Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells.

PubWeight™: 1.88‹?› | Rank: Top 3%

🔗 View Article (PMID 26871630)

Published in Cell on February 11, 2016

Authors

Pei-Chi Wei1, Amelia N Chang1, Jennifer Kao1, Zhou Du1, Robin M Meyers1, Frederick W Alt2, Bjoern Schwer3

Author Affiliations

1: Program in Cellular and Molecular Medicine, Boston Children's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
2: Program in Cellular and Molecular Medicine, Boston Children's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: alt@enders.tch.harvard.edu.
3: Program in Cellular and Molecular Medicine, Boston Children's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: bjoern.schwer@childrens.harvard.edu.

Articles citing this

Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A (2016) 0.96

High-resolution copy number variation analysis of schizophrenia in Japan. Mol Psychiatry (2016) 0.87

ZIKA virus elicits P53 activation and genotoxic stress in human neural progenitors similar to mutations involved in severe forms of genetic microcephaly and p53. Cell Death Dis (2016) 0.86

PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line. Proc Natl Acad Sci U S A (2016) 0.85

Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc (2016) 0.83

DNA polymerase θ (POLQ), double-strand break repair, and cancer. DNA Repair (Amst) (2016) 0.81

Conflict Resolution in the Genome: How Transcription and Replication Make It Work. Cell (2016) 0.81

Highly sensitive and unbiased approach for elucidating antibody repertoires. Proc Natl Acad Sci U S A (2016) 0.80

ATM-dependent pathways of chromatin remodelling and oxidative DNA damage responses. Philos Trans R Soc Lond B Biol Sci (2017) 0.79

Mosaicism in health and disease - clones picking up speed. Nat Rev Genet (2016) 0.79

When Genome Maintenance Goes Badly Awry. Mol Cell (2016) 0.77

Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry. Cell (2017) 0.76

A Mechanism for Somatic Brain Mosaicism. Cell (2016) 0.76

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science (2017) 0.76

Rescue from replication stress during mitosis. Cell Cycle (2017) 0.75

Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex is modulated by DNA end chemistry. Nucleic Acids Res (2016) 0.75

Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Res (2016) 0.75

Molecular biology: Breaks in the brain. Nature (2016) 0.75

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes. Nat Struct Mol Biol (2017) 0.75

Shining a light on early stress responses and late-onset disease vulnerability. Proc Natl Acad Sci U S A (2017) 0.75

A Signature of Genomic Instability Resulting from Deficient Replication Licensing. PLoS Genet (2017) 0.75

Activity-DEPendent Transposition. EMBO Rep (2017) 0.75

Tumor Suppressor Genes within Common Fragile Sites Are Active Players in the DNA Damage Response. PLoS Genet (2016) 0.75

Neurogenomics and the role of a large mutational target on rapid behavioral change. Biol Direct (2016) 0.75

Transcription-associated events affecting genomic integrity. Philos Trans R Soc Lond B Biol Sci (2017) 0.75

Environmental change drives accelerated adaptation through stimulated copy number variation. PLoS Biol (2017) 0.75

Transcription-replication conflicts at chromosomal fragile sites-consequences in M phase and beyond. Chromosoma (2016) 0.75

Retrotransposing Gremlins May Disrupt Our Brain's Genomes. Mol Syndromol (2016) 0.75

Fragile sites in cancer: more than meets the eye. Nat Rev Cancer (2017) 0.75

Genetic insights into the neurodevelopmental origins of schizophrenia. Nat Rev Neurosci (2017) 0.75

Physiological functions of programmed DNA breaks in signal-induced transcription. Nat Rev Mol Cell Biol (2017) 0.75

Examining non-LTR retrotransposons in the context of the evolving primate brain. BMC Biol (2017) 0.75

Expression and Structural Analyses of Human DNA Polymerase θ (POLQ). Methods Enzymol (2017) 0.75

TDP2 suppresses chromosomal translocations induced by DNA topoisomerase II during gene transcription. Nat Commun (2017) 0.75

Zika virus infection dysregulates human neural stem cell growth and inhibits differentiation into neuroprogenitor cells. Cell Death Dis (2017) 0.75

Articles cited by this

Integrative genomics viewer. Nat Biotechnol (2011) 42.83

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48

The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem (2010) 9.80

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33

Identification of a chromosome 18q gene that is altered in colorectal cancers. Science (1990) 8.32

A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription. Science (2006) 6.71

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell (2012) 6.07

Chromosome fragile sites. Annu Rev Genet (2007) 4.95

A critical role for DNA end-joining proteins in both lymphogenesis and neurogenesis. Cell (1998) 4.78

Interplay of p53 and DNA-repair protein XRCC4 in tumorigenesis, genomic stability and development. Nature (2000) 4.75

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res (2010) 4.67

Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol (2008) 4.50

Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocations. Cell (2002) 4.29

Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell (1983) 4.13

Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature (2012) 4.13

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell (2012) 4.02

Identification of early replicating fragile sites that contribute to genome instability. Cell (2013) 3.99

DNA ligase IV deficiency in mice leads to defective neurogenesis and embryonic lethality via the p53 pathway. Mol Cell (2000) 3.82

Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell (2011) 3.81

Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell (2011) 3.65

Mosaic copy number variation in human neurons. Science (2013) 3.57

Targeted disruption of the gene encoding DNA ligase IV leads to lethality in embryonic mice. Curr Biol (1999) 3.47

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol (2014) 2.99

DNA polymerase alpha inhibition by aphidicolin induces gaps and breaks at common fragile sites in human chromosomes. Hum Genet (1984) 2.92

Evidence for replicative repair of DNA double-strand breaks leading to oncogenic translocation and gene amplification. J Exp Med (2002) 2.86

Somatic mutation, genomic variation, and neurological disease. Science (2013) 2.72

Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol Cell (2011) 2.66

Antibody class switching mediated by yeast endonuclease-generated DNA breaks. Science (2006) 2.49

Generation of neuronal variability and complexity. Nature (2006) 2.39

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell (2015) 2.35

Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell (2013) 2.32

Topologically associating domains are stable units of replication-timing regulation. Nature (2014) 2.17

Transcription as a source of genome instability. Nat Rev Genet (2012) 1.94

Classical and alternative end-joining pathways for repair of lymphocyte-specific and general DNA double-strand breaks. Adv Immunol (2012) 1.83

Causes of genome instability. Annu Rev Genet (2013) 1.72

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. BMC Bioinformatics (2008) 1.51

Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell (2014) 1.43

Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes. Genome Res (2006) 1.40

XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient mice. Proc Natl Acad Sci U S A (2006) 1.38

Mobile DNA elements in the generation of diversity and complexity in the brain. Nat Rev Neurosci (2014) 1.35

DNA ligase IV suppresses medulloblastoma formation. Cancer Res (2002) 1.34

Mechanisms of ATM Activation. Annu Rev Biochem (2015) 1.33

Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes. Cell Rep (2013) 1.31

Maintaining genome stability in the nervous system. Nat Neurosci (2013) 1.24

The common fragile site FRA16D and its associated gene WWOX are highly conserved in the mouse at Fra8E1. Genes Chromosomes Cancer (2002) 1.22

Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes. Cell (2015) 1.17

Molecular profiling of common fragile sites in human fibroblasts. Nat Struct Mol Biol (2011) 1.14

De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining. PLoS Genet (2012) 1.07

Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching. Nature (2015) 1.05

Very large common fragile site genes and their potential role in cancer development. Cell Mol Life Sci (2014) 0.96

Unique and redundant functions of ATM and DNA-PKcs during V(D)J recombination. Cell Cycle (2011) 0.95

Updating the mechanisms of common fragile site instability: how to reconcile the different views? Cell Mol Life Sci (2014) 0.90

Characterization of FRA7B, a human common fragile site mapped at the 7p chromosome terminal region. Cancer Genet Cytogenet (2010) 0.85

Molecular characterization of common fragile sites as a strategy to discover cancer susceptibility genes. Cell Mol Life Sci (2014) 0.80