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1.
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
2.
Bioinformatics ; 37(Suppl_1): i272-i279, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34252966

RESUMO

MOTIVATION: The high-throughput chromosome conformation capture (Hi-C) technique has enabled genome-wide mapping of chromatin interactions. However, high-resolution Hi-C data requires costly, deep sequencing; therefore, it has only been achieved for a limited number of cell types. Machine learning models based on neural networks have been developed as a remedy to this problem. RESULTS: In this work, we propose a novel method, EnHiC, for predicting high-resolution Hi-C matrices from low-resolution input data based on a generative adversarial network (GAN) framework. Inspired by non-negative matrix factorization, our model fully exploits the unique properties of Hi-C matrices and extracts rank-1 features from multi-scale low-resolution matrices to enhance the resolution. Using three human Hi-C datasets, we demonstrated that EnHiC accurately and reliably enhanced the resolution of Hi-C matrices and outperformed other GAN-based models. Moreover, EnHiC-predicted high-resolution matrices facilitated the accurate detection of topologically associated domains and fine-scale chromatin interactions. AVAILABILITY AND IMPLEMENTATION: EnHiC is publicly available at https://github.com/wmalab/EnHiC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Cromatina , Software , Mapeamento Cromossômico , Cromossomos , Humanos , Conformação Molecular
3.
BMC Genomics ; 22(1): 499, 2021 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-34217222

RESUMO

BACKGROUND: Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear lamina dynamically act on chromatin at multiple levels. Here, we explore long-range interaction patterns between topologically associated domains (TADs) in several cell types. RESULTS: We find that TAD long-range interactions are connected to many key features of chromatin organization, including open and closed compartments, compaction and loop extrusion processes. Domains that form large TAD cliques tend to be repressive across cell types, when comparing gene expression, LINE/SINE repeat content and chromatin subcompartments. Further, TADs in large cliques are larger in genomic size, less dense and depleted of convergent CTCF motifs, in contrast to smaller and denser TADs formed by a loop extrusion process. CONCLUSIONS: Our results shed light on the organizational principles that govern repressive and active domains in the human genome.


Assuntos
Montagem e Desmontagem da Cromatina , Cromatina , Animais , Cromossomos , Expressão Gênica , Genoma Humano , Humanos
4.
Nat Commun ; 12(1): 4125, 2021 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-34226565

RESUMO

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence-absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the 'Pawnee' cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence-absence and functional annotation database among genomes and within the two outbred haplotypes of the 'Lakota' genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.


Assuntos
Carya/genética , Cromossomos , Genoma de Planta , Genômica , Melhoramento Vegetal , Diploide , Resistência à Doença/genética , Variação Genética , Genótipo , Haplótipos , Fenótipo
5.
Curr Protoc ; 1(7): e198, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34286910

RESUMO

The intricate folding of chromatin enables living organisms to store genomic material in an extremely small volume while facilitating proper cell function. Hi-C is a chromosome conformation capture (3C)-based technology to detect pair-wise chromatin interactions genome-wide, and has become a benchmark tool to study genome organization. In Hi-C, chromatin conformation is first captured by chemical cross-linking of cells. Cells are then lysed and subjected to restriction enzyme digestion, before the ends of the resulting fragments are marked with biotin. Fragments within close 3D proximity are ligated, and the biotin label is used to selectively enrich for ligated junctions. Finally, isolated ligation products are prepared for high-throughput sequencing, which enables the mapping of pair-wise chromatin interactions genome-wide. Over the past decade, "next-generation" sequencing has become cheaper and easier to perform, enabling more interactions to be sampled to obtain higher resolution in chromatin interaction maps. Here, we provide an in-depth guide to performing an up-to-date Hi-C procedure on mammalian cell lines. These protocols include recent improvements that increase the resolution potential of the assay, namely by enhancing cross-linking and using a restriction enzyme cocktail. These improvements result in a versatile Hi-C procedure that enables the detection of genome folding features at a wide range of distances. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Fixation of nuclear conformation Basic Protocol 2: Chromosome conformation capture Basic Protocol 3: Hi-C sequencing library preparation.


Assuntos
Cromatina , Cromossomos , Animais , Cromatina/genética , Cromossomos/genética , Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Conformação de Ácido Nucleico
6.
Sensors (Basel) ; 21(12)2021 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-34207789

RESUMO

Scheduling sensor nodes has an important role in real monitoring applications using sensor networks, lowering the power consumption and maximizing the network lifetime, while maintaining the satisfaction to application requirements. Nevertheless, this problem is usually very complex and not easily resolved by analytical methods. In a different manner, genetic algorithms (GAs) are heuristic search strategies that help to find the exact or approximate global optimal solution efficiently with a stochastic approach. Genetic algorithms are advantageous for their robustness to discrete and noisy objective functions, as they are only evaluated at independent points without requirements of continuity or differentiability. However, as explained in this paper, a time-based sensor network schedule cannot be represented by a chromosome with fixed length that is required in traditional genetic algorithms. Therefore, an extended genetic algorithm is introduced with variable-length chromosome (VLC) along with mutation and crossover operations in order to address this problem. Simulation results show that, with help of carefully defined fitness functions, the proposed scheme is able to evolve the individuals in the population effectively and consistently from generation to generation towards optimal ones, and the obtained network schedules are better optimized in comparison with the result of algorithms employing a fixed-length chromosome.


Assuntos
Redes de Comunicação de Computadores , Tecnologia sem Fio , Algoritmos , Cromossomos , Simulação por Computador , Humanos
7.
Nat Commun ; 12(1): 3708, 2021 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-34140506

RESUMO

3D genome alternations can dysregulate gene expression by rewiring enhancer-promoter interactions and lead to diseases. We report integrated analyses of 3D genome alterations and differential gene expressions in 18 newly diagnosed T-lineage acute lymphoblastic leukemia (T-ALL) patients and 4 healthy controls. 3D genome organizations at the levels of compartment, topologically associated domains and loop could hierarchically classify different subtypes of T-ALL according to T cell differentiation trajectory, similar to gene expressions-based classification. Thirty-four previously unrecognized translocations and 44 translocation-mediated neo-loops are mapped by Hi-C analysis. We find that neo-loops formed in the non-coding region of the genome could potentially regulate ectopic expressions of TLX3, TAL2 and HOXA transcription factors via enhancer hijacking. Importantly, both translocation-mediated neo-loops and NUP98-related fusions are associated with HOXA13 ectopic expressions. Patients with HOXA11-A13 expressions, but not other genes in the HOXA cluster, have immature immunophenotype and poor outcomes. Here, we highlight the potentially important roles of 3D genome alterations in the etiology and prognosis of T-ALL.


Assuntos
Cromossomos/metabolismo , Proteínas de Homeodomínio/genética , Leucemia-Linfoma de Células T do Adulto/genética , Conformação Molecular , Leucemia-Linfoma Linfoblástico de Células T Precursoras/genética , Linfócitos T/metabolismo , Translocação Genética , Acetilação , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Linhagem Celular Tumoral , Linhagem da Célula , Criança , Sequenciamento de Cromatina por Imunoprecipitação , Cromossomos/genética , Progressão da Doença , Elementos Facilitadores Genéticos , Perfilação da Expressão Gênica , Regulação Leucêmica da Expressão Gênica/genética , Regulação Leucêmica da Expressão Gênica/imunologia , Ontologia Genética , Hematopoese/genética , Histonas/metabolismo , Proteínas de Homeodomínio/metabolismo , Humanos , Imunofenotipagem , Leucemia-Linfoma de Células T do Adulto/metabolismo , Leucemia-Linfoma de Células T do Adulto/mortalidade , Leucemia-Linfoma de Células T do Adulto/patologia , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Complexo de Proteínas Formadoras de Poros Nucleares/genética , Complexo de Proteínas Formadoras de Poros Nucleares/metabolismo , Leucemia-Linfoma Linfoblástico de Células T Precursoras/metabolismo , Leucemia-Linfoma Linfoblástico de Células T Precursoras/mortalidade , Leucemia-Linfoma Linfoblástico de Células T Precursoras/patologia , Prognóstico , Linfócitos T/patologia , Adulto Jovem
8.
Zool Res ; 42(4): 417-422, 2021 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-34075735

RESUMO

The Chinese longsnout catfish ( Leiocassis longirostris Günther) is one of the most economically important freshwater fish in China. As wild populations have declined sharply in recent years, it is also a valuable model for research on sexual dimorphism, comparative biology, and conservation. However, the current lack of high-quality chromosome-level genome information for the species hinders the advancement of comparative genomic analysis and evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris. The total genome was 703.19 Mb, with 389 contigs and contig N50 length of 4.29 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome sequences (685.53 Mb) were scaffolded into 26 chromosomes ranging from 17.36 to 43.97 Mb, resulting in a chromosomal anchoring rate for the genome of 97.44%. In total, 23 708 protein-coding genes were identified in the genome. Phylogenetic analysis indicated that L. longirostris and its closest related species P. fulvidraco diverged approximately 26.6 million years ago. This high-quality reference genome of L. longirostris should pave the way for future genomic comparisons and evolutionary research.


Assuntos
Peixes-Gato/genética , Cromossomos/genética , Genoma , Animais , China , Filogenia , Especificidade da Espécie
9.
Nat Commun ; 12(1): 3551, 2021 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-34112792

RESUMO

Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere genome assemblies of a fungal pathogen of wheat to establish a nucleotide-level map of structural variation. We show that the recent emergence of pesticide resistance has been disproportionally driven by rearrangements. We use machine learning to train a model on structural variation events based on 30 chromosomal sequence features. We show that base composition and gene density are the major determinants of structural variation. Retrotransposons explain most inversion, indel and duplication events. We apply our model to Arabidopsis thaliana and show that our approach extends to more complex genomes. Finally, we analyze complete genomes of haploid offspring in a four-generation pedigree. Meiotic crossover locations are enriched for new rearrangements consistent with crossovers being mutational hotspots. The model trained on species-wide structural variation accurately predicts the position of >74% of newly generated variants along the pedigree. The predictive power highlights causality between specific sequence features and the induction of chromosomal rearrangements. Our work demonstrates that training sequence-derived models can accurately identify regions of intrinsic DNA instability in eukaryotic genomes.


Assuntos
Ascomicetos/genética , Ascomicetos/patogenicidade , Cromossomos/genética , Variação Genética , Genoma , Genômica/métodos , Aprendizado de Máquina , Meiose/genética , Arabidopsis/genética , Cromossomos/metabolismo , Simulação por Computador , Troca Genética , Eucariotos/genética , Evolução Molecular , Genes Duplicados , Estudo de Associação Genômica Ampla , Mutação INDEL , Modelos Genéticos , Linhagem , Filogenia , Polimorfismo Genético , Polimorfismo de Nucleotídeo Único , Retroelementos/genética , Inversão de Sequência
10.
Nat Commun ; 12(1): 3531, 2021 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-34112794

RESUMO

Camptothecin and its derivatives are widely used for treating malignant tumors. Previous studies revealed only a limited number of candidate genes for camptothecin biosynthesis in Camptotheca acuminata, and it is still poorly understood how its biosynthesis of camptothecin has evolved. Here, we report a high-quality, chromosome-level C. acuminata genome assembly. We find that C. acuminata experiences an independent whole-genome duplication and numerous genes derive from it are related to camptothecin biosynthesis. Comparing with Catharanthus roseus, the loganic acid O-methyltransferase (LAMT) in C. acuminata fails to convert loganic acid into loganin. Instead, two secologanic acid synthases (SLASs) convert loganic acid to secologanic acid. The functional divergence of the LAMT gene and positive evolution of two SLAS genes, therefore, both contribute greatly to the camptothecin biosynthesis in C. acuminata. Our results emphasize the importance of high-quality genome assembly in identifying genetic changes in the evolutionary origin of a secondary metabolite.


Assuntos
Camptotheca/metabolismo , Camptotecina/metabolismo , Cromossomos/metabolismo , Genoma de Planta , Metabolismo Secundário/genética , Camptotheca/enzimologia , Camptotheca/genética , Camptotecina/biossíntese , Cromossomos/genética , Sistema Enzimático do Citocromo P-450 , Evolução Molecular , Regulação da Expressão Gênica de Plantas/genética , Genes Duplicados , Genômica , Iridoides/metabolismo , Oxirredutases atuantes sobre Doadores de Grupo CH-CH , Filogenia , Proteína O-Metiltransferase/genética , Proteína O-Metiltransferase/metabolismo , RNA-Seq , Vimblastina/metabolismo
11.
Neuroscience ; 468: 199-210, 2021 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-34166762

RESUMO

Phosphatase and tensin homolog deleted on chromosome ten (PTEN) is a crucial regulator of neuronal development, neuronal survival, axonal regeneration, and synaptic plasticity. In this study we examined the potential role of PTEN in cognitive function in a mouse model of perioperative neurocognitive disorder (PND). Adult male C57BL/6J mice received intracerebroventricular injections of small interfering RNA (siRNA) against PTEN or control siRNA 3 days prior to exploratory laparotomy (n = 8 per group). A group of healthy mice not undergoing surgery included as additional control. Barnes maze and fear conditioning tests were conducted 7 days after surgery. Mice were then sacrificed to examine the expression of PTEN, AMP-activated protein kinase (AMPK), ionized calcium binding adaptor molecule (Iba)-1, B-cell lymphoma (Bcl)-2, Bcl2-associated X protein (Bax), interleukin (IL)-1ß, and tumor necrosis factor (TNF)-α in the hippocampus. The microglial activation was examined by immunohistochemistry using Iba-1 as a microglia maker. Nissl and terminal transferase deoxyuridine triphosphate nick-end labeling (TUNEL) staining were used to measure cell death and apoptosis. In comparison to the healthy controls, surgically treated mice had longer latency to identify the target box in both training and testing sessions in the Barnes maze test and shorter freezing time in the fear conditioning test. Surgically treated mice had increased expression of PTEN, AMPK, Bax, IL-1ß, and TNF-α, as well as increasing number of activated microglia and apoptosis neurons in the hippocampus. PTEN knockdown significantly attenuated the behavioral deficits in Barnes maze and fear conditioning tests, as well as over-expression of PTEN, AMPK, Bax, IL-1ß, and TNF-α induced by surgery. PTEN knockdown could attenuate cognitive deficits induced by trauma, likely through inhibiting the activation of microglia.


Assuntos
Transtornos Cognitivos , Animais , Cromossomos , Cognição , Masculino , Camundongos , Camundongos Endogâmicos C57BL , PTEN Fosfo-Hidrolase , Tensinas
12.
Mol Ecol ; 30(14): 3391-3393, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34145673

RESUMO

Despite the promise of ecological epigenetics, there remain few cases that clearly link epigenetic variation in wild animal populations to evolutionary change. In this issue of Molecular Ecology, Sun et al. provide such an example in white-throated sparrows-a fascinating system in which a large chromosomal rearrangement generates a "supergene" polymorphism linked to plumage colour, aggression and parenting behaviour. By combining whole genome bisulphite sequencing with RNA-sequencing and chromatin accessibility data, they show that the two alleles of this chromosomal polymorphism also exhibit substantial differences in DNA methylation levels, with implications for gene expression and transposable element activity. Their results provide a compelling case study for how genetic and epigenetic evolution proceed in concert. They also demonstrate the importance of integrating multiple types of genomic information to understand how gene regulation evolves, providing a model for future work in nonmodel species.


Assuntos
Pardais , Agressão , Alelos , Animais , Cromossomos , Epigênese Genética , Pardais/genética
13.
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
14.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(6): 569-572, 2021 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-34096028

RESUMO

OBJECTIVE: To assess the value of chromosomal microarray analysis (CMA) to verify a fetus with partial 18p deletion signaled by non-invasive prenatal testing. METHODS: G-banding chromosomal karyotyping analysis was carried out on amniotic fluid sample of the fetus and peripheral blood samples from the parents. Amniotic DNA was also subjected to CMA analysis. The fetus was also subjected to systematic ultrasound scan. RESULTS: The fetus was found to have a karyotype of 46,XX,18p+. CMA has revealed a 5 Mb deletion at 18p11.32-p11.31, a 2.9 Mb duplication at 18p11.31-p11.23, and a 2.5 Mb duplication at 18p11.23-p11.22. No chromosomal aberration or microdeletion/microduplication was detected in either parent. CONCLUSION: Non-invasive prenatal testing and CMA are both sensitive for the detection of chromosomal microdeletions and microduplications. CMA can help with clarification of genotype-phenotype correlation and facilitate prenatal diagnosis and genetic counseling for the family.


Assuntos
Deleção Cromossômica , Diagnóstico Pré-Natal , Cromossomos , Feminino , Feto , Humanos , Cariotipagem , Gravidez
15.
An Acad Bras Cienc ; 93(2): e20190426, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34105608

RESUMO

Cytogenetic analyses were performed on specimens of Leptodactylus bufonius from different localities in Argentina. Mitotic chromosomes were studied with Giemsa and differential staining techniques (Ag-NOR, C-banding, and CMA3/DAPI) and fluorescence in situ hybridization with the 18S DNAr probe. All specimens showed karyotypes with 2n = 2x = 22 and FN = 44. Secondary constrictions were present in the long arm of chromosome pair 8, coincident with Ag-NOR and hybridization signals of the 18S DNAr probe. The C-banding technique evidenced an important amount of heterochromatin with a sex-linked pericentromeric band in the short arm of chromosome pair 4. This heterochromatic band was heteromorphic in males but present in both homologues of females, and it was CMA3 positive (DAPI negative) at fluorescence staining. The occurrence of heteromorphic XY sex chromosomes in L. bufonius is the second known case in Leptodactylus and the fifth within the speciose family Leptodactylidae.


Assuntos
Anuros , Cromossomos Sexuais , Animais , Anuros/genética , Argentina , Bandeamento Cromossômico , Cromossomos/genética , Feminino , Hibridização in Situ Fluorescente , Masculino , Cromossomos Sexuais/genética
16.
Int J Mol Sci ; 22(11)2021 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-34067465

RESUMO

Cyclins and CDKs (Cyclin Dependent Kinases) are key players in the biology of eukaryotic cells, representing hubs for the orchestration of physiological conditions with cell cycle progression. Furthermore, as in the case of meiosis, cyclins and CDKs have acquired novel functions unrelated to this primal role in driving the division cycle. Meiosis is a specialized developmental program that ensures proper propagation of the genetic information to the next generation by the production of gametes with accurate chromosome content, and meiosis-specific cyclins are widespread in evolution. We have explored the diversification of CDK functions studying the meiosis-specific Crs1 cyclin in fission yeast. In addition to the reported role in DSB (Double Strand Break) formation, this cyclin is required for meiotic S-phase progression, a canonical role, and to maintain the architecture of the meiotic chromosomes. Crs1 localizes at the SPB (Spindle Pole Body) and is required to stabilize the cluster of telomeres at this location (bouquet configuration), as well as for normal SPB motion. In addition, Crs1 exhibits CDK(Cdc2)-dependent kinase activity in a biphasic manner during meiosis, in contrast to a single wave of protein expression, suggesting a post-translational control of its activity. Thus, Crs1 displays multiple functions, acting both in cell cycle progression and in several key meiosis-specific events.


Assuntos
Quinases Ciclina-Dependentes/genética , Ciclinas/genética , Meiose/genética , Fase S/genética , Cromossomos/genética , Processamento de Proteína Pós-Traducional/genética , Schizosaccharomyces/genética
17.
J Insect Sci ; 21(3)2021 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-33991100

RESUMO

The guarani group of Drosophila genus (Diptera: Drosophilidae) is formed by 24 species however the relationship of these species is not clear. In the present study are described the karyotypes of Drosophila sachapuyu Peñafiel and Rafael, 2018 and Drosophila zamorana Peñafiel and Rafael, 2018, two Andean species members of the guarani group. Mitotic chromosomes from cerebral ganglia of third stand larval were obtained by thermal shock and cell suspension techniques. The karyotype of D. sachapuyu, presents 2n = 10 (4R, 1V; X = R, Y = R) while D. zamorana exhibits karyotype 2n = 12 (5R, 1V; X = V, Y = R).


Assuntos
Drosophila , Cariótipo , Animais , Cromossomos , Drosophila/classificação , Drosophila/citologia , Drosophilidae/classificação , Equador , Filogenia
18.
Biophys J ; 120(12): 2521-2531, 2021 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-34023297

RESUMO

DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes proteins such as condensin. Here, however, we are interested in a different looping method whereby condensing agents (charge ≥+3) such as protamine proteins neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (≤1 µm) DNA fragments using atomic force microscopy. We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine's in vivo role for looping DNA into toroids and the mechanism of DNA condensation by condensing agents more broadly.


Assuntos
DNA , Protaminas , Cromossomos/metabolismo , DNA/genética , Repressores Lac/metabolismo , Conformação de Ácido Nucleico
19.
J Cell Sci ; 134(10)2021 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-34037217

RESUMO

The formation of crossovers between homologous chromosomes is key to sexual reproduction. In most species, crossovers are spaced further apart than would be expected if they formed independently, a phenomenon termed crossover interference. Despite more than a century of study, the molecular mechanisms implementing crossover interference remain a subject of active debate. Recent findings of how signaling proteins control the formation of crossovers and about the interchromosomal interface in which crossovers form offer new insights into this process. In this Review, we present a cell biological and biophysical perspective on crossover interference, summarizing the evidence that links interference to the spatial, dynamic, mechanical and molecular properties of meiotic chromosomes. We synthesize this physical understanding in the context of prevailing mechanistic models that aim to explain how crossover interference is implemented.


Assuntos
Troca Genética , Meiose , Cromossomos/genética
20.
Nucleic Acids Res ; 49(10): 5654-5670, 2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34048565

RESUMO

Integrons confer a rapid adaptation capability to bacteria. Integron integrases are able to capture and shuffle novel functions embedded in cassettes. Here, we investigated cassette recruitment in the Vibrio cholerae chromosomal integron during horizontal transfer. We demonstrated that the endogenous integrase expression is sufficiently triggered, after SOS response induction mediated by the entry of cassettes during conjugation and natural transformation, to mediate significant cassette insertions. These insertions preferentially occur at the attIA site, despite the presence of about 180 attC sites in the integron array. Thanks to the presence of a promoter in the attIA site vicinity, all these newly inserted cassettes are expressed and prone to selection. We also showed that the RecA protein is critical for cassette recruitment in the V. cholerae chromosomal integron but not in mobile integrons. Moreover, unlike the mobile integron integrases, that of V. cholerae is not active in other bacteria. Mobile integrons might have evolved from the chromosomal ones by overcoming host factors, explaining their large dissemination in bacteria and their role in antibioresistance expansion.


Assuntos
Cromossomos/metabolismo , Transferência Genética Horizontal/genética , Integrases/metabolismo , Integrons/genética , Vibrio cholerae/metabolismo , Cromossomos/genética , Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica/genética , Integrases/genética , Recombinases Rec A/genética , Recombinases Rec A/metabolismo , Recombinação Genética/genética , Vibrio cholerae/genética
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