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1.
Elife ; 102021 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-34406118

RESUMO

DNA loop extrusion by condensins and decatenation by DNA topoisomerase II (topo II) are thought to drive mitotic chromosome compaction and individualization. Here, we reveal that the linker histone H1.8 antagonizes condensins and topo II to shape mitotic chromosome organization. In vitro chromatin reconstitution experiments demonstrate that H1.8 inhibits binding of condensins and topo II to nucleosome arrays. Accordingly, H1.8 depletion in Xenopus egg extracts increased condensins and topo II levels on mitotic chromatin. Chromosome morphology and Hi-C analyses suggest that H1.8 depletion makes chromosomes thinner and longer through shortening the average loop size and reducing the DNA amount in each layer of mitotic loops. Furthermore, excess loading of condensins and topo II to chromosomes by H1.8 depletion causes hyper-chromosome individualization and dispersion. We propose that condensins and topo II are essential for chromosome individualization, but their functions are tuned by the linker histone to keep chromosomes together until anaphase.


Assuntos
Cromatina/metabolismo , Cromossomos/genética , DNA Topoisomerases Tipo II/genética , Histonas/genética , Adenosina Trifosfatases/metabolismo , Animais , Extratos Celulares/química , Cromossomos/ultraestrutura , Proteínas de Ligação a DNA/metabolismo , Feminino , Modelos Biológicos , Complexos Multiproteicos/metabolismo , Oócitos/química , Oócitos/metabolismo , Fuso Acromático/genética , Fuso Acromático/patologia , Fuso Acromático/ultraestrutura , Xenopus laevis
2.
Mol Cell ; 81(15): 3033-3037, 2021 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-34358454

RESUMO

Some biological questions are tough to solve through standard molecular and cell biological methods and naturally lend themselves to investigation by physical approaches. Below, a group of formally trained physicists discuss, among other things, how they apply physics to address biological questions and how physical approaches complement conventional biological approaches.


Assuntos
Biofísica/métodos , Modelos Biológicos , Física/métodos , Imagem Individual de Molécula , Biologia/educação , Biofísica/tendências , Cromossomos/química , Cromossomos/ultraestrutura , Simulação por Computador , Humanos , Proteínas Motores Moleculares/química , Origem da Vida , Física/educação , Imagem Individual de Molécula/métodos
3.
Int J Mol Sci ; 22(11)2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-34206020

RESUMO

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.


Assuntos
Cromossomos/genética , Linfócitos/citologia , Mitose/genética , Troca de Cromátide Irmã/genética , Núcleo Celular/genética , Cromossomos/ultraestrutura , Humanos , Cariotipagem , Linfócitos/ultraestrutura , Microscopia Eletrônica de Varredura
4.
Int J Mol Sci ; 22(11)2021 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-34072879

RESUMO

Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis-Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.


Assuntos
Cromatina/ultraestrutura , Cromossomos/ultraestrutura , DNA/genética , Imageamento Tridimensional , Cromatina/genética , Cromossomos/genética , DNA/ultraestrutura , Humanos , Modelos Moleculares
5.
Science ; 372(6545): 984-989, 2021 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-34045355

RESUMO

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.


Assuntos
Adenosina Trifosfatases/genética , Adenosina Trifosfatases/fisiologia , Evolução Biológica , Cromossomos/ultraestrutura , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/fisiologia , Eucariotos/genética , Genoma , Complexos Multiproteicos/genética , Complexos Multiproteicos/fisiologia , Adenosina Trifosfatases/química , Algoritmos , Animais , Nucléolo Celular/ultraestrutura , Núcleo Celular/ultraestrutura , Centrômero/ultraestrutura , Cromossomos/química , Cromossomos Humanos/química , Cromossomos Humanos/ultraestrutura , Proteínas de Ligação a DNA/química , Genoma Humano , Genômica , Heterocromatina/ultraestrutura , Humanos , Interfase , Mitose , Modelos Biológicos , Complexos Multiproteicos/química , Telômero/ultraestrutura
6.
Cytogenet Genome Res ; 161(1-2): 52-62, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33887732

RESUMO

With 82 species currently described, the genus Leptodactylus is the most diverse and representative one in the family Leptodactylidae. Concerning chromosomal organization, this genus represents an interesting and underexplored group since data from molecular cytogenetics are incipient, and little is known about the organization and distribution of repetitive DNA elements in the karyotypes. In this sense, this study aimed at providing a comparative analysis in 4 Leptodactylus species (L. macrosternum, L. pentadactylus, L. fuscus, and Leptodactylus cf. podicipinus), combining conventional cytogenetics (Giemsa staining, C-banding, and AgNOR staining) and mapping of molecular markers (18S rDNA, telomeric and microsatellite probes), to investigate mechanisms underlying their karyotype differentiation process. The results showed that all species had karyotypes with 2n = 22 and FN = 44, except for Leptodactylus cf. podicipinus which presented FN = 36. The 18S rDNA was observed in pair 8 of all analyzed species (corresponding to pair 4 in L. pentadactylus), coinciding with the secondary constrictions and AgNOR staining. FISH with microsatellite DNA probes demonstrated species-specific patterns, as well as an association of these repetitive sequences with constitutive heterochromatin blocks and ribosomal DNA clusters, revealing the dynamics of microsatellites in the genome of the analyzed species. In summary, our data demonstrate an ongoing process of genomic divergence inside species with almost similar karyotype, driven most likely by a series of pericentric inversions, followed by differential accumulation of repetitive sequences.


Assuntos
Anuros/genética , Cromossomos/ultraestrutura , DNA Ribossômico/genética , Cariotipagem , Repetições de Microssatélites , Animais , Bandeamento Cromossômico , Inversão Cromossômica , Análise Citogenética , Citogenética , Sondas de DNA , Feminino , Geografia , Heterocromatina/metabolismo , Hibridização in Situ Fluorescente , Cariótipo , Masculino , Meiose , Mitose , Região Organizadora do Nucléolo , Filogenia , Especificidade da Espécie
7.
Philos Trans A Math Phys Eng Sci ; 379(2199): 20200144, 2021 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-33896204

RESUMO

We report that high-density single-molecule super-resolution microscopy can be achieved with a conventional epifluorescence microscope set-up and a mercury arc lamp. The configuration termed as laser-free super-resolution microscopy (LFSM) is an extension of single-molecule localization microscopy (SMLM) techniques and allows single molecules to be switched on and off (a phenomenon termed as 'blinking'), detected and localized. The use of a short burst of deep blue excitation (350-380 nm) can be further used to reactivate the blinking, once the blinking process has slowed or stopped. A resolution of 90 nm is achieved on test specimens (mouse and amphibian meiotic chromosomes). Finally, we demonstrate that stimulated emission depletion and LFSM can be performed on the same biological sample using a simple commercial mounting medium. It is hoped that this type of correlative imaging will provide a basis for a further enhanced resolution. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.


Assuntos
Microscopia de Fluorescência/instrumentação , Imagem Individual de Molécula/instrumentação , Anfíbios , Animais , Cromossomos/química , Cromossomos/ultraestrutura , Desenho de Equipamento , Corantes Fluorescentes , Camundongos , Microscopia Confocal/instrumentação , Microscopia Confocal/métodos , Microscopia de Fluorescência/métodos , Compostos Orgânicos , Estudo de Prova de Conceito , Imagem Individual de Molécula/métodos , Complexo Sinaptonêmico/química , Complexo Sinaptonêmico/ultraestrutura , Xantenos
8.
Fertil Steril ; 116(2): 583-596, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-33926715

RESUMO

OBJECTIVE: To quantify the percentage of monopronuclear-derived blastocysts (MNBs) that are potentially useful for reproductive purposes using classic and state-of-the-art chromosome analysis approaches, and to study chromosomal distribution in the inner cell mass (ICM) and trophectoderm (TE) for intertissue/intratissue concordance comparison. DESIGN: Prospective experimental study. SETTING: Single-center in vitro fertilization clinic and reproductive genetics laboratory. PATIENT(S): A total of 1,128 monopronuclear zygotes were obtained between June 2016 and December 2018. INTERVENTION(S): MNBs were whole-fixed or biopsied to obtain a portion of ICM and 2 TE portions (TE1 and TE2) and were subsequently analyzed by fluorescence in situ hybridization, new whole-genome sequencing, and fingerprinting by single-nucleotide polymorphism array-based techniques (a-SNP). MAIN OUTCOME MEASURE(S): We assessed MNB rate, ploidy rate, and chromosomal constitution by new whole-genome sequencing, and parental composition by comparative a-SNP, performed in a "trio"-format (embryo/parents). The 24-chromosome distribution was compared between the TE and the ICM and within the TE. RESULT(S): A total of 18.4% of monopronuclear zygotes progressed to blastocysts; 77.6% of MNBs were diploid; 20% of MNBs were male and euploid, which might be reproductively useful. Seventy-five percent of MNBs were biparental and half of them were euploid, indicating that 40% might be reproductively useful. Intratissue concordance (TE1/TE2) was established for 93.3% and 73.3% for chromosome matching. Intertissue concordance (TE/ICM) was established for 78.8%, but 57.6% for chromosome matching. When segmental aneuploidy was not considered, intratissue concordance and chromosome matching increased to 100% and 80%, respectively, and intertissue concordance and chromosome matching increased to 84.8% and 75.8%, respectively. CONCLUSION(S): The a-SNP-trio strategy provides information about ploidy, euploidy, and parental origin in a single biopsy. This approach enabled us to identify 40% of MNBs with reproductive potential, which can have a significant effect in the clinical setting. Additionally, segmental aneuploidy is relevant for mismatched preimplantation genetic testing of aneuploidies, both within and between MNB tissues. Repeat biopsy might clarify whether segmental aneuploidy is a prone genetic character.


Assuntos
Blastocisto/ultraestrutura , Cromossomos/ultraestrutura , Ploidias , Polimorfismo de Nucleotídeo Único , Biópsia , Blastocisto/patologia , Massa Celular Interna do Blastocisto/ultraestrutura , Impressões Digitais de DNA , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Hibridização in Situ Fluorescente , Estudos Prospectivos
9.
PLoS Genet ; 17(4): e1009502, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33861748

RESUMO

Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the "karyograph", which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.


Assuntos
Cromossomos/genética , Evolução Molecular , Especiação Genética , Cariótipo , Animais , Centrômero/genética , Inversão Cromossômica/genética , Cromossomos/ultraestrutura , Peixes/genética , Humanos , Cadeias de Markov , Modelos Estatísticos , Filogenia
10.
Cytogenet Genome Res ; 161(1-2): 6-13, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33556945

RESUMO

Proechimys species are remarkable for their extensive chromosome rearrangements, representing a good model to understand genome evolution. Herein, we cytogenetically analyzed 3 different cytotypes of Proechimys gr. goeldii to assess their evolutionary relationship. We also mapped the transposable element SINE-B1 on the chromosomes of P. gr. goeldii in order to investigate its distribution among individuals and evaluate its possible contribution to karyotype remodeling in this species. SINE-B1 showed a dispersed distribution along chromosome arms and was also detected at the pericentromeric regions of some chromosomes, including pair 1 and the sex chromosomes, which are involved in chromosome rearrangements. In addition, we describe a new cytotype for P. gr. goeldii, reinforcing the significant role of gross chromosomal rearrangements during the evolution of the genus. The results of FISH with SINE-B1 suggest that this issue should be more deeply investigated for a better understanding of its role in the mechanisms involved in the wide variety of Proechimys karyotypes.


Assuntos
Cromossomos/ultraestrutura , Rearranjo Gênico , Roedores/genética , Elementos Nucleotídeos Curtos e Dispersos , Animais , Bandeamento Cromossômico , Evolução Molecular , Feminino , Genoma , Heterocromatina/química , Hibridização in Situ Fluorescente , Cariótipo , Masculino , Cromossomos Sexuais , América do Sul
11.
Cytogenet Genome Res ; 161(1-2): 70-81, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33601372

RESUMO

Basic and molecular cytogenetic techniques were carried out in 3 Neotropical region populations of catfishes, two of Trachelyopterus galeatus (one from the marshlands of Paraguay River basin and another from Lago Catalão, Amazon River basin) and one of Trachelyopterus porosus, a sympatric population to T. galeatus from the Amazon River basin. This study aimed to describe and understand the structure and evolution of Trachelyopterus B chromosomes, mainly through physical mapping of repetitive elements. A diploid number of 58 chromosomes was found for all individuals, as well as the presence of B chromosomes. For T. porosus this is the first report of a supernumerary. The sympatric species of T. galeatus and T. porosus from Amazon River had 1-3 B chromosomes and T. galeatus from Paraguay River had 1-2 B chromosomes, all of them showed intra- and interindividual numerical variation. Two females of T. porosus exhibited a new variant B chromosome (B2), previously not seen in Auchenipteridae, which might have originated from B1 chromosomes. All B chromosomes were entirely heterochromatic. In contrast to all complement A and B2 chromosomes, in which the telomeric sequences were found in the telomeric regions, B1 chromosomes of all populations were totally marked by (TTAGGG)n probes. (GATA)n sequence sites were found through all complement A chromosomes, but B1 and B2 chromosomes exhibited only a clustered block in one of the chromosome arms. The most frequent B chromosomes (B1) in all populations/species, including those previously studied in Auchenipteridae catfishes, share the following characteristics: totally heterochromatic, small, metacentric, with accumulation of repetitive (TTAGGG)n sequences, and a low number of (GATA)n copies, which might suggest a common ancient origin in Trachelyopterus species/populations.


Assuntos
Peixes-Gato/genética , Cromossomos/ultraestrutura , Animais , Brasil , Mapeamento Cromossômico , Análise Citogenética , Citogenética , Diploide , Feminino , Cariótipo , Masculino , Repetições de Microssatélites , Paraguai , Sequências Repetitivas de Ácido Nucleico , Telômero/ultraestrutura
12.
J Assist Reprod Genet ; 38(2): 387-396, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33398513

RESUMO

PURPOSE: To evaluate the factors that affect the incidence of euploid balanced embryos and interchromosomal effect (ICE) in carriers of different structural rearrangements. METHODS: This retrospective study includes 95 couples with reciprocal translocations (RecT) and 36 couples with Robertsonian translocations (RobT) undergoing Preimplantation Genetic Testing for Structural Rearrangements (PGT-SR) between March 2016 and July 2019. Next-generation sequencing (NGS) was the technique used coupled with trophectoderm (TE) biopsy. Only cases with females under 38 years were included. A total of 532 blastocysts were evaluated. RESULTS: The euploidy rate was similar in RobT when compared with RecT carriers [57/156 (36.5%) vs. 112/376 (29.8%), p = 0.127]. The pure ICE rate was significantly higher in RobT carriers [48/156 (30.8%) vs. 53/376 (14.1%), p < 0.001] than it was in RecT carriers. Female age was the independent factor for the probability of obtaining a euploid embryo in RecT and RobT carriers, and increasing female age decreases the probability of obtaining a euploid embryo. In RecT carriers, no significant differences were observed in euploidy rates, pure ICE, or combined ICE according to the length of the translocated fragment and the chromosome group. However, total ICE was significantly lower when there was a breakpoint in the short chromosome arm together with a breakpoint in the long arm [(44/158 (27.8%) for pq or qp, 51/155 (32.9%) for pp and 30/63 (47.6%) for qq; p = 0.02]. CONCLUSION: The incidence of euploid/balanced blastocysts was similar in both types of translocations. However, there was a significant increase in pure ICE in RobT compared to RecT carriers. In RecT carriers, the presence of the breakpoints in the long arm of the chromosomes involved in the rearrangement resulted in a higher total ICE.


Assuntos
Cromossomos/genética , Sequenciamento de Nucleotídeos em Larga Escala/tendências , Diagnóstico Pré-Implantação , Translocação Genética/genética , Adulto , Blastocisto/metabolismo , Blastocisto/patologia , Cromossomos/ultraestrutura , Hibridização Genômica Comparativa , Transferência Embrionária , Feminino , Fertilização In Vitro/tendências , Testes Genéticos/métodos , Humanos , Masculino , Ploidias , Gravidez , Taxa de Gravidez , Estudos Retrospectivos , Adulto Jovem
13.
Exp Cell Res ; 398(1): 112386, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-33220259

RESUMO

Here we describe novel spherical structures that are induced by cold shock on the lampbrush chromosomes (LBCs) of Xenopus laevis oocytes. We call these structures cold bodies or C-bodies. C-bodies are distributed symmetrically on homologous LBCs, with a pattern similar to that of 5S rDNA. Neither active transcription nor translation is necessary for their formation. Similar protrusions occur on the edges of some nucleoli. Endogenous LBCs as well as those derived from injected sperm form C-bodies under cold shock conditions. The function of C-bodies is unknown.


Assuntos
Estruturas do Núcleo Celular/ultraestrutura , Núcleo Celular/ultraestrutura , Cromossomos/ultraestrutura , Resposta ao Choque Frio , Oócitos/ultraestrutura , Animais , Núcleo Celular/genética , Núcleo Celular/metabolismo , Estruturas do Núcleo Celular/metabolismo , Cromossomos/genética , Feminino , Oócitos/metabolismo , Xenopus laevis
14.
Genes (Basel) ; 11(12)2020 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-33352937

RESUMO

The ice cod Arctogadus glacialis (Peters, 1872) is one of the few fish species endemic to the Arctic. With a circumpolar distribution, the species is confined to the fjords and shelves of the Arctic seas. Biological information on A. glacialis is scarce, with genomic information restricted to microsatellites. Within the frame of the TUNU-Programme: Arctic Ocean Fishes-Diversity, Adaptation and Conservation, we studied A. glacialis at the chromosomal level to explore fish diversity and evolutionary aspects. The analysis of over 50 individuals from the Northeast Greenland fjords between latitudes 71°09' N and 76°42' N revealed a remarkable intraspecific diversity epitomized by chromosome numbers spanning from 28 to 33, the occurrence of putative B chromosomes, and diversified patterns of distribution of heterochromatin and rDNAs. The number of B chromosomes followed a latitudinal gradient from 0-2 in the north to 2-5 in the south. Considering the benthic and rather stationary life history of this species, the observed chromosomal differences might have arisen independently, possibly driven and/or fostered by the dynamics of repetitive sequences, and are being fixed in relatively isolated fjord populations. The resulting latitudinal cline we observe today might have repercussions on the fate of local populations facing the ongoing climate-driven environmental changes.


Assuntos
Cromossomos , Gadiformes/genética , Adaptação Fisiológica , Animais , Regiões Árticas , Mapeamento Cromossômico , Cromossomos/ultraestrutura , Mudança Climática , DNA Ribossômico/genética , Diploide , Feminino , Deriva Genética , Genoma , Groenlândia , Heterocromatina/genética , Cariótipo , Masculino , Mitose
15.
Cytogenet Genome Res ; 160(9): 539-553, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33227787

RESUMO

The family Aspredinidae comprises a clade of complex systematic relationships, both from molecular and morphological approaches. In this study, conventional and molecular cytogenetic studies coupled with nucleotide sequencing were performed in 6 Aspredininae species (Amaralia hypsiura, Bunocephalus cf. aloikae, Bunocephalus amaurus, Bunocephalus aff. coracoideus, Bunocephalus verrucosus, and Platystacus cotylephorus) from different locations of the Amazon hydrographic basin. Our results showed highly divergent diploid numbers (2n) among the species, ranging from 49 to 74, including the occurrence of an XX/X0 sex chromosome system. A neighbor-joining phylogram based on the cytochrome c oxidase I (COI) showed that Bunocephalus coracoideus is not a monophyletic clade, but closely related to B. verrucosus. The karyotypic data associated with COI suggest an ancestral karyotype for Aspredinidae with a reduced 2n, composed of bi-armed chromosomes and a trend toward chromosomal fissions resulting in higher diploid number karyotypes, mainly composed of acrocentric chromosomes. Evolutionary relationships were discussed under a phylogenetic context with related species from different Siluriformes families. The karyotype features and chromosomal diversity of Aspredinidae show an amazing differentiation, making this family a remarkable model for investigating the evolutionary dynamics in siluriforms as well as in fish as a whole.


Assuntos
Peixes-Gato/genética , Cromossomos/genética , Animais , Evolução Biológica , Brasil , Peixes-Gato/classificação , Cromossomos/ultraestrutura , Código de Barras de DNA Taxonômico , DNA Ribossômico/genética , Diploide , Evolução Molecular , Feminino , Hibridização in Situ Fluorescente , Cariotipagem , Masculino , Filogenia , RNA Ribossômico 18S/genética , RNA Ribossômico 5S/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico , Cromossomos Sexuais/genética , Cromossomos Sexuais/ultraestrutura , Especificidade da Espécie
16.
J Cell Mol Med ; 24(22): 12900-12909, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33052009

RESUMO

Long non-coding RNAs (lncRNAs), as part of the family of non-protein-coding transcripts, are implicated in the occurrence and progression of several cardiovascular diseases (CVDs). With recent advances in lncRNA research, these molecules are purported to regulate gene expression at multiple levels, thereby producing beneficial or detrimental biological effects during CVD pathogenesis. At the transcriptional level, lncRNAs affect gene expression by interacting with DNA and proteins, for example, components of chromatin-modifying complexes, or transcription factors affecting chromatin status. These potential mechanisms suggest that lncRNAs guide proteins to specific gene loci (eg promoter regions), or forestall proteins to specific genomic sites via DNA binding. Additionally, some lncRNAs are required for correct chromatin conformation, which occurs via chromatin looping in enhancer-like models. At the post-transcriptional level, lncRNAs interact with RNA molecules, mainly microRNAs (miRNAs) and mRNAs, potentially regulating CVD pathophysiological processes. Moreover, lncRNAs appear to post-transcriptionally modulate gene expression by participating in mRNA splicing, stability, degradation and translation. Thus, the purpose of this review is to provide a comprehensive summary of lncRNAs implicated in CVD biological processes, with an emphasis on potential mechanisms of action.


Assuntos
Doenças Cardiovasculares/genética , Doenças Cardiovasculares/imunologia , RNA Longo não Codificante/genética , Animais , Apoptose , Biomarcadores/metabolismo , Doenças Cardiovasculares/metabolismo , Cromatina/metabolismo , Cromossomos/ultraestrutura , DNA/química , Elementos Facilitadores Genéticos/genética , Fibrose/metabolismo , Humanos , MicroRNAs/metabolismo , Miócitos Cardíacos/citologia , Regiões Promotoras Genéticas , Ligação Proteica , Processamento Pós-Transcricional do RNA , RNA Longo não Codificante/metabolismo , RNA não Traduzido/metabolismo
17.
Am J Med Genet A ; 182(11): 2529-2532, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32779332

RESUMO

Copy number variants (CNVs) are significant causes of rare and undiagnosed diseases. Parallel detection of single nucleotide variants (SNVs) and CNVs with exome analysis, if feasible, would shorten the diagnostic closure in a timely manner. We validated such "parallel" approach through a cohort study of 791 undiagnosed patients. In addition to routine exome analysis, we applied an innovative algorithm EXCAVATOR2 which enhances sensitivity by paradoxically exploiting read depth data that covers nonexonic regions where baits were not originally intended to hybridize. About 48 patients had copy number variations, 42 deletions, and 6 duplications with a resolution of 0.51-14.7 mega base pairs. Importantly from a clinical standpoint, we identified three patients with "dual diagnosis" due to concurrent pathogenic CNV and SNV. We suggest "hitting two birds with one stone" approach to exome data is an efficient strategy in deciphering undiagnosed patients and may well be considered as a first-tier genetic test.


Assuntos
Variações do Número de Cópias de DNA , Exoma , Polimorfismo de Nucleotídeo Único , Sequenciamento Completo do Exoma , Algoritmos , Cromossomos/ultraestrutura , Deleção de Genes , Testes Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Curva ROC , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
18.
PLoS Biol ; 18(8): e3000817, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32813728

RESUMO

During meiosis, chromosomes adopt a specialized organization involving assembly of a cohesin-based axis along their lengths, with DNA loops emanating from this axis. We applied novel, quantitative, and widely applicable cytogenetic strategies to elucidate the molecular bases of this organization using Caenorhabditis elegans. Analyses of wild-type (WT) chromosomes and de novo circular minichromosomes revealed that meiosis-specific HORMA-domain proteins assemble into cohorts in defined numbers and co-organize the axis together with 2 functionally distinct cohesin complexes (REC-8 and COH-3/4) in defined stoichiometry. We further found that REC-8 cohesins, which load during S phase and mediate sister-chromatid cohesion, usually occur as individual complexes, supporting a model wherein sister cohesion is mediated locally by a single cohesin ring. REC-8 complexes are interspersed in an alternating pattern with cohorts of axis-organizing COH-3/4 complexes (averaging 3 per cohort), which are insufficient to confer cohesion but can bind to individual chromatids, suggesting a mechanism to enable formation of asymmetric sister-chromatid loops. Indeed, immunofluorescence/fluorescence in situ hybridization (immuno-FISH) assays demonstrate frequent asymmetry in genomic content between the loops formed on sister chromatids. We discuss how features of chromosome axis/loop architecture inferred from our data can help to explain enigmatic, yet essential, aspects of the meiotic program.


Assuntos
Caenorhabditis elegans/genética , Proteínas de Ciclo Celular/genética , Cromátides/ultraestrutura , Proteínas Cromossômicas não Histona/genética , Cromossomos/ultraestrutura , Meiose , Complexo Sinaptonêmico/ultraestrutura , Animais , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Ciclo Celular/metabolismo , Cromátides/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Segregação de Cromossomos , Cromossomos/metabolismo , Análise Citogenética , Hibridização in Situ Fluorescente , Fase S/genética , Complexo Sinaptonêmico/metabolismo
19.
Nat Commun ; 11(1): 3531, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32669601

RESUMO

Homologous recombination (HR) factors were recently implicated in DNA replication fork remodeling and protection. While maintaining genome stability, HR-mediated fork remodeling promotes cancer chemoresistance, by as-yet elusive mechanisms. Five HR cofactors - the RAD51 paralogs RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3 - recently emerged as crucial tumor suppressors. Albeit extensively characterized in DNA repair, their role in replication has not been addressed systematically. Here, we identify all RAD51 paralogs while screening for modulators of RAD51 recombinase upon replication stress. Single-molecule analysis of fork progression and architecture in isogenic cellular systems shows that the BCDX2 subcomplex restrains fork progression upon stress, promoting fork reversal. Accordingly, BCDX2 primes unscheduled degradation of reversed forks in BRCA2-defective cells, boosting genomic instability. Conversely, the CX3 subcomplex is dispensable for fork reversal, but mediates efficient restart of reversed forks. We propose that RAD51 paralogs sequentially orchestrate clinically relevant transactions at replication forks, cooperatively promoting fork remodeling and restart.


Assuntos
Replicação do DNA , Rad51 Recombinase/metabolismo , Proteína BRCA2/metabolismo , Linhagem Celular Tumoral , Estruturas Cromossômicas/metabolismo , Cromossomos/ultraestrutura , Dano ao DNA , Reparo do DNA , Proteínas de Ligação a DNA/metabolismo , Instabilidade Genômica , Recombinação Homóloga , Humanos , Microscopia , Mutagênicos , Mutação , Osteossarcoma/metabolismo , RNA Interferente Pequeno/metabolismo
20.
PLoS Genet ; 16(7): e1008918, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32730246

RESUMO

Holocentric chromosomes possess multiple kinetochores along their length rather than the single centromere typical of other chromosomes [1]. They have been described for the first time in cytogenetic experiments dating from 1935 and, since this first observation, the term holocentric chromosome has referred to chromosomes that: i. lack the primary constriction corresponding to centromere observed in monocentric chromosomes [2]; ii. possess multiple kinetochores dispersed along the chromosomal axis so that microtubules bind to chromosomes along their entire length and move broadside to the pole from the metaphase plate [3]. These chromosomes are also termed holokinetic, because, during cell division, chromatids move apart in parallel and do not form the classical V-shaped figures typical of monocentric chromosomes [4-6]. Holocentric chromosomes evolved several times during both animal and plant evolution and are currently reported in about eight hundred diverse species, including plants, insects, arachnids and nematodes [7,8]. As a consequence of their diffuse kinetochores, holocentric chromosomes may stabilize chromosomal fragments favouring karyotype rearrangements [9,10]. However, holocentric chromosome may also present limitations to crossing over causing a restriction of the number of chiasma in bivalents [11] and may cause a restructuring of meiotic divisions resulting in an inverted meiosis [12].


Assuntos
Caenorhabditis elegans/genética , Cromossomos/genética , Cinetocoros/ultraestrutura , Meiose/genética , Animais , Caenorhabditis elegans/citologia , Centrômero/genética , Centrômero/ultraestrutura , Cromátides/genética , Cromátides/ultraestrutura , Segregação de Cromossomos/genética , Cromossomos/ultraestrutura , Cariótipo , Plantas/genética
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