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1.
Mutat Res Rev Mutat Res ; 792: 108475, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37931775

RESUMO

Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.


Assuntos
Variação Estrutural do Genoma , Genômica , Humanos , Aberrações Cromossômicas , Genoma Humano , Análise de Sequência de DNA
2.
NAR Genom Bioinform ; 5(2): lqad042, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37181851

RESUMO

Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to comparable strategies for rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from samples with known SV properties, we demonstrate that duplex sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple source molecules. In contrast, tagmentation libraries coupled with data filtering based on strand family size greatly reduced both artifact classes and enabled efficient and specific detection of single-molecule SV junctions. The throughput of SV capture sequencing (svCapture) and base-level accuracy of DuplexSeq provided detailed views of the microhomology profile and limited occurrence of de novo SNVs near the junctions of hundreds of newly created SVs, suggesting end joining as a possible formation mechanism. The open source svCapture pipeline enables rare SV detection as a routine addition to SNVs/indels in properly prepared capture sequencing libraries.

3.
Nucleic Acids Res ; 49(13): 7507-7524, 2021 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-34181717

RESUMO

Impaired replication progression leads to de novo copy number variant (CNV) formation at common fragile sites (CFSs). We previously showed that these hotspots for genome instability reside in late-replicating domains associated with large transcribed genes and provided indirect evidence that transcription is a factor in their instability. Here, we compared aphidicolin (APH)-induced CNV and CFS frequency between wild-type and isogenic cells in which FHIT gene transcription was ablated by promoter deletion. Two promoter-deletion cell lines showed reduced or absent CNV formation and CFS expression at FHIT despite continued instability at the NLGN1 control locus. APH treatment led to critical replication delays that remained unresolved in G2/M in the body of many, but not all, large transcribed genes, an effect that was reversed at FHIT by the promoter deletion. Altering RNase H1 expression did not change CNV induction frequency and DRIP-seq showed a paucity of R-loop formation in the central regions of large genes, suggesting that R-loops are not the primary mediator of the transcription effect. These results demonstrate that large gene transcription is a determining factor in replication stress-induced genomic instability and support models that CNV hotspots mainly result from the transcription-dependent passage of unreplicated DNA into mitosis.


Assuntos
Hidrolases Anidrido Ácido/genética , Variações do Número de Cópias de DNA , Replicação do DNA , Proteínas de Neoplasias/genética , Transcrição Gênica , Hidrolases Anidrido Ácido/biossíntese , Animais , Afidicolina/farmacologia , Linhagem Celular , Sítios Frágeis do Cromossomo , Loci Gênicos , Humanos , Camundongos , Mutação , Proteínas de Neoplasias/biossíntese , Regiões Promotoras Genéticas , Estruturas R-Loop , Ribonuclease H/metabolismo , Estresse Fisiológico
4.
Cell Res ; 30(11): 944-945, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32665662
5.
Hum Genet ; 137(11-12): 921-939, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30450527

RESUMO

Juvenile segmental progeroid syndromes are rare, heterogeneous disorders characterized by signs of premature aging affecting more than one tissue or organ starting in childhood. Hutchinson-Gilford progeria syndrome (HGPS), caused by a recurrent de novo synonymous LMNA mutation resulting in aberrant splicing and generation of a mutant product called progerin, is a prototypical example of such disorders. Here, we performed a joint collaborative study using massively parallel sequencing and targeted Sanger sequencing, aimed at delineating the underlying genetic cause of 14 previously undiagnosed, clinically heterogeneous, non-LMNA-associated juvenile progeroid patients. The molecular diagnosis was achieved in 11 of 14 cases (~ 79%). Furthermore, we firmly establish biallelic mutations in POLR3A as the genetic cause of a recognizable, neonatal, Wiedemann-Rautenstrauch-like progeroid syndrome. Thus, we suggest that POLR3A mutations are causal for a portion of under-diagnosed early-onset segmental progeroid syndromes. We additionally expand the clinical spectrum associated with PYCR1 mutations by showing that they can somewhat resemble HGPS in the first year of life. Moreover, our results lead to clinical reclassification in one single case. Our data emphasize the complex genetic and clinical heterogeneity underlying progeroid disorders.


Assuntos
Retardo do Crescimento Fetal/genética , Progéria/genética , Pirrolina Carboxilato Redutases/genética , RNA Polimerase III/genética , Adolescente , Processamento Alternativo/genética , Criança , Feminino , Retardo do Crescimento Fetal/diagnóstico , Retardo do Crescimento Fetal/patologia , Predisposição Genética para Doença , Humanos , Lactente , Lamina Tipo A/genética , Masculino , Mutação , Fenótipo , Progéria/diagnóstico , Progéria/patologia , Progéria/fisiopatologia , delta-1-Pirrolina-5-Carboxilato Redutase
6.
Environ Mol Mutagen ; 59(8): 698-714, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30218578

RESUMO

Copy number variants (CNVs) are important in genome variation and genetic disease, with new mutations arising frequently in the germline and somatic cells. Replication stress caused by aphidicolin and hydroxyurea (HU) is a potent inducer of de novo CNVs in cultured mammalian cells. HU is used extensively for long-term management of sickle cell disease. Here, we examined the effects of HU treatment on germline CNVs in vivo in male mice to explore whether replication stress can act as a CNV mutagen in germline mitotic divisions as in cultured cells and whether this would support a concern for increased CNV mutations in offspring of men treated with HU. Several trials of HU administration were performed by oral gavage and subcutaneous pump, with CNVs characterized in C57BL/6 x C3H/HeJ hybrid mouse offspring by microarray and mate-pair sequencing. HU had a short half-life of ~14 min and a narrow dose window over which studies could be performed while maintaining fertility. Tissue histopathology and reticulocyte micronucleus assays verified that doses had a substantial tissue and genetic toxicity. CNVs were readily detected in offspring that originated in both paternal and maternal mouse strains, as de novo and inherited events. However, HU did not increase CNV formation above baseline levels. These results reveal a high rate of CNV mutagenesis in the mouse germline but do not support the hypothesis that HU would increase CNV formation during mammalian spermatogenesis, perhaps due to highly toxic effects on sperm development or experimental variables related to HU pharmacology in mice. Environ. Mol. Mutagen. 59:698-714, 2018. © 2018 Wiley Periodicals, Inc.


Assuntos
Variações do Número de Cópias de DNA/genética , Replicação do DNA/genética , Células Germinativas/efeitos dos fármacos , Hidroxiureia/toxicidade , Espermatogênese/efeitos dos fármacos , Espermatozoides/crescimento & desenvolvimento , Animais , Variações do Número de Cópias de DNA/efeitos dos fármacos , Dano ao DNA/efeitos dos fármacos , Dano ao DNA/genética , Replicação do DNA/efeitos dos fármacos , Masculino , Camundongos , Camundongos Endogâmicos C3H , Camundongos Endogâmicos C57BL
7.
Nat Rev Cancer ; 17(8): 489-501, 2017 07 25.
Artigo em Inglês | MEDLINE | ID: mdl-28740117

RESUMO

Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.


Assuntos
Instabilidade Cromossômica , Sítios Frágeis do Cromossomo , Variações do Número de Cópias de DNA , Neoplasias/genética , Oncogenes/genética , Anáfase , Animais , Quebra Cromossômica , Quebras de DNA de Cadeia Dupla , Replicação do DNA , Rearranjo Gênico , Humanos , Metáfase
8.
Head Neck ; 39(5): 840-852, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-28236344

RESUMO

BACKGROUND: Human papillomavirus (HPV)-positive oropharyngeal cancer is generally associated with excellent response to therapy, but some HPV-positive tumors progress despite aggressive therapy. The purpose of this study was to evaluate viral oncogene expression and viral integration sites in HPV16- and HPV18-positive squamous cell carcinoma lines. METHODS: E6/E7 alternate transcripts were assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Detection of integrated papillomavirus sequences (DIPS-PCR) and sequencing identified viral insertion sites and affected host genes. Cellular gene expression was assessed across viral integration sites. RESULTS: All HPV-positive cell lines expressed alternate HPVE6/E7 splicing indicative of active viral oncogenesis. HPV integration occurred within cancer-related genes TP63, DCC, JAK1, TERT, ATR, ETV6, PGR, PTPRN2, and TMEM237 in 8 head and neck squamous cell carcinoma (HNSCC) lines but UM-SCC-105 and UM-GCC-1 had only intergenic integration. CONCLUSION: HPV integration into cancer-related genes occurred in 7 of 9 HPV-positive cell lines and of these 6 were from tumors that progressed. HPV integration into cancer-related genes may be a secondary carcinogenic driver in HPV-driven tumors. © 2017 Wiley Periodicals, Inc. Head Neck 39: 840-852, 2017.


Assuntos
Carcinoma de Células Escamosas/virologia , Neoplasias de Cabeça e Pescoço/virologia , Papillomavirus Humano 16/fisiologia , Papillomavirus Humano 18/fisiologia , Integração Viral/fisiologia , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/patologia , Técnicas de Cultura de Células , Linhagem Celular Tumoral , Neoplasias de Cabeça e Pescoço/genética , Neoplasias de Cabeça e Pescoço/patologia , Humanos , Proteínas Oncogênicas Virais/metabolismo
9.
JIMD Rep ; 34: 55-61, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-27518780

RESUMO

Holocarboxylase synthetase (HLCS) deficiency is a rare autosomal recessive disorder that presents with multiple life-threatening metabolic derangements including metabolic acidosis, ketosis, and hyperammonemia. A majority of HLCS deficiency patients respond to biotin therapy; however, some patients show only a partial or no response to biotin therapy. Here, we report a neonatal presentation of HLCS deficiency with partial response to biotin therapy. Sequencing of HLCS showed a novel heterozygous mutation in exon 5, c.996G>C (p.Gln332His), which likely abolishes the normal intron 6 splice donor site. Cytogenetic analysis revealed that the defect of the other allele is a paracentric inversion on chromosome 21 that disrupts HLCS. This case illustrates that in addition to facilitating necessary family testing, a molecular diagnosis can optimize management by providing a better explanation of the enzyme's underlying defect. It also emphasizes the potential benefit of a karyotype in cases in which molecular genetic testing fails to provide an explanation.

10.
J Med Genet ; 54(3): 212-216, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27920058

RESUMO

BACKGROUND: Hutchinson-Gilford progeria syndrome (HGPS) is a fatal sporadic autosomal dominant premature ageing disease caused by single base mutations that optimise a cryptic splice site within exon 11 of the LMNA gene. The resultant disease-causing protein, progerin, acts as a dominant negative. Disease severity relies partly on progerin levels. METHODS AND RESULTS: We report a novel form of somatic mosaicism, where a child possessed two cell populations with different HGPS disease-producing mutations of the same nucleotide-one producing severe HGPS and one mild HGPS. The proband possessed an intermediate phenotype. The mosaicism was initially discovered when Sanger sequencing showed a c.1968+2T>A mutation in blood DNA and a c.1968+2T>C in DNA from cultured fibroblasts. Deep sequencing of DNA from the proband's blood revealed 4.7% c.1968+2T>C mutation, and 41.3% c.1968+2T>A mutation. CONCLUSIONS: We hypothesise that the germline mutation was c.1968+2T>A, but a rescue event occurred during early development, where the somatic mutation from A to C at 1968+2 provided a selective advantage. This type of mosaicism where a partial phenotypic rescue event results from a second but milder disease-causing mutation in the same nucleotide has not been previously characterised for any disease.


Assuntos
Núcleo Celular/genética , Lamina Tipo A/genética , Progéria/genética , Adolescente , Núcleo Celular/patologia , Células Cultivadas , Criança , Pré-Escolar , Éxons/genética , Feminino , Fibroblastos/patologia , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Lactente , Masculino , Mosaicismo , Progéria/patologia
11.
Nature ; 532(7597): 46-7, 2016 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-27007850
12.
Genome Res ; 25(2): 189-200, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25373142

RESUMO

Copy number variants (CNVs) resulting from genomic deletions and duplications and common fragile sites (CFSs) seen as breaks on metaphase chromosomes are distinct forms of structural chromosome instability precipitated by replication inhibition. Although they share a common induction mechanism, it is not known how CNVs and CFSs are related or why some genomic loci are much more prone to their occurrence. Here we compare large sets of de novo CNVs and CFSs in several experimental cell systems to each other and to overlapping genomic features. We first show that CNV hotpots and CFSs occurred at the same human loci within a given cultured cell line. Bru-seq nascent RNA sequencing further demonstrated that although genomic regions with low CNV frequencies were enriched in transcribed genes, the CNV hotpots that matched CFSs specifically corresponded to the largest active transcription units in both human and mouse cells. Consistently, active transcription units >1 Mb were robust cell-type-specific predictors of induced CNV hotspots and CFS loci. Unlike most transcribed genes, these very large transcription units replicated late and organized deletion and duplication CNVs into their transcribed and flanking regions, respectively, supporting a role for transcription in replication-dependent lesion formation. These results indicate that active large transcription units drive extreme locus- and cell-type-specific genomic instability under replication stress, resulting in both CNVs and CFSs as different manifestations of perturbed replication dynamics.


Assuntos
Sítios Frágeis do Cromossomo , Variações do Número de Cópias de DNA , Replicação do DNA , Transcrição Gênica , Animais , Linhagem Celular , Quebra Cromossômica , Mapeamento Cromossômico , Loci Gênicos , Instabilidade Genômica , Humanos , Hibridização in Situ Fluorescente , Camundongos , Especificidade de Órgãos , Reprodutibilidade dos Testes
13.
Cancer Genet ; 207(4): 133-40, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24813807

RESUMO

It has emerged that palindrome-mediated genomic instability generates DNA-based rearrangements. The presence of palindromic AT-rich repeats (PATRRs) at the translocation breakpoints suggested a palindrome-mediated mechanism in the generation of several recurrent constitutional rearrangements: the t(11;22), t(17;22), and t(8;22). To date, all reported PATRR-mediated translocations include the PATRR on chromosome 22 (PATRR22) as a translocation partner. Here, the constitutional rearrangement, t(3;8)(p14.2;q24.1), segregating with renal cell carcinoma in two families, is examined. The chromosome 8 breakpoint lies in PATRR8 in the first intron of the RNF139 (TRC8) gene, whereas the chromosome 3 breakpoint is located in an AT-rich palindromic sequence in intron 3 of the FHIT gene (PATRR3). Thus, the t(3;8) is the first PATRR-mediated, recurrent, constitutional translocation that does not involve PATRR22. Furthermore, we detect de novo translocations similar to the t(11;22) and t(8;22), involving PATRR3 in normal sperm. The breakpoint on chromosome 3 is in proximity to FRA3B, the most common fragile site in the human genome and a site of frequent deletions in tumor cells. However, the lack of involvement of PATRR3 sequence in numerous FRA3B-related deletions suggests that there are several different DNA sequence-based etiologies responsible for chromosome 3p14.2 genomic rearrangements.


Assuntos
Carcinoma de Células Renais/genética , Cromossomos Humanos Par 3/genética , Cromossomos Humanos Par 8/genética , Neoplasias Renais/genética , Translocação Genética , Sequência Rica em At/genética , Hidrolases Anidrido Ácido/genética , Animais , Sequência de Bases , Carcinoma de Células Renais/patologia , Linhagem Celular , Pontos de Quebra do Cromossomo , Humanos , Sequências Repetidas Invertidas/genética , Neoplasias Renais/patologia , Masculino , Camundongos , Dados de Sequência Molecular , Proteínas de Neoplasias/genética , Receptores de Superfície Celular/genética , Análise de Sequência de DNA
14.
Environ Mol Mutagen ; 55(2): 103-13, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24327335

RESUMO

Despite their importance to human genetic variation and disease, little is known about the molecular mechanisms and environmental risk factors that impact copy number variant (CNV) formation. While it is clear that replication stress can lead to de novo CNVs, for example, following treatment of cultured mammalian cells with aphidicolin (APH) and hydroxyurea (HU), the effect of different types of mutagens on CNV induction is unknown. Here we report that ionizing radiation (IR) in the range of 1.5-3.0 Gy effectively induces de novo CNV mutations in cultured normal human fibroblasts. These IR-induced CNVs are found throughout the genome, with the same hotspot regions seen after APH- and HU-induced replication stress. IR produces duplications at a higher frequency relative to deletions than do APH and HU. At most hotspots, these duplications are physically shifted from the regions typically deleted after APH or HU, suggesting different pathways involved in their formation. CNV breakpoint junctions from irradiated samples are characterized by microhomology, blunt ends, and insertions like those seen in spontaneous and APH/HU-induced CNVs and most nonrecurrent CNVs in vivo. The similarity to APH/HU-induced CNVs suggests that low-dose IR induces CNVs through a replication-dependent mechanism, as opposed to replication-independent repair of DSBs. Consistent with this mechanism, a lower yield of CNVs was observed when cells were held for 48 hr before replating after irradiation. These results predict that any environmental DNA damaging agent that impairs replication is capable of creating CNVs.


Assuntos
Variações do Número de Cópias de DNA/efeitos da radiação , Pontos de Checagem do Ciclo Celular , Linhagem Celular , Pontos de Quebra do Cromossomo , Replicação do DNA , Fibroblastos/citologia , Fibroblastos/efeitos da radiação , Deleção de Genes , Duplicação Gênica , Genoma Humano , Humanos , Polimorfismo de Nucleotídeo Único
15.
Am J Med Genet A ; 161A(8): 1882-96, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23824832

RESUMO

Deletion of the distal segment of 9p causes a syndrome comprising trigonocephaly, minor anomalies, and intellectual disability. Patients with this condition also frequently present with genitourinary abnormalities including cryptorchidism, hypospadias, ambiguous genitalia, or 46,XY testicular dysgenesis. The region responsible for the gonadal dysgenesis has been localized to 9p24.3 with the likely responsible gene identified as DMRT1. Similar to patients with other molecular causes of 46,XY gonadal dysgenesis, patients with partial del 9p have an increased risk of gonadoblastoma. We present two patients with 46,XY gonadal dysgenesis due to partial 9p monosomy. Both patients were also diagnosed with gonadoblastoma following gonadectomy at an early age. Chromosomal microarray analyses refined the cytogenetic abnormalities and allowed potential genotype-phenotype relationships to be determined. We also review the literature as it pertains to partial 9p monosomy, genital abnormalities and gonadoblastoma and note that a large percentage of affected patients present with two copy number variations. We propose that a two-hit mechanism may be involved in the incomplete penetrance and variable expressivity of partial 9p monosomy and an abnormal genital phenotype. The significant percentage of gonadoblastoma in patients with 46,XY complete gonadal dysgenesis due to partial 9p monosomy also continues to support the necessity of gonadectomy in this patient population.


Assuntos
Disgenesia Gonadal 46 XY/genética , Gonadoblastoma/genética , Deleção Cromossômica , Cromossomos Humanos Par 9/genética , Feminino , Disgenesia Gonadal 46 XY/patologia , Gonadoblastoma/patologia , Humanos , Lactente , Recém-Nascido , Cariotipagem , Literatura de Revisão como Assunto
16.
Hum Mol Genet ; 22(24): 4901-13, 2013 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-23863462

RESUMO

SNM1B/Apollo is a DNA nuclease that has important functions in telomere maintenance and repair of DNA interstrand crosslinks (ICLs) within the Fanconi anemia (FA) pathway. SNM1B is required for efficient localization of key repair proteins, such as the FA protein, FANCD2, to sites of ICL damage and functions epistatically to FANCD2 in cellular survival to ICLs and homology-directed repair. The FA pathway is also activated in response to replication fork stalling. Here, we sought to determine the importance of SNM1B in cellular responses to stalled forks in the absence of a blocking lesion, such as ICLs. We found that depletion of SNM1B results in hypersensitivity to aphidicolin, a DNA polymerase inhibitor that causes replication stress. We observed that the SNM1B nuclease is required for efficient localization of the DNA repair proteins, FANCD2 and BRCA1, to subnuclear foci upon aphidicolin treatment, thereby indicating SNM1B facilitates direct repair of stalled forks. Consistent with a role for SNM1B subsequent to recognition of the lesion, we found that SNM1B is dispensable for upstream events, including activation of ATR-dependent signaling and localization of RPA, γH2AX and the MRE11/RAD50/NBS1 complex to aphidicolin-induced foci. We determined that a major consequence of SNM1B depletion is a marked increase in spontaneous and aphidicolin-induced chromosomal gaps and breaks, including breakage at common fragile sites. Thus, this study provides evidence that SNM1B functions in resolving replication stress and preventing accumulation of genomic damage.


Assuntos
Sítios Frágeis do Cromossomo , Enzimas Reparadoras do DNA/metabolismo , Replicação do DNA , Instabilidade Genômica , Proteínas Nucleares/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Afidicolina/farmacologia , Proteína BRCA1/metabolismo , Linhagem Celular , Núcleo Celular/metabolismo , Sobrevivência Celular/efeitos dos fármacos , Sobrevivência Celular/genética , Cromatina/metabolismo , Dano ao DNA , Reparo do DNA , Enzimas Reparadoras do DNA/química , Enzimas Reparadoras do DNA/genética , Exodesoxirribonucleases , Proteína do Grupo de Complementação D2 da Anemia de Fanconi/metabolismo , Expressão Gênica , Histonas/metabolismo , Humanos , Complexos Multiproteicos/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/genética , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Transporte Proteico , Proteína de Replicação A/metabolismo , Transdução de Sinais/efeitos dos fármacos , Ubiquitinação
17.
Cancer Cell ; 23(2): 137-9, 2013 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-23410970

RESUMO

Chromosome rearrangements in B lymphocytes can be initiated by AID-associated double strand breaks (DSBs), with others arising by unclear mechanisms. A recent study by Barlow and colleagues in Cell reports on genomic regions, termed early replicating fragile sites, that may explain many AID-independent DSBs and creates a compelling link between replication stress, transcription, and chromosome rearrangements.

18.
Mutat Res ; 752(1): 6-9, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-22935230

RESUMO

Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis (ENIGMA) met in October 2011 to propose the necessary foundational studies, which include sequencing of parent-offspring trios from highly exposed human populations, and controlled dose-response experiments in animals. These studies will establish background levels of variability in germline mutation rates and identify environmental agents that influence these rates and heritable disease. Guidance for the types of exposures to examine come from rodent studies that have identified agents such as cancer chemotherapeutic drugs, ionizing radiation, cigarette smoke, and air pollution as germ-cell mutagens. Research is urgently needed to establish the health consequences of parental exposures on subsequent generations.


Assuntos
Interação Gene-Ambiente , Doenças Genéticas Inatas/genética , Genômica , Animais , Poluentes Ambientais/toxicidade , Mutação em Linhagem Germinativa , Humanos , Efeitos da Radiação , Produtos do Tabaco/efeitos adversos
19.
PLoS Genet ; 8(9): e1002981, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23028374

RESUMO

Spontaneous copy number variant (CNV) mutations are an important factor in genomic structural variation, genomic disorders, and cancer. A major class of CNVs, termed nonrecurrent CNVs, is thought to arise by nonhomologous DNA repair mechanisms due to the presence of short microhomologies, blunt ends, or short insertions at junctions of normal and de novo pathogenic CNVs, features recapitulated in experimental systems in which CNVs are induced by exogenous replication stress. To test whether the canonical nonhomologous end joining (NHEJ) pathway of double-strand break (DSB) repair is involved in the formation of this class of CNVs, chromosome integrity was monitored in NHEJ-deficient Xrcc4(-/-) mouse embryonic stem (ES) cells following treatment with low doses of aphidicolin, a DNA replicative polymerase inhibitor. Mouse ES cells exhibited replication stress-induced CNV formation in the same manner as human fibroblasts, including the existence of syntenic hotspot regions, such as in the Auts2 and Wwox loci. The frequency and location of spontaneous and aphidicolin-induced CNV formation were not altered by loss of Xrcc4, as would be expected if canonical NHEJ were the predominant pathway of CNV formation. Moreover, de novo CNV junctions displayed a typical pattern of microhomology and blunt end use that did not change in the absence of Xrcc4. A number of complex CNVs were detected in both wild-type and Xrcc4(-/-) cells, including an example of a catastrophic, chromothripsis event. These results establish that nonrecurrent CNVs can be, and frequently are, formed by mechanisms other than Xrcc4-dependent NHEJ.


Assuntos
Variações do Número de Cópias de DNA/genética , Reparo do DNA por Junção de Extremidades/genética , Proteínas de Ligação a DNA/genética , Células-Tronco Embrionárias , Animais , Afidicolina/farmacologia , Proteínas do Citoesqueleto , Quebras de DNA de Cadeia Dupla , Replicação do DNA/efeitos dos fármacos , Humanos , Camundongos , Proteínas Nucleares/genética , Oxirredutases/genética , Fatores de Transcrição , Oxidorredutase com Domínios WW
20.
Am J Med Genet A ; 158A(10): 2591-601, 2012 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22903861

RESUMO

We identified a novel 6.33 Mb deletion of 1q21.3q23.3 (hg18; chr1: 153035245-159367106) in two siblings presenting with blepharophimosis, ptosis, microbrachycephaly, severe psychomotor, and intellectual disability. Additional common features include small corpus callosum, normal birth length and head circumference, postnatal growth restriction, low anterior hairline, upturned nose, bilateral preauricular pits, widely spaced teeth, gingival hypertrophy, left ventricular dilatation with decreased biventricular systolic function, delayed bone age, 5th finger clinodactyly, short 3rd digit, hyperconvex nails, obstructive and central sleep apnea, and bilateral heel contractures. Fluorescence in situ hybridization (FISH) performed in the mother of both children showed an apparently balanced, intrachromosomal insertional translocation of 1q21.3q23.3 to 1q42.12. The sibling recurrence likely arose by a maternal meiotic crossing over on the rearranged chromosome 1 between the deleted region and the insertion. We hypothesize that the decreased cardiac function and contractures may be related to LMNA haploinsufficiency. This case illustrates the importance of FISH when attempting to determine inheritance of a copy-number variation and emphasize the value of evaluating known haploinsufficiency phenotypes for genes in deleted regions.


Assuntos
Deleção Cromossômica , Cromossomos Humanos Par 1/genética , Irmãos , Translocação Genética , Anormalidades Múltiplas/genética , Anormalidades Múltiplas/patologia , Adolescente , Blefarofimose/genética , Blefarofimose/patologia , Blefaroptose/genética , Blefaroptose/patologia , Criança , Deficiências do Desenvolvimento/genética , Deficiências do Desenvolvimento/patologia , Feminino , Cardiopatias Congênitas/genética , Cardiopatias Congênitas/patologia , Humanos , Hibridização in Situ Fluorescente , Deficiência Intelectual/genética , Deficiência Intelectual/patologia , Masculino , Mutagênese Insercional
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