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1.
Semin Cell Dev Biol ; 134: 112-124, 2023 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-35307283

RESUMO

In brown algae, the extracellular matrix (ECM) and its constitutive polymers play crucial roles in specialized functions, including algal growth and development. In this review we offer an integrative view of ECM construction in brown algae. We briefly report the chemical composition of its main constituents, and how these are interlinked in a structural model. We examine the ECM assembly at the tissue and cell level, with consideration on its structure in vivo and on the putative subcellular sites for the synthesis of its main constituents. We further discuss the biosynthetic pathways of two major polysaccharides, alginates and sulfated fucans, and the progress made beyond the candidate genes with the biochemical validation of encoded proteins. Key enzymes involved in the elongation of the glycan chains are still unknown and predictions have been made at the gene level. Here, we offer a re-examination of some glycosyltransferases and sulfotransferases from published genomes. Overall, our analysis suggests novel investigations to be performed at both the cellular and biochemical levels. First, to depict the location of polysaccharide structures in tissues. Secondly, to identify putative actors in the ECM synthesis to be functionally studied in the future.


Assuntos
Feófitas , Feófitas/genética , Feófitas/química , Feófitas/metabolismo , Polissacarídeos/química , Polissacarídeos/metabolismo , Genoma , Matriz Extracelular/metabolismo
2.
Semin Cell Dev Biol ; 134: 4-13, 2023 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-35339358

RESUMO

Extremophiles have always garnered great interest because of their exotic lifestyles and ability to thrive at the physical limits of life. In hot springs environments, the Cyanidiophyceae red algae are the only photosynthetic eukaryotes able to live under extremely low pH (0-5) and relatively high temperature (35ºC to 63ºC). These extremophiles live as biofilms in the springs, inhabit acid soils near the hot springs, and form endolithic populations in the surrounding rocks. Cyanidiophyceae represent a remarkable source of knowledge about the evolution of extremophilic lifestyles and their genomes encode specialized enzymes that have applied uses. Here we review the evolutionary origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. Currently, Cyanidiophyceae comprise a single order (Cyanidiales), three families, four genera, and nine species, including the well-known Cyanidioschyzon merolae and Galdieria sulphuraria. These algae have small, gene-rich genomes that are analogous to those of prokaryotes they live and compete with. There are few spliceosomal introns and evidence exists for horizontal gene transfer as a driver of local adaptation to gain access to external fixed carbon and to extrude toxic metals. Cyanidiophyceae offer a variety of commercial opportunities such as phytoremediation to detoxify contaminated soils or waters and exploitation of their mixotrophic lifestyles to support the efficient production of bioproducts such as phycocyanin and floridosides. In terms of exobiology, Cyanidiophyceae are an ideal model system for understanding the evolutionary effects of foreign gene acquisition and the interactions between different organisms inhabiting the same harsh environment on the early Earth. Finally, we describe ongoing research with C. merolae genetics and summarize the unique insights they offer to the understanding of algal biology and evolution.


Assuntos
Extremófilos , Rodófitas , Humanos , Eucariotos , Extremófilos/genética , Rodófitas/genética , Genoma , Solo , Filogenia
3.
Zool Res ; 44(1): 78-89, 2023 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-36349358

RESUMO

Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.


Assuntos
Bass , Animais , Bass/genética , Análise de Sequência de DNA/veterinária , Genoma , América do Norte , China
4.
Gene ; 850: 146933, 2023 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-36191824

RESUMO

Channel catfish is an important species for aquaculture that exhibits a sexually dimorphic growth in favor of males. Genetic sexing and development of sex markers are crucial for the early identification of sex and of particular genotypes (YY males) for the production of all-male population in channel catfish aquaculture. In this study, we sequenced genomic DNA from pools of males and pools of females to better characterize the sex determining region (SDR) of channel catfish and to develop sex-specific markers for genetic sexing. Performing comparative analyses on male and female pooled genomic reads, we identified a large SDR (∼8.3 Mb) in the middle of channel catfish linkage group 4 (LG04). This non-recombining SDR contains a high-density of male-specific (Y chromosome) fixed single nucleotide polymorphisms (SNPs) along with âˆ¼ 185 kb male-specific insertions or deletions. This SDR contains 95 annotated protein-encoding genes, including the recently reported putative channel catfish master sex determining (MSD) gene, breast cancer anti-estrogen resistance protein 1 (bcar1), located at one edge of the SDR. No sex-specific SNPs and/or indels were found in the coding sequence of bcar1, but one male-specific SNP was identified in its first intron. Based on this genomic information, we developed a PCR-based sex-specific genetic test. Genotyping results confirmed strong linkage between phenotypic sexes and the identified SDR in channel catfish. Our results confirm, using a Pool-Seq approach, that channel catfish is male heterogametic (XX-XY) with a large SDR on the LG04 sex chromosome. Furthermore, our genotyping primers can be used to identify XX, XY, and YY fish that will facilitate future research on sex determination and aquaculture applications in channel catfish.


Assuntos
Ictaluridae , Animais , Masculino , Feminino , Ictaluridae/genética , Genótipo , Ligação Genética , Genoma , Cromossomo Y
5.
Methods Mol Biol ; 2562: 273-289, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36272083

RESUMO

The availability of the chromosome-scale axolotl genome sequences has made it possible to explore genome evolution, perform cross-species comparisons, and use additional sequencing data to analyze both genome-wide features and individual genes. Here, we will focus on the UCSC genome browser and demonstrate in a step-by-step manner how to use it to integrate different data to approach a broad question of the Fgf8 locus evolution and analyze the neighborhood of a gene that was reported missing in axolotl - Pax3.


Assuntos
Ambystoma mexicanum , Bases de Dados Genéticas , Animais , Software , Genoma , Internet
6.
Methods Mol Biol ; 2562: 291-318, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36272084

RESUMO

The gigantic 32Gb Axolotl genome inspires fascinating questions such as: how such a big genome is organized and packed in nuclei and how regulation of gene transcription can happen over such large genomic distances. Currently, there are many technical challenges when we investigate chromatin architecture in axolotl. For example, probing promoter-enhancer interactions in such a large genome. Chromatin capture methods (e.g., Chromatin Conformation Capture) have been used in a variety of species. The large size of the axolotl nuclei and its genome requires the adaptation of such methods. Here, we describe a detailed protocol for high-throughput genome-wide conformation capture (Hi-C) using axolotl limb cells. This Hi-C library preparation protocol can also be used to prepare libraries from other nonmodel organisms such as Lungfish and Cephalopods. We believe that our protocol could be useful for a variety of animal systems including other salamanders.


Assuntos
Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Animais , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Cromossomos/genética , Cromatina/genética , Genômica/métodos , Conformação de Ácido Nucleico
7.
Methods Mol Biol ; 2562: 335-349, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36272086

RESUMO

Clustered regularly interspaced short palindromic repeats (CRISPR) is a powerful tool that enables editing of the axolotl genome. In this chapter, we will cover how to retrieve gene sequences, confirm annotation, design CRISPR targets, analyze indels, and screen for Crispant axolotls. This is a comprehensive guide on how to use CRISPR on your favorite gene and gain insights into its function.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Animais , Sistemas CRISPR-Cas/genética , Ambystoma mexicanum/genética , Genoma , Mutação , RNA Guia/genética
8.
Methods Mol Biol ; 2562: 471-479, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36272095

RESUMO

As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to image tissues live and other methods enhance the spectrum of biological questions accessible to all researchers. Here I provide a personal perspective on what I consider exciting future questions open for investigation.


Assuntos
Genoma , Urodelos , Animais , Genômica , Edição de Genes
9.
Gene ; 851: 146965, 2023 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-36261090

RESUMO

As a classical molecular marker, microsatellite (simple sequence repeat, SSR) has been widely used in the study of genetics and evolution of mammals. However, there are widespread problems about lack of comparative analysis and low quality of genomic data. Based on high-quality chromosome-level genomes, we compared the SSR distribution patterns of 81 mammals species belonging to 13 orders in evolution landscape. In this study, the number of SSRs decreased with the increase of repetition times, and the terminal of exon/intron were enrichment areas of SSRs. We also found that the proportion and dominant repeat units of each type of P-SSR varied among mammalian branches, which could become the evolutionary dynamics for them to adapt to diverse environmental pressures. In particular, the phylogenetic PCA results demonstrated the particularity of some mammals (Tachyglossus aculeatus and Ornithorhynchus anatinus) in evolutionary status, which was consistent with morphological cognition. Meanwhile, there were significant differences in the GC content of each category of P-SSR across mammalian taxa. Besides, the CVs (coefficient of variations) of the RCNs of trinucleotide and hexanucleotide P-SSRs were at a low level in the exon regions, while the dinucleotide or tetranucleotide P-SSRs were at a high level. Furthermore, the results of functional annotation showed that signal transduction played a pivotal role in mammalian biological activities. In conclusion, our research will help to improve the characteristic information of mammalian SSRs and explore their evolutionary background.


Assuntos
Genoma , Repetições de Microssatélites , Animais , Filogenia , Repetições de Microssatélites/genética , Genoma/genética , Mamíferos/genética , Cromossomos , Genoma de Planta
10.
Gene ; 851: 146974, 2023 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-36309242

RESUMO

Allopolyploid genomes are divided into compartments called subgenomes that are derived from lower ploidy ancestors. In African clawed frogs of the subgenus Xenopus (genus Xenopus), allotetraploid species have two subgenomes (L and S) with morphologically distinct homoeologous chromosomes. In allotetraploid species of the sister subgenus Silurana, independently evolved subgenomes also exist, but their cytogenetics has not been investigated in detail. We used a diverse suite of cytogenetic and molecular FISH techniques on an allotetraploid species in Silurana-Xenopus calcaratus-to explore evolutionary dynamics of chromosome morphology and rearrangements. We find that the subgenomes of X. calcaratus have distinctive characteristics, with a more conserved a-subgenome resembling the closely related genome of the diploid species X. tropicalis, and a more rapidly evolving b-subgenome having more pronounced changes in chromosome structure, including diverged heterochromatic blocks, repetitive sequences, and deletion of a nucleolar secondary constriction. Based on these cytogenetic differences, we propose a chromosome nomenclature for X. calcaratus that may apply to other allotetraploids in subgenus Silurana, depending on as yet unresolved details of their evolutionary origins. These findings highlight the potential for large-scale asymmetry in subgenome evolution following allopolyploidization.


Assuntos
Cromossomos , Diploide , Animais , Xenopus laevis , Xenopus/genética , Cromossomos/genética , Genoma/genética , Evolução Molecular , Genoma de Planta
11.
Semin Cell Dev Biol ; 133: 96-106, 2023 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-35249812

RESUMO

The nuclear envelope (NE) protects but also organizes the eukaryotic genome. In this review we will discuss recent literature on how the NE disassembles and reassembles, how it varies in surface area and protein composition and how this translates into chromatin organization and gene expression in the context of animal development.


Assuntos
Células Eucarióticas , Membrana Nuclear , Animais , Membrana Nuclear/metabolismo , Genoma
12.
Methods Mol Biol ; 2599: 59-68, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36427143

RESUMO

Genomic DNA wraps around core histones to form nucleosomes, which provides steric constraints on how transcription factors (TFs) can interact with gene regulatory sequences. It is increasingly apparent that well-positioned, accessible nucleosomes are an inherent feature of active enhancers and can facilitate cooperative TF binding, referred to as nucleosome-mediated cooperativity. Thus, profiling chromatin and nucleosome properties (accessibility, positioning, and occupancy) on the genome is crucial to understand cell-type-specific gene regulation. Here we describe a simplified protocol to profile accessible nucleosomes in the mammalian genome using low-level and high-level micrococcal nuclease (MNase) digestion followed by genome-wide sequencing.


Assuntos
Cromatina , Nucleossomos , Animais , Nucleossomos/genética , Cromatina/genética , Nuclease do Micrococo/metabolismo , Genoma , Histonas/genética , Histonas/metabolismo , Mamíferos/genética , Mamíferos/metabolismo
13.
Methods Mol Biol ; 2599: 113-125, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36427146

RESUMO

Chromosome conformation capture technology and its derivatives have been widely used to study genome organization. Among them, Hi-C (chromosome conformation capture coupling with high-throughput sequencing) is popular in dissecting chromatin architecture on the genome-wide level. However, the intrinsic limitations prevent its application when it comes to rare samples. Here, we present easy Hi-C, a biotin-free technology that dramatically reduces DNA loss and is suitable for low-input samples.


Assuntos
Cromossomos , Genoma , Mapeamento Cromossômico/métodos , Cromatina/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos
14.
Methods Mol Biol ; 2590: 183-200, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36335500

RESUMO

Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly available sequence data for sample HG005 of the Genome in a Bottle project.


Assuntos
Cromossomos , Genoma , Haplótipos , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Polimorfismo de Nucleotídeo Único , Algoritmos
15.
Methods Mol Biol ; 2590: 201-218, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36335501

RESUMO

Haplotype-resolved genome assemblies remain a challenge in practice. Here, we provide a step-by-step guide on gamete binning, a method to generate haplotype-resolved genome assemblies for diploid species. The protocol starts by phasing heterozygous variants to individual haplotypes of specific chromosomes using the genome information of individual haploid gametes of the focal individual. Using phased variants, the whole-genome sequencing reads from the diploid genome can be genotyped and assigned into groups, which represent the individual haplotypes of each of the chromosomes. Finally, haplotype-specific chromosomes can be assembled independently using standard assembly tools. First applications of gamete binning revealed a haplotyping accuracy over 99%, which outperformed sequence-only or Hi-C-based haplotype-resolved genome assemblies.Availability: github.com/schneebergerlab/GameteBinning_prac .


Assuntos
Diploide , Genoma , Haplótipos/genética , Sequenciamento Completo do Genoma , Células Germinativas , Análise de Sequência de DNA
16.
Semin Cell Dev Biol ; 135: 59-72, 2023 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-35331626

RESUMO

Histone variants represent chromatin components that diversify the structure and function of the genome. The variants of H2A, primarily H2A.X, H2A.Z and macroH2A, are well-established participants in DNA damage response (DDR) pathways, which function to protect the integrity of the genome. Through their deposition, post-translational modifications and unique protein interaction networks, these variants guard DNA from endogenous threats including replication stress and genome fragility as well as from DNA lesions inflicted by exogenous sources. A growing body of work is now providing a clearer picture on the involvement and mechanistic basis of H2A variant contribution to genome integrity. Beyond their well-documented role in gene regulation, we review here how histone H2A variants promote genome stability and how alterations in these pathways contribute to human diseases including cancer.


Assuntos
Cromatina , Histonas , Humanos , Histonas/genética , Histonas/metabolismo , Cromatina/genética , Genoma , Processamento de Proteína Pós-Traducional/genética , DNA/genética
17.
Semin Cell Dev Biol ; 135: 35-42, 2023 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-35570098

RESUMO

H2A variants are histones that carry out specialized nucleosome function during the eukaryote genome packaging. Most genes encoding H2A histone variants arose in the distant past, and have highly conserved domains and structures. Yet, novel H2A variants have continued to arise throughout the radiation of eukaryotes and disturbed the apparent tranquility of nucleosomes. These species-specific H2A variants contributed to the functional diversification of nucleosomes through changes in both their structure and expression patterns. In this short review, we discuss the evolutionary trajectories of these histone renegades in plants and animal genomes.


Assuntos
Histonas , Nucleossomos , Animais , Histonas/genética , Histonas/metabolismo , Nucleossomos/genética , Plantas/genética , Plantas/metabolismo , Genoma , Evolução Biológica
18.
Gene ; 851: 147010, 2023 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-36349576

RESUMO

Copy number variation (CNV), as one of the important variations in the biological genome, refers to the deletion and duplication of genomic segments between 1 kb and 50 kb caused by genomic rearrangements. Currently, many copy number variations have been found to be significantly associated with important economic traits such as growth, development and reproduction of cattle. However, the study of MUC19 gene has not been reported. In this study, we detected an appropriate correlation between MUC19 gene and growth traits of Chinese cattle. We detected the distribution of MUC19-CNV across Qinchuan cattle (QC), Pinan cattle (PN), Xianan cattle (XN), Yunling cattle (YL), Guyuan cattle (GY), Jiaxian cattle (JX), and analyzed the association between types of MUC19-CNV and growth traits through SPSS20.0 software and method of ANOVA. The results showed that various types of CNV were present in each breed of cattle, but there were discrepancies in the distribution of copy number variant types. The Association analysis result showed that CNV of MUC19 gene showed a postive effect in cattle growth traits: the copy number of MUC19 was significantly correlated with hip width of PN cattle (P < 0.01), height at hip cross and withers height of PN cattle (P < 0.05), hip width and body length of JX cattle (P < 0.05), Huckle bone width of YL cattle (P < 0.05).


Assuntos
Variações do Número de Cópias de DNA , Polimorfismo de Nucleotídeo Único , Bovinos/genética , Animais , Variações do Número de Cópias de DNA/genética , Fenótipo , Genoma , China
19.
Methods Mol Biol ; 2577: 93-101, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36173568

RESUMO

Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.


Assuntos
Cromatina , Transposases , Cromatina/genética , Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA/métodos , Transposases/química , Transposases/genética
20.
Methods Mol Biol ; 2577: 229-240, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36173577

RESUMO

The CRISPR-Cpf1 also known as Cas12a is an RNA-guided endonuclease similar to CRISPR-Cas9. Combining the CRISPR-Cpf1 with optogenetics technology, we have engineered photoactivatable Cpf1 (paCpf1) to precisely control the genome sequence in a spatiotemporal manner. We also identified spontaneously activated split Cpf1 and thereby developed a potent dCpf1 split activator, which has the potential to activate endogenous target genes. Here we describe a method for optogenetic endogenous genome editing using paCpf1 in mammalian cells. Furthermore, we show a method for endogenous gene activation using dCpf1 split activator in mammalian cells and mice.


Assuntos
Endonucleases , Edição de Genes , Animais , Sistemas CRISPR-Cas/genética , Endonucleases/genética , Endonucleases/metabolismo , Edição de Genes/métodos , Genoma , Mamíferos/metabolismo , Camundongos , RNA , Ativação Transcricional
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