RESUMO
The Structural Maintenance of Chromosomes (SMC) protein complexes are DNA-binding molecular machines required to shape chromosomes into functional units and to safeguard the genome through cell division. These ring-shaped multi-subunit protein complexes, which are present in all kingdoms of life, achieve this by organizing chromosomes in three-dimensional space. Mechanistically, the SMC complexes hydrolyze ATP to either stably entrap DNA molecules within their lumen, or rapidly reel DNA into large loops, which allow them to link two stretches of DNA in cis or trans. In this chapter, the canonical structure of the SMC complexes is first introduced, followed by a description of the composition and general functions of the main types of eukaryotic and prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.
Assuntos
Cromossomos , Cromossomos/química , Complexos Multiproteicos/metabolismo , Complexos Multiproteicos/química , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ciclo Celular/genética , DNA/química , DNA/metabolismo , DNA/genética , Proteínas Cromossômicas não Histona/metabolismo , Proteínas Cromossômicas não Histona/química , Trifosfato de Adenosina/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteínas de Ligação a DNA/químicaRESUMO
Three-dimensional (3D) chromosome structures are closely related to various chromosomal functions, and deep analysis of the structures is crucial for the elucidation of the functions. In recent years, chromosome conformation capture (3C) techniques combined with next-generation sequencing analysis have been developed to comprehensively reveal 3D chromosome structures. Micro-C is one such method that can detect the structures at nucleosome resolution. In this chapter, I provide a basic method for Micro-C analysis. I present and discuss a series of data analyses ranging from mapping to basic downstream analyses, including loop detection.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Software , Fluxo de Trabalho , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Cromossomos/genética , Biologia Computacional/métodos , Mapeamento Cromossômico/métodos , Nucleossomos/química , Nucleossomos/genética , Nucleossomos/metabolismoRESUMO
Hi-C is a popular ligation-based technique to detect 3D physical chromosome structure within the nucleus using cross-linking and next-generation sequencing. As an unbiased genome-wide assay based on chromosome conformation capture, it provides rich insights into chromosome structure, dynamic chromosome folding and interactions, and the regulatory state of a cell. Bioinformatics analyses of Hi-C data require dedicated protocols as most genome alignment tools assume that both paired-end reads will map to the same chromosome, resulting in large two-dimensional matrices as processed data. Here, we outline the necessary steps to generate high-quality aligned Hi-C data by separately mapping each read while correcting for biases from restriction enzyme digests. We introduce our own custom open-source pipeline, which enables users to select an aligner of their choosing with high accuracy and performance. This enables users to generate high-resolution datasets with fast turnaround and fewer unmapped reads. Finally, we discuss recent innovations in experimental techniques, bioinformatics techniques, and their applications in clinical testing for diagnostics.
Assuntos
Mapeamento Cromossômico , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , Software , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Biologia Computacional/métodos , Humanos , Mapeamento Cromossômico/métodos , Cromossomos/genética , Genômica/métodos , Cromatina/genética , Cromatina/químicaRESUMO
We describe an approach for reconstructing three-dimensional (3D) structures from single-cell Hi-C data. This approach has been inspired by a method of recurrence plots and visualization tools for nonlinear time series data. Some examples are also presented.
Assuntos
Análise de Célula Única , Análise de Célula Única/métodos , Imageamento Tridimensional/métodos , Humanos , Software , Cromossomos/genética , AlgoritmosRESUMO
Biomolecules contain various heterogeneities in their structures and local chemical properties, and their functions emerge through the dynamics encoded by these heterogeneities. Molecular dynamics model-based studies will greatly contribute to the elucidation of such chemical/mechanical structure-dynamics-function relationships and the mechanisms that generate them. Coarse-grained molecular dynamics models with appropriately designed nonuniform local interactions play an important role in considering the various phenomena caused by large molecular complexes consisting of various proteins and DNA such as nuclear chromosomes. Therefore, in this chapter, we will introduce a method for constructing a coarse-grained molecular dynamics model that simulates the global behavior of each chromosome in the nucleus of a mammalian cell containing many giant chromosomes.
Assuntos
Núcleo Celular , Simulação de Dinâmica Molecular , Núcleo Celular/metabolismo , Núcleo Celular/química , Animais , Humanos , Cromossomos/química , DNA/química , DNA/metabolismo , MamíferosRESUMO
Hi-C is a powerful method for obtaining genome-wide chromosomal structural information. The typical Hi-C analysis utilizes a two-dimensional (2D) contact matrix, which poses challenges for quantitative comparisons, visualizations, and integrations across multiple datasets. Here, we present a protocol for extracting one-dimensional (1D) features from chromosome structure data by HiC1Dmetrics. Leveraging these 1D features enables integrated analysis of Hi-C and epigenomic data.
Assuntos
Epigenômica , Epigenômica/métodos , Humanos , Cromossomos/genética , Software , Biologia Computacional/métodosRESUMO
BACKGROUND: Chromosome organization plays an important role in biological processes such as replication, regulation, and transcription. One way to study the relationship between chromosome structure and its biological functions is through Hi-C studies, a genome-wide method for capturing chromosome conformation. Such studies generate vast amounts of data. The problem is exacerbated by the fact that chromosome organization is dynamic, requiring snapshots at different points in time, further increasing the amount of data to be stored. We present a novel approach called the High-Efficiency Contact Matrix Compressor (HiCMC) for efficient compression of Hi-C data. RESULTS: By modeling the underlying structures found in the contact matrix, such as compartments and domains, HiCMC outperforms the state-of-the-art method CMC by approximately 8% and the other state-of-the-art methods cooler, LZMA, and bzip2 by over 50% across multiple cell lines and contact matrix resolutions. In addition, HiCMC integrates domain-specific information into the compressed bitstreams that it generates, and this information can be used to speed up downstream analyses. CONCLUSION: HiCMC is a novel compression approach that utilizes intrinsic properties of contact matrix, such as compartments and domains. It allows for a better compression in comparison to the state-of-the-art methods. HiCMC is available at https://github.com/sXperfect/hicmc .
Assuntos
Cromossomos , Humanos , Cromossomos/química , Algoritmos , Biologia Computacional/métodos , SoftwareRESUMO
Horseshoe bats (genus Rhinolophus, family Rhinolophidae) represent an important group within chiropteran phylogeny due to their distinctive traits, including constant high-frequency echolocation, rapid karyotype evolution, and unique immune system. Advances in evolutionary biology, supported by high-quality reference genomes and comprehensive whole-genome data, have significantly enhanced our understanding of species origins, speciation mechanisms, adaptive evolutionary processes, and phenotypic diversity. However, genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data, with only a single published genome of R. ferrumequinum currently available. In this study, we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat ( R. affinis). Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae. Notably, we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway, DNA repair, and apoptosis, which displayed signs of rapid evolution. In addition, we observed an expansion of the major histocompatibility complex class II (MHC-II) region and a higher copy number of the HLA- DQB2 gene in horseshoe bats compared to other chiropteran species. Based on whole-genome resequencing and population genomic analyses, we identified multiple candidate loci (e.g., GLI3) associated with variations in echolocation call frequency across R. affinis subspecies. This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.
Assuntos
Quirópteros , Ecolocação , Genoma , Animais , Quirópteros/genética , Quirópteros/virologia , Quirópteros/fisiologia , SARS-CoV-2/fisiologia , SARS-CoV-2/genética , Cromossomos/genéticaRESUMO
BACKGROUND: B chromosomes are extra non-essential elements present in several eukaryotes. Unlike A chromosomes which are essential and present in all individuals of a species, B chromosomes are not necessary for normal functioning of an organism. Formerly regarded as genetically inactive, B chromosomes have been discovered to not only express their own genes, but also to exert influence on gene expression in A chromosomes. Recent studies have shown that, in some Psalidodon (Characiformes, Characidae) species, B chromosomes might be associated with phenotypic effects, such as changes in the reproductive cycle and gene expression. METHODS AND RESULTS: In this study, we aimed to establish stable reference genes for RT-qPCR experiments conducted on gonads of three fish species within Psalidodon genus, both in the presence and absence of B chromosomes. The stability of five selected reference genes was assessed using NormFinder, geNorm, BestKeeper, and RefFinder algorithms. We determined ppiaa and pgk1 as the most stable genes in P. fasciatus, whereas ppiaa and hmbsa showed the highest stability in P. bockmanni. For P. paranae, tbp and hprt1 were the most stable genes in females, and ppiaa and hprt1 were the most stable in males. CONCLUSIONS: We determined the most stable reference genes in gonads of three Psalidodon species considering the presence of B chromosomes. This is the first report of reference gene stability in the genus and provides valuable tools to better understand the effects of B chromosomes at gene expression level.
Assuntos
Cromossomos , Animais , Masculino , Feminino , Cromossomos/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reação em Cadeia da Polimerase em Tempo Real/normas , Padrões de Referência , Perfilação da Expressão Gênica/métodos , Perfilação da Expressão Gênica/normas , Gônadas/metabolismo , Characidae/genética , Caraciformes/genéticaRESUMO
Involved in mitotic condensation, interaction of transcriptional regulatory elements and isolation of structural domains, loop formation has become a paradigm in the deciphering of chromatin architecture and its functional role. Despite the emergence of increasingly powerful genome visualization techniques, the high variability in cell populations and the randomness of conformations still make loop detection a challenge. We introduce an approach for determining the presence and frequency of loops in a collection of experimental conformations obtained by multiplexed super-resolution imaging. Based on a spectral approach, in conjunction with neural networks, this method offers a powerful tool to detect loops in large experimental data sets, both at the population and single-cell levels. The method's performance is confirmed on experimental FISH data where Hi-C and other loop detection results are available. The method is then applied to recently published experimental data, where it provides a detailed and statistically quantified description of the global architecture of the chromosomal region under study.
Assuntos
Cromatina , Hibridização in Situ Fluorescente , Cromatina/metabolismo , Cromatina/genética , Hibridização in Situ Fluorescente/métodos , Humanos , Animais , Redes Neurais de Computação , Conformação de Ácido Nucleico , Cromossomos/genéticaRESUMO
Abalone (family Haliotidae) are an ecologically and economically significant group of marine gastropods that can be found in tropical and temperate waters. To date, only a few Haliotis genomes are available, all belonging to temperate species. Here, we provide the first chromosome-scale abalone genome assembly and the first reference genome of the tropical abalone Haliotis asinina. The combination of PacBio long-read HiFi sequencing and Dovetail's Omni-C sequencing allowed the chromosome-level assembly of this genome, while PacBio Isoform sequencing across five tissue types enabled the construction of high-quality gene models. This assembly resulted in 16 pseudo-chromosomes spanning over 1.12 Gb (98.1% of total scaffolds length), N50 of 67.09 Mb, the longest scaffold length of 105.96 Mb, and a BUSCO completeness score of 97.6%. This study identified 25,422 protein-coding genes and 61,149 transcripts. In an era of climate change and ocean warming, this genome of a heat-tolerant species can be used for comparative genomics with a focus on thermal resistance. This high-quality reference genome of H. asinina is a valuable resource for aquaculture, fisheries, and ecological studies.
Assuntos
Cromossomos , Gastrópodes , Genoma , Gastrópodes/genética , AnimaisRESUMO
Tritrichomonas foetus is a parasitic protist responsible for bovine trichomonosis, a reproductive disease associated with significant economic burden to the livestock industry throughout the world. Here, we present a chromosome-level reference genome of T. foetus -KV-1 (ATCC 30924) using short-read (Illumina Miseq), long-read (Oxford Nanopore) and chromatin-linked (Hi-C) sequencing. This is the first chromosome-level genome of a parasitic protist of the order Tritrichomonadida and the second within the Parabasalia lineage, after Trichomonas vaginalis, the human-associated causative agent of the sexually transmitted infection in humans. Our constructed genome is 148 Mb in size, with a N50 length of the scaffolds of 22.9 Mb. The contigs are anchored in five super-scaffolds, corresponding to the expected five chromosomes of the species and covering 78% of the genome assembly. We predict 41,341 protein-coding genes, of which 95.10% have been functionally annotated. This high-quality genome assembly serves as a valuable reference genome for T. foetus to support future studies in functional genomics, genetic conservation and taxonomy.
Assuntos
Doenças dos Bovinos , Genoma de Protozoário , Tritrichomonas foetus , Tritrichomonas foetus/genética , Animais , Bovinos , Doenças dos Bovinos/parasitologia , Cromossomos , Infecções Protozoárias em Animais/parasitologiaRESUMO
Living in the intertidal environment, littorinid snails are excellent models for understanding genetic mechanisms underlying adaptation to harsh fluctuating environments. Furthermore, the karyotypes of littorinid snails, with the same chromosome number as the presumed bilaterian ancestor, make them valuable for investigating karyotype evolution from the bilaterian ancestor to mollusks. Here, we generated high-quality, chromosome-scale genome assemblies for 2 littorinid marine snails, Littorina brevicula (927.94 Mb) and Littoraria sinensis (882.51 Mb), with contig N50 of 3.43 Mb and 2.31 Mb, respectively. Comparative genomic analyses identified 92 expanded gene families and 85 positively selected genes as potential candidates possibly associated with intertidal adaptation in the littorinid lineage, which were functionally enriched in stimulus responses, innate immunity, and apoptosis process regulation and might be involved in cellular homeostasis maintenance in stressful intertidal environments. Genome macrosynteny analyses indicated that 4 fissions and 4 fusions led to the evolution from the 17 presumed bilaterian ancestral chromosomes to the 17 littorinid chromosomes, implying that the littorinid snails have a highly conserved karyotype with the bilaterian ancestor. Based on the most parsimonious reconstruction of the common ancestral karyotype of scallops and littorinid snails, 3 chromosomal fissions and 1 chromosomal fusion from the bilaterian ancient linkage groups were shared by the bivalve scallop and gastropoda littorinid snails, indicating that the chromosome-scale ancient gene linkages were generally preserved in the mollusk genomes for over 500 million years. The highly conserved karyotype makes the littorinid snail genomes valuable resources for understanding early bilaterian evolution and biology.
Assuntos
Cromossomos , Evolução Molecular , Cariótipo , Caramujos , Animais , Caramujos/genética , Caramujos/classificação , Cromossomos/genética , Adaptação Fisiológica/genética , Genoma , Filogenia , Genômica/métodos , Evolução BiológicaRESUMO
During eukaryotic cell division, a microtubule-based structure called the spindle exerts forces on chromosomes. The best-studied spindle forces, including those responsible for the separation of sister chromatids, are directed parallel to the spindle's long axis. By contrast, little is known about forces perpendicular to the spindle axis, which determine the metaphase plate configuration and thus the location of chromosomes in the subsequent nucleus. Using live-cell microscopy, we find that metaphase chromosomes are spatially anti-correlated in mouse oocyte spindles, evidence of previously unknown long-range forces acting perpendicular to the spindle axis. We explain this observation by showing that the spindle's microtubule network behaves as a nematic liquid crystal and that deformation of the nematic field around embedded chromosomes causes long-range repulsion between them.
Assuntos
Microtúbulos , Oócitos , Fuso Acromático , Animais , Fuso Acromático/metabolismo , Oócitos/metabolismo , Oócitos/citologia , Camundongos , Microtúbulos/metabolismo , Metáfase , Cromossomos , Cromossomos de Mamíferos/metabolismo , FemininoRESUMO
In nature, diploids and tetraploids are two common types of polyploid evolution. Misgurnus anguillicaudatus (mud loach) is a remarkable fish species that exhibits both diploid and tetraploid forms. However, reconstructing the four haplotypes of its autotetraploid genome remains unresolved. Here, we generated the first haplotype-resolved, chromosome-level genome of autotetraploid M. anguillicaudatus with a size of 4.76 Gb, contig N50 of 6.78 Mb, and scaffold N50 of 44.11 Mb. We identified approximately 2.9 Gb (61.03% of genome) of repetitive sequences and predicted 91,485 protein-coding genes. Moreover, allelic gene expression levels indicated the absence of significant dominant haplotypes within the autotetraploid loach genome. This genome will provide a valuable biological model for unraveling the mechanisms of polyploid formation and evolution, adaptation to environmental changes, and benefit for aquaculture applications and biodiversity conservation.
Assuntos
Cipriniformes , Genoma , Haplótipos , Tetraploidia , Animais , Cipriniformes/genética , Cromossomos , PoliploidiaRESUMO
The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.
Assuntos
Cromossomos , Genoma , Pectinidae , Pectinidae/genética , Animais , Genoma MitocondrialRESUMO
Chromosomal chaos may have aided their moves to fresh water and land.
Assuntos
Cromossomos , Evolução Molecular , Rearranjo Gênico , Oligoquetos , Animais , Cromossomos/genética , Genoma , Oligoquetos/anatomia & histologia , Oligoquetos/genéticaRESUMO
Discinaceae holds significant importance within the Pezizales, representing a prominent group of macroascomycetes distributed globally. However, there is a dearth of genomic studies focusing on this family, resulting in gaps in our understanding of its evolution, development, and ecology. Here we utilized state-of-the-art genome assembly methodologies, incorporating third-generation single-molecule fluorescence and Hi-C-assisted methods, to elucidate the genomic landscapes of Gyromitra esculenta and Paragyromitra xinjiangensis. The genome sizes of two species were determined to be 47.10 Mb and 48.20 Mb, with 23 and 22 scaffolds, respectively. 10,438 and 11,469 coding proteins were identified, with functional annotations encompassing over 96.47% and 94.40%, respectively. Assessment of completeness using BUSCO revealed that 98.71% and 98.89% of the conserved proteins were identified. The application of comparative genomic technology has helped in identifying traits associated with of heterothallic life cycle traits and elucidating unique patterns of chromosomal evolution. Additionally, we identified potential saprotrophic nutritional modes and systematic phylogenetic relationships between the two species. Therefore, this study provides crucial genomic insights into the evolution, nutritional type, and ecological roles of species within the Pezizales.
Assuntos
Ascomicetos , Genoma Fúngico , Ascomicetos/genética , Cromossomos , Fluorescência , Tamanho do Genoma , Genômica , FilogeniaRESUMO
Endemic to the upper and middle reaches of the Yangtze River in China, elongate loach (Leptobotia elongata) has become a vulnerable species mainly due to overfishing and habitat destruction. Thus far, no genome data of this species are reported. As a result, lacking of such genomic information has restricted practical conservation and utilization of this economic fish. Here, we constructed chromosome-level genome assemblies for both male and female elongate loach by integration of MGI, PacBio HiFi and Hi-C sequencing technologies. Two primary genome assemblies (586-Mb and 589-Mb) were obtained for female and male fishes, respectively. Indeed, 98.22% and 98.61% of the contig sequences were anchored onto 25 chromosomes, with identification of 26.22% and 25.92% repeat contents in both assembled genomes. Meanwhile, a total of 25,215 and 25,253 protein-coding genes were annotated, of which 97.41% and 98.8% could be predicted with functions. Taken together, our genome data presented here provide a valuable genomic resource for in-depth evolutionary and functional research, as well as molecular breeding and conservation of this economic fish species.
Assuntos
Cromossomos , Cipriniformes , Genoma , Animais , Feminino , Masculino , Cipriniformes/genética , ChinaRESUMO
Interphase chromosomes reside within distinct nuclear regions known as chromosome territories (CTs). Recent observations from Hi-C analyses, a method mapping chromosomal interactions, have revealed varied decay in contact probabilities among different chromosomes. Our study explores the relationship between this contact decay and the particular shapes of the chromosome territories they occupy. For this, we employed molecular dynamics (MD) simulations to examine how confined polymers, resembling chromosomes, behave within different confinement geometries similar to chromosome territory boundaries. Our simulations unveil so far unreported relationships between contact probabilities and end-to-end distances varying based on different confinement geometries. These findings highlight the crucial impact of chromosome territories on shaping the larger-scale properties of 3D genome organization. They emphasize the intrinsic connection between the shapes of these territories and the contact behaviors exhibited by chromosomes. Understanding these correlations is key to accurately interpret Hi-C and microscopy data, and offers vital insights into the foundational principles governing genomic organization.