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1.
Nat Commun ; 11(1): 2071, 2020 04 29.
Artículo en Inglés | MEDLINE | ID: mdl-32350247

RESUMEN

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.


Asunto(s)
Bovinos/genética , Variación Genética , Genoma , Haplotipos/genética , Alelos , Desequilibrio Alélico , Animales , Secuencia de Bases , Cromosomas de los Mamíferos/genética , Femenino , Sitios Genéticos , Mutación INDEL/genética , Masculino , Anotación de Secuencia Molecular , Polimorfismo de Nucleótido Simple/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Secuencias Repetitivas de Ácidos Nucleicos/genética
2.
BMC Bioinformatics ; 21(1): 164, 2020 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-32349660

RESUMEN

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.


Asunto(s)
Biología Computacional/métodos , ARN Circular/genética , Programas Informáticos , Sitios de Unión/genética , Regulación de la Expresión Génica , Genoma , Estudio de Asociación del Genoma Completo , Humanos , Intrones/genética , MicroARNs/genética , MicroARNs/metabolismo , Polimorfismo de Nucleótido Simple/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética
3.
BMC Bioinformatics ; 21(1): 207, 2020 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-32448146

RESUMEN

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.


Asunto(s)
Genoma de Plastidios , Programas Informáticos , Secuencia de Bases , Secuencias Repetitivas de Ácidos Nucleicos/genética , Reproducibilidad de los Resultados
4.
BMC Bioinformatics ; 21(1): 197, 2020 May 19.
Artículo en Inglés | MEDLINE | ID: mdl-32429835

RESUMEN

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.


Asunto(s)
Anfibios/genética , ADN Mitocondrial/química , Genoma Mitocondrial , Animales , Secuencias Invertidas Repetidas , Secuencias Repetitivas de Ácidos Nucleicos
5.
Adv Exp Med Biol ; 1241: 101-124, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32383118

RESUMEN

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.


Asunto(s)
Daño del ADN , ADN/metabolismo , Enfermedades Neurodegenerativas/genética , Secuencias Repetitivas de Ácidos Nucleicos , Animales , Reparación del ADN , Epigénesis Genética , Humanos
6.
PLoS Negl Trop Dis ; 14(3): e0008147, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32155159

RESUMEN

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.


Asunto(s)
ADN de Helmintos/sangre , Equinococosis/diagnóstico , Echinococcus/genética , Técnicas de Diagnóstico Molecular/métodos , Plasma/química , Secuencias Repetitivas de Ácidos Nucleicos , Adulto , Animales , ADN de Helmintos/química , ADN de Helmintos/genética , ADN de Helmintos/aislamiento & purificación , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Masculino , Sensibilidad y Especificidad
7.
PLoS Negl Trop Dis ; 14(3): e0008127, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32203502

RESUMEN

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.


Asunto(s)
Armadillos/microbiología , Lepra/epidemiología , Lepra/veterinaria , Mycobacterium leprae/aislamiento & purificación , Animales , Animales Salvajes/microbiología , Brasil/epidemiología , ADN Bacteriano/análisis , Bases de Datos Factuales , Mapeo Geográfico , Mycobacterium leprae/genética , Reacción en Cadena de la Polimerasa , Prevalencia , Secuencias Repetitivas de Ácidos Nucleicos , Zoonosis/epidemiología , Zoonosis/microbiología
8.
Nucleic Acids Res ; 48(8): 4492-4506, 2020 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-32128583

RESUMEN

The telomere repeats containing RNA (TERRA) is transcribed from the C-rich strand of telomere DNA and comprises of UUAGGG nucleotides repeats in humans. The TERRA RNA repeats can exist in single stranded, RNA-DNA hybrid and G-quadruplex forms in the cell. Interaction of TERRA RNA with hnRNPA1 has been proposed to play critical roles in maintenance of telomere DNA. hnRNPA1 contains an N-terminal UP1 domain followed by an RGG-box containing C-terminal region. RGG-motifs are emerging as key protein motifs that recognize the higher order nucleic acid structures as well as are known to promote liquid-liquid phase separation of proteins. In this study, we have shown that the RGG-box of hnRNPA1 specifically recognizes the TERRA RNA G-quadruplexes that have loops in their topology, whereas it does not interact with the single-stranded RNA. Our results show that the N-terminal UP1 domain in the presence of the RGG-box destabilizes the loop containing TERRA RNA G-quadruplex efficiently compared to the RNA G-quadruplex that lacks loops, suggesting that unfolding of G-quadruplex structures by UP1 is structure dependent. Furthermore, we have compared the telomere DNA and TERRA RNA G-quadruplex binding by the RGG-box of hnRNPA1 and discussed its implications in telomere DNA maintenance.


Asunto(s)
G-Cuádruplex , Ribonucleoproteína Nuclear Heterogénea A1/química , Ribonucleoproteína Nuclear Heterogénea A1/metabolismo , ARN/química , Telómero , Unión Proteica , Dominios Proteicos , ARN/metabolismo , Secuencias Repetitivas de Ácidos Nucleicos
9.
PLoS Genet ; 16(3): e1008673, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32203508

RESUMEN

Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in chromosome dynamics and genome stability. However, our current understanding of 3D genome organization does not include PCH domains because of technical challenges associated with repetitive sequences enriched in PCH genomic regions. We investigated the 3D architecture of Drosophila melanogaster PCH domains and their spatial associations with the euchromatic genome by developing a novel analysis method that incorporates genome-wide Hi-C reads originating from PCH DNA. Combined with cytogenetic analysis, we reveal a hierarchical organization of the PCH domains into distinct "territories." Strikingly, H3K9me2-enriched regions embedded in the euchromatic genome show prevalent 3D interactions with the PCH domain. These spatial contacts require H3K9me2 enrichment, are likely mediated by liquid-liquid phase separation, and may influence organismal fitness. Our findings have important implications for how PCH architecture influences the function and evolution of both repetitive heterochromatin and the gene-rich euchromatin.


Asunto(s)
Centrosoma/metabolismo , Eucromatina/genética , Heterocromatina/metabolismo , Animales , Estructuras Cromosómicas/metabolismo , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Eucromatina/metabolismo , Genoma/genética , Heterocromatina/genética , Heterocromatina/ultraestructura , Histonas/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética
10.
Cytogenet Genome Res ; 160(3): 141-147, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32146462

RESUMEN

Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.


Asunto(s)
Anuros/genética , ADN Satélite/genética , Genoma/genética , Cromosomas Sexuales/genética , Animales , Centrómero/genética , Evolución Molecular , Heterocromatina/genética , Hibridación Fluorescente in Situ , Filogenia , Secuencias Repetitivas de Ácidos Nucleicos/genética , Análisis de Secuencia de ADN
11.
PLoS One ; 15(3): e0230390, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32176736

RESUMEN

The aim of the study was to detect and genetically characterize Arcobacter butzleri in pet red-footed tortoises suspected for Campylobacter spp., using molecular techniques. A written consent from tortoise owners was obtained, after explaining the advantages of the research to tortoise owners of Grenada. Fecal samples were collected from 114 tortoises from five parishes of the country and cultured for Campylobacter spp. using selective culture techniques. A. butzleri was isolated from 4.39% of pet tortoises. Total thirteen isolates were obtained; all identified as A. butzleri by a universal and a species-specific Polymerase Chain Reaction (PCR) and direct sequencing. Genetic characterization of these isolates was performed based on Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) that generated eight different genetic fingerprints with a discriminatory power of 0.91. Campylobacter species were not detected molecularly in any of the culture-positive samples. This is the first report of infection of pet tortoises in Grenada, West Indies with A. butzleri. This study emphasizes on the risk of zoonotic transmission of A. butzleri by exotic pets, which is a serious concern for public health.


Asunto(s)
Arcobacter/genética , Campylobacter/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Tortugas/microbiología , Animales , Campylobacter/aislamiento & purificación , Dermatoglifia del ADN/métodos , ADN Bacteriano/genética , ADN Bacteriano/aislamiento & purificación , Heces/microbiología , Tortugas/genética
12.
Gene ; 738: 144477, 2020 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-32061764

RESUMEN

The wide variation found in the size of eukaryotic genomes is largely related to the accumulation of repetitive sequences. Studies show that these sequences can go through an evolutionary process (molecular co-optation) and acquire new genomic functions. Cytogenetic studies reveal a wide karyotypic variation between chelonians (order Testudines) (2n = 26-68), attributed mainly to the number of microchromosomes. The study of repetitive DNAs has the potential to provide data on the dynamics of these sequences, and how they influence the organization of the genome. Here, we reveal the first in situ mapping data of 45S rDNA, histone H3 genes, and telomeric sequences, for a species of the genus Rhinoclemmys, R. punctularia. The karyotype described here for R. punctularia is different from previous reports for the diploid complement of this species, with differences probably attributable to centric fissions and pericentric inversions or centromere repositioning. The 45S rDNA are on a single chromosome pair (like in other turtles), telomeric sequences are in terminal position on all the chromosomes, and histone H3 is dispersed in low copy number, with clusters in pericentromeric regions of three chromosome pairs. We report on the presence of a Gypsy retrotransposon insert located within H3 histone of R. punctularia, and the H3 region sequenced contained the open reading frame of the histone sequence. Comparative modeling revealed a functional pattern for the protein, thus suggesting that the Gypsy element might have been recruited for new functions in the genome of this species.


Asunto(s)
Secuencias Repetitivas de Ácidos Nucleicos/genética , Retroelementos/genética , Tortugas/genética , Animales , Mapeo Cromosómico , Citogenética/métodos , ADN Ribosómico/genética , Diploidia , Evolución Molecular , Femenino , Histonas/genética , Hibridación Fluorescente in Situ , Cariotipo , Cariotipificación/métodos , Masculino , ARN Ribosómico/genética , Telómero/genética
13.
Nat Cell Biol ; 22(2): 235-245, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-32015436

RESUMEN

PIWI-interacting RNAs (piRNAs) promote fertility in many animals. However, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets but, rather, is mediated by epigenetic silencing of all of the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway restores histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that sRNA-mediated silencing of histone genes impairs the fertility of piRNA mutants and may serve to maintain piRNAs across evolution.


Asunto(s)
Proteínas Argonauta/genética , Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Silenciador del Gen , Histonas/genética , ARN Interferente Pequeño/genética , Animales , Animales Modificados Genéticamente , Proteínas Argonauta/deficiencia , Proteínas Argonauta/metabolismo , Evolución Biológica , Sistemas CRISPR-Cas , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Fertilidad/genética , Edición Génica , Histonas/metabolismo , Patrón de Herencia , Mutación , ARN sin Sentido/genética , ARN sin Sentido/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN Interferente Pequeño/metabolismo , Secuencias Repetitivas de Ácidos Nucleicos
14.
Nat Commun ; 11(1): 733, 2020 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-32024817

RESUMEN

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.


Asunto(s)
Mutación , Neoplasias/genética , Telómero/genética , Estudios de Casos y Controles , Proteínas Co-Represoras/genética , Genoma Humano , Humanos , Chaperonas Moleculares/genética , ARN Largo no Codificante , Secuencias Repetitivas de Ácidos Nucleicos , Telomerasa/genética , Secuenciación Completa del Genoma , Proteína Nuclear Ligada al Cromosoma X/genética
15.
Cytogenet Genome Res ; 160(1): 29-37, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32092757

RESUMEN

The fish family Cynodontidae belongs to the superfamily Curimatoidea, together with the Hemiodontidae, Serrasalmidae, Parodontidae, Prochilodontidae, Chilodontidae, Curimatidae, and Anostomidae. The majority of the species of this superfamily that have been analyzed to date have a diploid chromosome number of 2n = 54. Differentiated sex chromosomes (with female heterogamety) have been observed only in the Prochilodontidae, Parodontidae, and Anostomidae. The present study provides the first description of differentiated sex chromosomes in the cynodontid species Cynodon gibbus, which has a ZZ/ZW system, and shows that repetitive DNA has played a fundamental role in the differentiation of these sex chromosomes.


Asunto(s)
Characiformes/genética , Cromosomas Sexuales , Animales , Bandeo Cromosómico , ADN , Evolución Molecular , Femenino , Heterocromatina/química , Hibridación Fluorescente in Situ , Cariotipificación , Masculino , Hibridación de Ácido Nucleico , Secuencias Repetitivas de Ácidos Nucleicos
16.
Cytogenet Genome Res ; 160(3): 134-140, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32092753

RESUMEN

Reptiles show a remarkable diversity of sex determination mechanisms and sex chromosome systems, derived from different autosomal pairs. The origin of the ZW sex chromosomes of Lacerta agilis, a widespread Eurasian lizard species, is a matter of discussion: is it a small macrochromosome from the 11-18 group common to all lacertids, or does this species have a unique ZW pair derived from the large chromosome 5? Using independent molecular cytogenetic methods, we investigated the karyotype of L. agilis exigua from Siberia, Russia, to identify the sex chromosomes. FISH with a flow-sorted chromosome painting probe derived from L. strigata and specific to chromosomes 13, 14, and Z confirmed that the Z chromosome of L. agilis is a small macrochromosome, the same as in L. strigata. FISH with the telomeric probe showed an extensive accumulation of the telomere-like repeat in the W chromosome in agreement with previous studies, excluding the possibility that the lineages of L. agilis studied in different works could have different sex chromosome systems due to a putative intra-species polymorphism. Our results reinforce the idea of the stability of the sex chromosomes and lack of evidence for sex-chromosome turnovers in known species of Lacertidae.


Asunto(s)
Evolución Biológica , Lagartos/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Cromosomas Sexuales/genética , Animales , Hibridación Fluorescente in Situ , Federación de Rusia
17.
Proc Natl Acad Sci U S A ; 117(9): 4858-4863, 2020 03 03.
Artículo en Inglés | MEDLINE | ID: mdl-32075918

RESUMEN

We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ∼350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% in these eight cancer types, while only 1% of 812 healthy controls scored positive.


Asunto(s)
Aneuploidia , Neoplasias , Secuencias Repetitivas de Ácidos Nucleicos , Biomarcadores de Tumor , ADN Tumoral Circulante , ADN/genética , Esófago , Humanos , Biopsia Líquida , Mutación , Neoplasias/diagnóstico , Neoplasias/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Secuenciación Completa del Genoma
18.
Cancer Sci ; 111(4): 1385-1391, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31957195

RESUMEN

Cancer studies primarily focus on the characterization of the key driver genes and the underlying pathways. However, the contribution of other cancer-associated genes located in the genomic neighborhood of the driver genes could help to understand further aspects of cancer progression. Given the frequent involvement of chromosome 3 in multiple human cancers, in particular in the form of the prognostically highly relevant monosomy 3 in uveal melanoma (UM), we investigated the cumulative impact of cancer-associated genes on chromosome 3. Our analysis showed that these genes are enriched with repetitive elements with genes surrounded by distinctive repeats (MIR, hAT-Charlie, ERVL-MaLR, LINE-2, and simple/low complexity) in the promoter being more precisely associated with cancer-related pathways than the ones with major transposable elements (SINE/Alu and LINE-1). Additionally, these genes showed strong intrachromosomal chromatin interactions in 3D nuclear organization. Further investigations revealed a genomic hotspot in the vicinity of BAP1 locus, which is affected in 27 types of different cancers and contains abundant noncoding RNAs that are often expressed in a tissue-specific manner. The cross-species comparison of these cancer-associated genes revealed mostly a shared synteny in closer primates. However, near to the BAP1 locus signs of chromosomal inversions were observed during the course of evolution. To our knowledge, this is the first study to characterize the entire genomic neighborhood of cancer-associated genes located on any single chromosome. Based on our results, we hypothesize that monosomy of chromosome 3 will have important clinical and molecular consequences in the respective diseases and in particular in UM.


Asunto(s)
Cromatina/genética , Evolución Molecular , Melanoma/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Neoplasias de la Úvea/genética , Elementos Alu/genética , Animales , Inversión Cromosómica/genética , Cromosomas Humanos Par 3/genética , Biología Computacional , Humanos , Elementos de Nucleótido Esparcido Largo/genética , Melanoma/patología , Primates/genética , Regiones Promotoras Genéticas/genética , Proteínas Supresoras de Tumor/genética , Ubiquitina Tiolesterasa/genética , Neoplasias de la Úvea/patología
19.
Appl Microbiol Biotechnol ; 104(5): 1891-1904, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31932894

RESUMEN

The genus Colletotrichum comprises species with different lifestyles but is mainly known for phytopathogenic species that infect crops of agronomic relevance causing considerable losses. The fungi of the genus Colletotrichum are distributed in species complexes and within each complex some species have particularities regarding their lifestyle. The most commonly found and described lifestyles in Colletotrichum are endophytic and hemibiotrophic phytopathogenic. Several of these phytopathogenic species show wide genetic variability, which makes long-term maintenance of resistance in plants difficult. Different mechanisms may play an important role in the emergence of genetic variants but are not yet fully understood in this genus. These mechanisms include heterokaryosis, a parasexual cycle, sexual cycle, transposable element activity, and repeat-induced point mutations. This review provides an overview of the genus Colletotrichum, the species complexes described so far and the most common lifestyles in the genus, with a special emphasis on the mechanisms that may be responsible, at least in part, for the emergence of new genotypes under field conditions.


Asunto(s)
Colletotrichum/crecimiento & desarrollo , Colletotrichum/genética , Variación Genética/genética , Enfermedades de las Plantas/microbiología , Elementos Transponibles de ADN/genética , Endófitos , Genoma Fúngico/genética , Especificidad del Huésped , Secuencias Repetitivas de Ácidos Nucleicos/genética , Especificidad de la Especie
20.
PLoS One ; 15(1): e0227275, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-31923209

RESUMEN

The aim of this work was to determine current cagA gene EPIYA motifs present in Colombian Helicobacter pylori isolates using a fast and reliable molecular test. DNA from eighty-five Helicobacter pylori-cagA positive strains were analyzed. Strains were obtained from patients diagnosed with functional dyspepsia at Clínica Fundadores in Bogotá. The 3' region of the cagA gene was amplified through conventional Polymerase Chain Reaction (PCR). Obtained amplicons were sequenced using the Sanger method and analyzed with bioinformatics tools. Additionally, a significant Spearman correlation coefficient was determined between the patients' age and the number of EPIYA-C repeats; with p values < 0.05 considered significant. Estimates were obtained using a 95% CI. The 3´ variable region of the cagA gene was amplified and PCR products of the following sizes corresponded to the following EPIYA motifs: 400 bp: EPIYA AB, 500 bp: EPIYA ABC, 600 bp: EPIYA ABCC and 700 bp: ABCCC. A single PCR band was observed for 58 out of 85 Helicobacter pylori isolates, with an EPIYA distribution motif as follows: 7/85 AB (8.2%), 34/85 ABC (40%), 26/85 ABCC (30.6%) and 18/85 ABCCC (21.2%). However, in 27 out of 85 Helicobacter pylori isolates, two or more bands were observed, where the most predominant cagA genotype were ABC-ABCC (26%, 7/27) and ABCC-ABCCC (22.2%, 6/27). A direct proportionality between the number of EPIYA-C repeats and an increase in the patients' age was observed, finding a greater number of EPIYA ABCC and ABCCC repeats in the population over 50 years old. All isolates were of the Western cagA type and 51.8% of them were found to have multiple EPIYA-C repeats. These standardized molecular test allowed to identify the number of EPIYA C motifs based on band size.


Asunto(s)
Secuencias de Aminoácidos/genética , Antígenos Bacterianos/genética , Proteínas Bacterianas/genética , Pruebas Diagnósticas de Rutina/normas , Genes Bacterianos/genética , Infecciones por Helicobacter/diagnóstico , Infecciones por Helicobacter/epidemiología , Helicobacter pylori/genética , Adulto , Anciano , Colombia/epidemiología , ADN Bacteriano/genética , Dispepsia/microbiología , Femenino , Genotipo , Infecciones por Helicobacter/microbiología , Humanos , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa/normas , Secuencias Repetitivas de Ácidos Nucleicos/genética , Análisis de Secuencia de ADN/normas
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