x
更新日期:2021-01-08 00:00:00
abstract:BACKGROUND:Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-4-r28
更新日期:2012-04-24 00:00:00
abstract::Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...
journal_title:Genome biology
pub_type: 评论,信件
doi:10.1186/s13059-015-0709-y
更新日期:2015-07-11 00:00:00
abstract::Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-5-212
更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symb...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-6-r36
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE dis...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-7-preprint0006
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0578-9
更新日期:2015-01-29 00:00:00
abstract::Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-7-r58
更新日期:2006-01-01 00:00:00
abstract::The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific oppo...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-4-r39
更新日期:2013-04-29 00:00:00
abstract:BACKGROUND:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-3-r53
更新日期:2014-03-25 00:00:00