Chromatin organization is a major influence on regional mutation rates in human cancer cells

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Nature

• Publication date

  2012-07-22

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1038/nature11273PMID 22820252
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The large‐scale distribution of somatic mutations in cancer genomes

  2012cited by this paper
• The UCSC Genome Browser database: extensions and updates 2013

  2012cited by this paper
• The UCSC Genome Browser database: extensions and updates 2011

  2011cited by this paper
• A high-resolution map of human evolutionary constraint using 29 mammals

  2011cited by this paper
• Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

  2011cited by this paper
• Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome

  2011cited by this paper
• Quantifying the Variation in the Effective Population Size Within a Genome

  2011cited by this paper
• The mutation spectrum revealed by paired genome sequences from a lung cancer patient

  2010cited by this paper
• A comprehensive catalogue of somatic mutations from a human cancer genome

  2010cited by this paper
• A map of human genome variation from population-scale sequencing

  2010cited by this paper
• The genomic complexity of primary human prostate cancer

  2010cited by this paper
• Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

  2009cited by this paper
• A small cell lung cancer genome reports complex tobacco exposure signatures

  2009cited by this paper
• Human mutation rate associated with DNA replication timing

  2009cited by this paper
• Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

  2009cited by this paper
• Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq

  2008cited by this paper
• ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin.

  2008cited by this paper
• Dynamic regulation of nucleosome positioning in the human genome.

  2008cited by this paper
• Combinatorial patterns of histone acetylations and methylations in the human genome

  2008cited by this paper
• DNA sequencing of a cytogenetically normal acute myeloid leukemia genome

  2008cited by this paper
• Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.

  2008cited by this paper
• Chromatin structure and evolution in the human genome

  2007cited by this paper
• High-resolution profiling of histone methylations in the human genome.

  2007cited by this paper
• Beyond the sequence: cellular organization of genome function.

  2007cited by this paper
• Database resources of the National Center for Biotechnology Information

  2006cited by this paper
• Cellular machineries for chromosomal DNA repair.

  2004cited by this paper
• Mutation rate variation in the mammalian genome.

  2003cited by this paper
• A high-resolution recombination map of the human genome

  2002cited by this paper
• Human SNP variability and mutation rate are higher in regions of high recombination.

  2002cited by this paper
• Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes

  1989cited by this paper
• Mutation rates differ among regions of the mammalian genome

  1989cited by this paper

• Predicting mutation-rate variation across the genome using epigenetic data

  2026cites this paper
• Mutation Rate Variation Across Genomic Regions in \textit{Arabidopsis thaliana}

  2026cites this paper
• Non-B DNA structures and their contributions to genetic diversity, aging, and disease

  2026cites this paper
• Epimutations: raw material for evolution?

  2026cites this paper
• Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability

  2025cites this paper
• SKI regulates rRNA transcription and pericentromeric heterochromatin to ensure centromere integrity and genome stability

  2025cites this paper
• Checkpoint Blockade Combinations in High Tumor Mutational Burden/Load Tumors: Insights from the Atezolizumab + Bevacizumab and Nivolumab + Ipilimumab Cohorts in DRUP.

  2025cites this paper
• Improved genome assembly of whale shark, the world’s biggest fish: revealing “chromocline” in intragenomic heterogeneity

  2025cites this paper
• Element-specific estimation of background mutation rates in whole cancer genomes through transfer learning

  2025cites this paper
• Triple-positive breast cancer: navigating heterogeneity and advancing multimodal therapies for improving patient outcomes

  2025cites this paper
• The Noncoding Mutational Landscape of Pancreatic Cancer Reveals Recurrent Somatic Mutations in Enhancer Regions

  2025cites this paper
• Reconstructing the lifelong history of cells and tissues via somatic mutation analysis

  2025cites this paper
• Lysine Acetyltransferase 6 in Health and Disease

  2025cites this paper
• A predictive chromatin architecture nexus regulates transcription and DNA damage repair

  2025cites this paper
• Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes

  2025cites this paper
• Passenger mutations link cellular origin and transcriptional identity in human lung adenocarcinomas

  2025cites this paper
• Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organization

  2025cites this paper
• Biologically-informed regional subset analysis with CatBoost for robust tissue-of-origin prediction

  2025cites this paper
• The Potential of NGTs to Overcome Constraints in Plant Breeding and Their Regulatory Implications

  2025cites this paper
• Poisson process factorization for mutational signature analysis with genomic covariates

  2025cites this paper
• Influence of H3K9 methylation on gene mutation rates in yeast: Advancing epigenetic research with controlled experimental design.

  2025cites this paper
• Transposable elements and heterochromatic regions are enriched for structural variation and sequence divergence in the genome of wild-type Caenorhabditis elegans

  2025cites this paper
• Transcription start sites experience a high influx of heritable variants fueled by early development

  2025cites this paper
• Clinical implications of DNA ploidy, stroma, and nucleotyping in predicting peritoneal metastasis risk for gastric cancer

  2025cites this paper
• SATB1 in cancer progression and metastasis: mechanisms and therapeutic potential

  2025cites this paper
• TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states

  2025cites this paper
• Evaluating topography of mutational signatures with SigProfilerTopography

  2025cites this paper
• Genetic determinants and genomic consequences of non-leukemogenic somatic point mutations

  2025influential citation
• Linear covariation between germline and somatic mutation rates across ciliates and mammals.

  2025cites this paper
• Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast

  2025cites this paper
• The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations

  2024cites this paper
• Sodium arsenite-induced DNA methylation alterations exacerbated by p53 knockout in MCF7 cells

  2024cites this paper
• OpenNucleome for high-resolution nuclear structural and dynamical modeling

  2024cites this paper
• Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair

  2024cites this paper
• Chromosomal instability is associated with prognosis and efficacy of bevacizumab after resection of colorectal cancer liver metastasis

  2024cites this paper
• Cancer treatment monitoring using cell-free DNA fragmentomes

  2024cites this paper
• Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations

  2024influential citation
• Exploring prognostic values of DNA ploidy, stroma-tumor fraction and nucleotyping in stage II colon cancer patients

  2024cites this paper
• Combination of DNA ploidy, stroma, and nucleotyping predicting prognosis and tailoring adjuvant chemotherapy duration in stage III colon cancer

  2024cites this paper
• Clinical Interest in Exome-Based Analysis of Somatic Mutational Signatures for Non-Small Cell Lung Cancer

  2024cites this paper
• Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers

  2024cites this paper
• Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer

  2024cites this paper
• Identifying key genes in cancer networks using persistent homology

  2024cites this paper
• ERCC2 mutations alter the genomic distribution pattern of somatic mutations and are independently prognostic in bladder cancer

  2024cites this paper
• HJURP is recruited to double-strand break sites and facilitates DNA repair by promoting chromatin reorganization

  2024cites this paper
• Convergent evolution of epigenome recruited DNA repair across the Tree of Life

  2024cites this paper
• Comparing the predictors of mutability among healthy human tissues inferred from mutations in single cell genome data

  2024cites this paper
• Tissue-Predisposition to Cancer Driver Mutations

  2024cites this paper
• [Heterochromatin and epigenetic control of repeat sequences].

  2024cites this paper
• Evaluating topography of mutational signatures with SigProfilerTopography

  2024cites this paper
• H3K4me1 recruits DNA repair proteins in plants.

  2024cites this paper
• Extrinsic and intrinsic drivers of natural killer cell clonality

  2024cites this paper
• MoCoLo: a testing framework for motif co-localization

  2024cites this paper
• DNA Repair in Nucleosomes: Insights from Histone Modifications and Mutants

  2024cites this paper
• High-Resolution Genomic Profiling of Liver Cancer Links Etiology With Mutation and Epigenetic Signatures

  2023cites this paper
• Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico

  2023cites this paper
• Epigenetic inheritance in adaptive evolution

  2023cites this paper
• Genome-wide contributions of the MutSα- and MutSβ-dependent DNA mismatch repair pathways to the maintenance of genetic stability in Saccharomyces cerevisiae

  2023cites this paper
• A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH

  2023cites this paper
• Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs in A. thaliana

  2023cites this paper
• The frequency of somatic mutations in cancer predicts the phenotypic relevance of germline mutations

  2023cites this paper
• Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation

  2023cites this paper
• Prognostic analysis of mutated genes and insight into effects of DNA damage and repair on mutational strand asymmetries in gastric cancer

  2023cites this paper
• Reactions of deoxyribonucleotide bases with sulfooxymethyl or halomethyl polycyclic aromatic hydrocarbons induce unwinding of DNA supercoils

  2023cites this paper
• Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements

  2023cites this paper
• The genetic determinants of recurrent somatic mutations in 43,693 blood genomes

  2023cites this paper
• Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs.

  2023cites this paper
• Stem cell mutations, associated cancer risk, and consequences for regenerative medicine

  2023cites this paper
• Predicting regional somatic mutation rates using DNA motifs

  2023cites this paper
• Methylation across the central dogma in health and diseases: new therapeutic strategies

  2023cites this paper
• Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

  2023cites this paper
• OpenNucleome for high resolution nuclear structural and dynamical modeling

  2023cites this paper
• Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation

  2023cites this paper
• Developmental priming of cancer susceptibility

  2023cites this paper
• Regularized sequence-context mutational trees capture variation in mutation rates across the human genome

  2023cites this paper
• Hotspot propensity across mutational processes

  2023cites this paper
• The impact of chromatin on double-strand break repair: Imaging tools and discoveries.

  2023cites this paper
• Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa

  2023cites this paper
• Topography of mutational signatures in human cancer

  2023cites this paper
• AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples

  2023cites this paper
• Prognostic Value of Chromatin Structure Typing in Early-Stage Non-Small Cell Lung Cancer

  2023cites this paper
• Mitigating age-related somatic mutation burden

  2023cites this paper
• Cell-type specificity of the human mutation landscape with respect to DNA replication dynamics

  2023cites this paper
• Chromosome damage in regions with different levels of air pollution

  2023cites this paper
• Genomic mutation landscape of skin cancers from DNA repair-deficient xeroderma pigmentosum patients

  2023cites this paper
• Boveri and beyond: Chromothripsis and genomic instability from mitotic errors.

  2023cites this paper
• Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver events of human cancer

  2023cites this paper
• The Adaptability of Chromosomal Instability in Cancer Therapy and Resistance

  2022cites this paper
• A 3D genome atlas of genetic variants and their pathological effects

  2022cites this paper
• Regional mutational signature activities in cancer genomes

  2022cites this paper
• DNA replication initiation shapes the mutational landscape and expression of the human genome

  2022cites this paper
• The H3K4me1 histone mark recruits DNA repair to functionally constrained genomic regions in plants

  2022cites this paper
• Form and function of archaeal genomes

  2022cites this paper
• Multilevel view on chromatin architecture alterations in cancer

  2022cites this paper
• Analysis of Skin Cancers from Xeroderma Pigmentosum Patients Reveals Heterogeneous UV-Induced Mutational Profiles Shaped by DNA Repair

  2022cites this paper
• Multifactorial heterogeneity of the human mutation landscape related to DNA replication dynamics

  2022cites this paper
• Mechanisms governing the accessibility of DNA damage proteins to constitutive heterochromatin

  2022cites this paper
• Effects of replication domains on genome-wide UV-induced DNA damage and repair

  2022cites this paper
• Redistribution of mutation rates across chromosomal domains in human 1 cancer genomes 2

  2022cites this paper
• Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin

  2022cites this paper