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1.
Nucleic Acids Res ; 48(14): 7883-7898, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32609810

RESUMO

Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled circular DNA in Saccharomyces cerevisiae populations sampled when young and after extensive aging. Young cells possessed highly diverse circular DNA populations but 94% of the circular DNA were lost after ∼15 divisions, whereas rDNA circles underwent massive accumulation to >95% of circular DNA. Circles present in both young and old cells were characterized by replication origins including circles from unique regions of the genome and repetitive regions: rDNA and telomeric Y' regions. We further observed that circles can have flexible inheritance patterns: [HXT6/7circle] normally segregates to mother cells but in low glucose is present in up to 50% of cells, the majority of which must have inherited this circle from their mother. Interestingly, [HXT6/7circle] cells are eventually replaced by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting circular DNAs are intermediates in chromosomal amplifications. In conclusion, the heterogeneity of circular DNA offers flexibility in adaptation, but this heterogeneity is remarkably diminished with age.


Assuntos
Senescência Celular/genética , Replicação do DNA , DNA Circular/química , Saccharomyces cerevisiae/genética , DNA Circular/análise , Variação Genética , Padrões de Herança , Proteínas de Transporte de Monossacarídeos/genética , Sequências Repetitivas de Ácido Nucleico , Origem de Replicação , Proteínas de Saccharomyces cerevisiae/genética
2.
Proc Natl Acad Sci U S A ; 117(29): 17130-17134, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32636262

RESUMO

Supergenes underlie striking polymorphisms in nature, yet the evolutionary mechanisms by which they arise and persist remain enigmatic. These clusters of linked loci can spread in populations because they captured coadapted alleles or by selfishly distorting the laws of Mendelian inheritance. Here, we show that the supergene haplotype associated with multiple-queen colonies in Alpine silver ants is a maternal effect killer. All eggs from heterozygous queens failed to hatch when they did not inherit this haplotype. Hence, the haplotype specific to multiple-queen colonies is a selfish genetic element that enhances its own transmission by causing developmental arrest of progeny that do not carry it. At the population level, such transmission ratio distortion favors the spread of multiple-queen colonies, to the detriment of the alternative haplotype associated with single-queen colonies. Hence, selfish gene drive by one haplotype will impact the evolutionary dynamics of alternative forms of colony social organization. This killer hidden in a social supergene shows that large nonrecombining genomic regions are prone to cause multifarious effects across levels of biological organization.


Assuntos
Formigas/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Genes de Insetos/genética , Herança Materna/genética , Comportamento Social , Animais , Formigas/crescimento & desenvolvimento , Formigas/fisiologia , Evolução Molecular , Feminino , Haplótipos/genética , Masculino , Meiose/genética , Sequências Reguladoras de Ácido Nucleico/genética , Sequências Repetitivas de Ácido Nucleico/genética
3.
PLoS One ; 15(6): e0234306, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32555615

RESUMO

Moraxella catarrhalis is a human-adapted, opportunistic bacterial pathogen of the respiratory mucosa. Although asymptomatic colonization of the nasopharynx is common, M. catarrhalis can ascend into the middle ear, where it is a prevalent causative agent of otitis media in children, or enter the lower respiratory tract, where it is associated with acute exacerbations of chronic obstructive pulmonary disease in adults. Phase variation is the high frequency, random, reversible switching of gene expression that allows bacteria to adapt to different host microenvironments and evade host defences, and is most commonly mediated by simple DNA sequence repeats. Bioinformatic analysis of five closed M. catarrhalis genomes identified 17 unique simple DNA sequence repeat tracts that were variable between strains, indicating the potential to mediate phase variable expression of the associated genes. Assays designed to assess simple sequence repeat variation under conditions mimicking host infection demonstrated that phase variation of uspA1 (ubiquitous surface protein A1) from high to low expression occurs over 72 hours of biofilm passage, while phase variation of uspA2 (ubiquitous surface protein A2) to high expression variants occurs during repeated exposure to human serum, as measured by mRNA levels. We also identify and confirm the variable expression of two novel phase variable genes encoding a Type III DNA methyltransferase (modO), and a conserved hypothetical permease (MC25239_RS00020). These data reveal the repertoire of phase variable genes mediated by simple sequence repeats in M. catarrhalis and demonstrate that modulation of expression under conditions mimicking human infection is attributed to changes in simple sequence repeat length.


Assuntos
Regulação Bacteriana da Expressão Gênica/genética , Moraxella catarrhalis/genética , Aderência Bacteriana/genética , Proteínas da Membrana Bacteriana Externa/genética , Proteínas da Membrana Bacteriana Externa/metabolismo , Expressão Gênica/genética , Humanos , Repetições de Microssatélites/genética , Moraxella catarrhalis/patogenicidade , Infecções por Moraxellaceae , Otite Média/microbiologia , Sequências Repetitivas de Ácido Nucleico/genética
4.
PLoS One ; 15(6): e0235127, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32579599

RESUMO

Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant protein production. We previously isolated a sequence (B-3-31) that alleviates RIGS from the human genome. Here, we developed an assay system for evaluating the influence of repeat sequences on gene expression, based on in vitro ligation followed by our original gene amplification technology in animal cells. Using this assay, we found that the repeat of B-3-31, three core sequences of replication initiation regions (G5, C12, and D8) and two matrix attachment regions (AR1 and 32-3), activated the co-amplified plasmid-encoded d2EGFP gene in both human and hamster cell lines. This upregulation effect persisted for up to 82 days, which was confirmed to be repeat-induced, and was thus designated as a repeat-induced gene activation (RIGA). In clear contrast, the repeat of three bacterial sequences (lambda-phage, Amp, and ColE1) and three human retroposon sequences (Alu, 5'-untranslated region, and ORF1 of a long interspersed nuclear element) suppressed gene expression, thus reflecting RIGS. RIGS was CpG-independent. We suggest that RIGA might be associated with replication initiation. The discovery of RIGS and RIGA has implications for the repeat in mammalian genome, as well as practical value in recombinant production.


Assuntos
Inativação Gênica , Genoma Humano/genética , Regiões de Interação com a Matriz/genética , Origem de Replicação/genética , Ativação Transcricional , Animais , Sequência de Bases , Células CHO , Linhagem Celular Tumoral , Cricetinae , Cricetulus , Regulação da Expressão Gênica , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Humanos , Hibridização in Situ Fluorescente/métodos , Plasmídeos/genética , Sequências Repetitivas de Ácido Nucleico/genética , Retroelementos/genética
5.
Proc Natl Acad Sci U S A ; 117(25): 14251-14258, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32513732

RESUMO

Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and other maladaptive processes. Here, we demonstrate an integral role for H1 linker histones in silencing repetitive elements in mouse embryonic stem cells. Strong H1 depletion causes a profound de-repression of several classes of repetitive sequences, including major satellite, LINE-1, and ERV. Activation of repetitive sequence transcription is accompanied by decreased H3K9 trimethylation of repetitive sequence chromatin. H1 linker histones interact directly with Suv39h1, Suv39h2, and SETDB1, the histone methyltransferases responsible for H3K9 trimethylation of chromatin within these regions, and stimulate their activity toward chromatin in vitro. However, we also implicate chromatin compaction mediated by H1 as an additional, dominant repressive mechanism for silencing of repetitive major satellite sequences. Our findings elucidate two distinct, H1-mediated pathways for silencing heterochromatin.


Assuntos
Cromatina/metabolismo , Histonas/metabolismo , Sequências Repetitivas de Ácido Nucleico/fisiologia , Animais , Epigenômica , Heterocromatina/metabolismo , Histona-Lisina N-Metiltransferase/metabolismo , Metilação , Metiltransferases/metabolismo , Camundongos , Células-Tronco Embrionárias Murinas/metabolismo , Proteínas Repressoras/metabolismo
6.
Neurology ; 94(23): e2441-e2447, 2020 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-32467133

RESUMO

OBJECTIVE: Facioscapulohumeral muscular dystrophy (FSHD) is a heterogenetic disorder predominantly characterized by progressive facial and scapular muscle weakness. Patients with FSHD either have a contraction of the D4Z4 repeat on chromosome 4q35 or mutations in D4Z4 chromatin modifiers SMCHD1 and DNMT3B, both causing D4Z4 chromatin relaxation and inappropriate expression of the D4Z4-encoded DUX4 gene in skeletal muscle. In this study, we tested the hypothesis whether LRIF1, a known SMCHD1 protein interactor, is a disease gene for idiopathic FSHD2. METHODS: Clinical examination of a patient with idiopathic FSHD2 was combined with pathologic muscle biopsy examination and with genetic, epigenetic, and molecular studies. RESULTS: A homozygous LRIF1 mutation was identified in a patient with a clinical phenotype consistent with FSHD. This mutation resulted in the absence of the long isoform of LRIF1 protein, D4Z4 chromatin relaxation, and DUX4 and DUX4 target gene expression in myonuclei, all molecular and epigenetic hallmarks of FSHD. In concordance, LRIF1 was shown to bind to the D4Z4 repeat, and knockdown of the LRIF1 long isoform in muscle cells results in DUX4 and DUX4 target gene expression. CONCLUSION: LRIF1 is a bona fide disease gene for FSHD2. This study further reinforces the unifying genetic mechanism, which postulates that FSHD is caused by D4Z4 chromatin relaxation, resulting in inappropriate DUX4 expression in skeletal muscle.


Assuntos
Proteínas de Ciclo Celular/genética , Distrofia Muscular Facioescapuloumeral/genética , Biópsia , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Células Cultivadas , Cromatina/ultraestrutura , Proteínas Cromossômicas não Histona/metabolismo , Cromossomos Humanos Par 4/genética , Códon sem Sentido , Consanguinidade , Fibroblastos , Mutação da Fase de Leitura , Duplicação Gênica , Regulação da Expressão Gênica , Proteínas de Homeodomínio/biossíntese , Proteínas de Homeodomínio/genética , Homozigoto , Humanos , Masculino , Pessoa de Meia-Idade , Fibras Musculares Esqueléticas/metabolismo , Músculo Esquelético/patologia , Linhagem , Isoformas de Proteínas/genética , Sequências Repetitivas de Ácido Nucleico
7.
Nat Commun ; 11(1): 2288, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32385271

RESUMO

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Endogamia , Zea mays/genética , Sequência de Bases , Elementos de DNA Transponíveis/genética , Genoma de Planta , Sequências Repetitivas de Ácido Nucleico/genética
8.
Nat Commun ; 11(1): 2447, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32415081

RESUMO

Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporation remain poorly characterized. Here, by using ribose-seq and Ribose-Map techniques, we built and analyzed high-throughput sequencing libraries of rNMPs derived from mitochondrial and nuclear DNA of budding and fission yeast. We reveal both common and unique features of rNMP sites among yeast species and strains, and between wild type and different ribonuclease H-mutant genotypes. We demonstrate that the rNMPs are not randomly incorporated in DNA. We highlight signatures and patterns of rNMPs, including sites within trinucleotide-repeat tracts. Our results uncover that the deoxyribonucleotide immediately upstream of the rNMPs has a strong influence on rNMP distribution, suggesting a mechanism of rNMP accommodation by DNA polymerases as a driving force of rNMP incorporation. Consistently, we find deoxyadenosine upstream from the most abundant genomic rCMPs and rGMPs. This study establishes a framework to better understand mechanisms of rNMP incorporation in DNA.


Assuntos
Citosina/metabolismo , DNA Fúngico/genética , Desoxiadenosinas/metabolismo , Genoma Fúngico , Guanosina/metabolismo , Ribonucleotídeos/metabolismo , Saccharomyces cerevisiae/genética , Sequência de Bases , Núcleo Celular/genética , DNA Mitocondrial/genética , Genoma Mitocondrial , Sequências Repetitivas de Ácido Nucleico/genética , Ribonuclease H/metabolismo , Schizosaccharomyces/genética
9.
Nat Commun ; 11(1): 2223, 2020 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-32376862

RESUMO

Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable to the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.


Assuntos
Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Homeodomínio/química , Proteínas de Homeodomínio/metabolismo , Motivos de Nucleotídeos/genética , Arabidopsis/química , Arabidopsis/genética , Proteínas de Arabidopsis/genética , DNA/metabolismo , Dimerização , Proteínas de Homeodomínio/genética , Brotos de Planta/genética , Ligação Proteica , Sequências Repetitivas de Ácido Nucleico/genética , Fatores de Transcrição/química , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
10.
BMC Bioinformatics ; 21(1): 207, 2020 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-32448146

RESUMO

BACKGROUND: Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on genome structure and evolution. The average coverage depth of a genome assembly is often used as an indicator of assembly quality. Visualizing coverage depth across a draft genome is a critical step, which allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Despite the interplay between genome structure and assembly quality, no contemporary, user-friendly software tool can visualize the coverage depth of a plastid genome assembly while taking its quadripartite genome structure into account. A software tool is needed that fills this void. RESULTS: We introduce 'PACVr', an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as the individual plastome genes. By using a variable window approach, the tool allows visualizations on different calculation scales. It also confirms sequence equality of, as well as visualizes gene synteny between, the inverted repeat regions of the input genome. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be invoked from a Unix shell, facilitating its use in automated quality control. We illustrate the application of PACVr on four empirical datasets and compare visualizations generated by PACVr with those of alternative software tools. CONCLUSIONS: PACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) gene synteny across the inverted repeat regions. It contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences. The software, example datasets, technical documentation, and a tutorial are available with the package at https://cran.r-project.org/package=PACVr.


Assuntos
Genomas de Plastídeos , Software , Sequência de Bases , Sequências Repetitivas de Ácido Nucleico/genética , Reprodutibilidade dos Testes
11.
Nat Commun ; 11(1): 2071, 2020 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-32350247

RESUMO

Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.


Assuntos
Bovinos/genética , Variação Genética , Genoma , Haplótipos/genética , Alelos , Desequilíbrio Alélico , Animais , Sequência de Bases , Cromossomos de Mamíferos/genética , Feminino , Loci Gênicos , Mutação INDEL/genética , Masculino , Anotação de Sequência Molecular , Polimorfismo de Nucleotídeo Único/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Sequências Repetitivas de Ácido Nucleico/genética
12.
BMC Bioinformatics ; 21(1): 197, 2020 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-32429835

RESUMO

BACKGROUND: Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians. RESULTS: This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry. CONCLUSIONS: Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.


Assuntos
Anfíbios/genética , DNA Mitocondrial/química , Genoma Mitocondrial , Animais , Sequências Repetidas Invertidas , Sequências Repetitivas de Ácido Nucleico
13.
Adv Exp Med Biol ; 1241: 101-124, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32383118

RESUMO

The mammalian genome mostly contains repeated sequences. Some of these repeats are in the regulatory elements of genes, and their instability, particularly the propensity to change the repeat unit number, is responsible for 36 well-known neurodegenerative human disorders. The mechanism of repeat expansion has been an unsolved question for more than 20 years. There are a few hypotheses describing models of mutation development. Every hypothesis is based on assumptions about unusual secondary structures that violate DNA metabolism processes in the cell. Some models are based on replication errors, and other models are based on mismatch repair or base excision repair errors. Additionally, it has been shown that epigenetic regulation of gene expression can influence the probability and frequency of expansion. In this review, we consider the molecular bases of repeat expansion disorders and discuss possible mechanisms of repeat expansion during cell metabolism.


Assuntos
Dano ao DNA , DNA/metabolismo , Doenças Neurodegenerativas/genética , Sequências Repetitivas de Ácido Nucleico , Animais , Reparo do DNA , Epigênese Genética , Humanos
14.
BMC Bioinformatics ; 21(1): 164, 2020 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-32349660

RESUMO

BACKGROUND: Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functional analysis of circRNAs are scarce. RESULTS: We present circRNAprofiler, an R-based computational framework that runs after circRNAs have been identified. It allows to combine circRNAs detected by multiple publicly available annotation-based circRNA detection tools and to analyze their expression, genomic context, evolutionary conservation, biogenesis and putative functions. CONCLUSIONS: Overall, the circRNA analysis workflow implemented by circRNAprofiler is highly automated and customizable, and the results of the analyses can be used as starting point for further investigation in the role of specific circRNAs in any physiological or pathological condition.


Assuntos
Biologia Computacional/métodos , RNA Circular/genética , Software , Sítios de Ligação/genética , Regulação da Expressão Gênica , Genoma , Estudo de Associação Genômica Ampla , Humanos , Íntrons/genética , MicroRNAs/genética , MicroRNAs/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Sequências Repetitivas de Ácido Nucleico/genética
15.
Nat Commun ; 11(1): 1964, 2020 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327641

RESUMO

Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.


Assuntos
Evolução Molecular , Nematoides/genética , Infecções por Nematoides/parasitologia , Cromossomos Sexuais/genética , Animais , Brugia Malayi/genética , Caenorhabditis elegans/genética , Mapeamento Cromossômico , Feminino , Regulação da Expressão Gênica , Genoma Helmíntico/genética , Humanos , Masculino , Nematoides/classificação , Sequências Repetitivas de Ácido Nucleico/genética , Processos de Determinação Sexual/genética
16.
Nat Commun ; 11(1): 1980, 2020 04 24.
Artigo em Inglês | MEDLINE | ID: mdl-32332764

RESUMO

The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. Here, we introduce a method to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our analytical approach reveals insights into the contribution of DNA repair towards indel mutagenesis in human cells.


Assuntos
Quebras de DNA de Cadeia Dupla , Reparo do DNA , Neoplasias/genética , Sequências Repetitivas de Ácido Nucleico , Motivos de Aminoácidos , Biologia Computacional , Análise Mutacional de DNA , Replicação do DNA , Deleção de Genes , Regulação Neoplásica da Expressão Gênica , Variação Genética , Genoma Humano , Genômica , Humanos , Mutação INDEL , Mutagênese , Neoplasias/metabolismo , Polinucleotídeos/genética , Análise de Sequência de RNA , Transcrição Genética
17.
Nucleic Acids Res ; 48(9): 4601-4613, 2020 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-32266374

RESUMO

While the histone variant H2A.Z is known to be required for mitosis, it is also enriched in nucleosomes surrounding the transcription start site of active promoters, implicating H2A.Z in transcription. However, evidence obtained so far mainly rely on correlational data generated in actively dividing cells. We have exploited a paradigm in which transcription is uncoupled from the cell cycle by developing an in vivo system to inactivate H2A.Z in terminally differentiated post-mitotic muscle cells. ChIP-seq, RNA-seq and ATAC-seq experiments performed on H2A.Z KO post-mitotic muscle cells show that this histone variant is neither required to maintain nor to activate transcription. Altogether, this study provides in vivo evidence that in the absence of mitosis H2A.Z is dispensable for transcription and that the enrichment of H2A.Z on active promoters is a marker but not an active driver of transcription.


Assuntos
Histonas/fisiologia , Músculo Esquelético/metabolismo , Transcrição Genética , Ativação Transcricional , Animais , Diferenciação Celular , Células Cultivadas , Cromatina , Sequenciamento de Cromatina por Imunoprecipitação , Histonas/genética , Histonas/metabolismo , Camundongos , Fibras Musculares Esqueléticas , Músculo Esquelético/citologia , RNA-Seq , Sequências Repetitivas de Ácido Nucleico , Sítio de Iniciação de Transcrição
18.
Mol Phylogenet Evol ; 147: 106766, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32119996

RESUMO

A recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.


Assuntos
Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Homologia de Sequência do Ácido Nucleico , Animais , Bases de Dados Genéticas , Evolução Molecular , Marcadores Genéticos , Magnoliopsida/genética , Especificidade da Espécie
19.
PLoS Negl Trop Dis ; 14(3): e0008127, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32203502

RESUMO

Understanding the prevalence of M. leprae infection in armadillos is important because of evidence from Brazil and other countries of an association between contact with armadillos and the development of Hansen's Disease (leprosy). Our aim was to characterize studies which have investigated natural M. leprae infection in wild armadillos in Brazil, and to quantify and explore variability in the reported prevalence of infection. We conducted a systematic review (PROSPERO CRD42019155277) of publications in MEDLINE, EMBASE, Global Health, Scopus, LILACS, Biblioteca Digital Brasileira de Teses e Dissertações, Catálogo de Teses e Dissertações de CAPES, and Biblioteca Virtual em Saúde up to 10/2019 using Mesh and text search terms (in English, Portuguese, Spanish, and French). The 10 included studies represented a total sample of 302 armadillos comprising 207 (69%) Dasypus novemcinctus, 67 (22%) Euphractus sexcinctus, 16 (5%) Priodontes maximus, 10 (3%) Cabassous unicinctus, and 2 (1%) Cabassous tatouay from 7 different states. Methods used included histopathology (4 studies), PGL-1 and LID-1 antigen detection (4 studies) and examination for clinical signs of disease (4 studies). Eight studies used PCR of which 7 targeted the RLEP repetitive element and 3 tested for inhibitory substances. M. leprae prevalence by PCR ranged from 0% (in 3 studies) to 100% in one study, with a summary estimate of 9.4% (95% CI 0.4% to 73.1%) and a predictive interval of 0-100%. The average prevalence is equivalent to 1 in 10 armadillos in Brazil being infected with M. leprae, but wide variation in sample estimates means that the prevalence in any similar study would be entirely unpredictable. We propose instead that future studies aim to investigate transmission and persistence of M. leprae within and between armadillo populations, meanwhile adopting the precautionary principle to protect human health and an endangered species in Brazil.


Assuntos
Tatus/microbiologia , Hanseníase/epidemiologia , Hanseníase/veterinária , Mycobacterium leprae/isolamento & purificação , Animais , Animais Selvagens/microbiologia , Brasil/epidemiologia , DNA Bacteriano/análise , Bases de Dados Factuais , Mapeamento Geográfico , Mycobacterium leprae/genética , Reação em Cadeia da Polimerase , Prevalência , Sequências Repetitivas de Ácido Nucleico , Zoonoses/epidemiologia , Zoonoses/microbiologia
20.
PLoS Negl Trop Dis ; 14(3): e0008147, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32155159

RESUMO

BACKGROUND: Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625. CONCLUSIONS/SIGNIFICANCE: This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential non-invasive screening and diagnosis of echinococcosis.


Assuntos
DNA de Helmintos/sangue , Equinococose/diagnóstico , Echinococcus/genética , Técnicas de Diagnóstico Molecular/métodos , Plasma/química , Sequências Repetitivas de Ácido Nucleico , Adulto , Animais , DNA de Helmintos/química , DNA de Helmintos/genética , DNA de Helmintos/isolamento & purificação , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Masculino , Sensibilidade e Especificidade
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