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BackgroundDuring mitosis, chromatin engages in a dynamic cycle of condensation and decondensation. Condensation into distinct units to ensure high fidelity segregation is followed by rapid and reproducible decondensation to produce functional daughter cells. Factors contributing to the reproducibility of chromatin structure between cell generations are not well understood. We investigated local metaphase chromosome condensation along mitotic chromosomes within genomic intervals showing differential accessibility (DA) between homologs. DA was originally identified using short sequence-defined single copy (sc) DNA probes of ResultsWe evaluated multiple adjacent scFISH probes at 6 different DA loci from chromosomal regions 2p23, 3p24, 12p12, 15q22, 15q24 and 20q13 within peripheral blood T-lymphocytes. DA was organized within domains that extend beyond the defined boundaries of individual scFISH probes. Based on hybridizations of 2 to 4 scFISH probes per domain, domains ranged in length from 16.0 kb to 129.6 kb. Transcriptionally inert chromosomal DA regions in T-lymphocytes also demonstrated conservation of DA in bone marrow and fibroblast cells.ConclusionsWe identified novel chromosomal regions with allelic differences in metaphase chromosome accessibility and demonstrated that these accessibility differences appear to be aggregated into contiguous domains extending beyond individual scFISH probes. These domains are encompassed by previously established topologically associated domain (TAD) boundaries. DA appears to be a conserved feature of human metaphase chromosomes across different stages of lymphocyte differentiation and germ cell origin, consistent with its proposed role in maintenance of intergenerational cellular chromosome memory.

With the introduction of systems theory to genetics, numerous opportunities for genomic research have been identified. Consequences of DNA sequence variations are systematically evaluated using the network- or pathway-based analysis, a technological basis of systems biology or, more precisely, systems genomics. Despite comprehensive descriptions of advantages offered by systems genomic approaches, pathway-based analysis is uncommon in cytogenetic (cytogenomic) studies, i.e. genome analysis at the chromosomal level. Here, we would like to express our opinion that current cytogenomics benefits from the application of systems biology methodology. Accordingly, systems cytogenomics appears to be a biomedical area requiring more attention than it actually receives.

Global medical associations (ACOG, ISUOG, ACMG) recommend diagnostic prenatal testing for the detection and prevention of genetic disorders. Historically, cytogenetic methods such as karyotype analysis, fluorescent in situ hybridization (FISH), and chromosomal microarray (CMA) are utilized worldwide to diagnose common syndromes. However, the limitations of each of these methods, either performed in tandem or simultaneously, demonstrates the need of a revolutionary technology that can alleviate the need of multiple technologies. Optical genome mapping (OGM) is a novel technology that fills this void by being able to detect all classes of structural variations (SVs), including copy number variations (CNVs). OGM is being adopted by laboratories as a next-generation cytogenomic tool for both postnatal constitutional genetic disorders and hematological malignancies. This commentary highlights the potential of OGM to become a standard of care in prenatal genetic testing by its ability to identify large balanced and unbalanced SVs (currently the strength of karyotyping and metaphase FISH), CNVs (by CMA), repeat contraction disorders (by Southern blotting) and multiple repeat expansion disorders (by PCR based methods or Southern blotting). Also, next-generation sequencing (NGS) methods are excellent at detecting sequence variants but are unable to accurately detect the repeat regions of the genome which limits the ability to detect all classes of SVs. Notably, multiple molecular methods are used to identify repeat expansion and contraction disorders in routine clinical laboratories around the world. With non-invasive prenatal screening test (NIPT) as the standard of care screening assay for all global pregnancies, we anticipate OGM as a high-resolution cytogenomic diagnostic tool employed following a positive NIPT screen or for high-risk pregnancies with an abnormal ultrasound. Accurate detection of all types of genetic disorders by OGM, such as liveborn aneuploidies, sex chromosome anomalies, microdeletion/microduplication syndromes, repeat expansion/contraction disorders is key to reducing the global burden of genetic disorders.

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.

Made available in DSpace on 2020-12-10T19:40:32Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-12-01 Fundacao Araucaria (Fundacao Araucaria de Apoio ao Desenvolvimento Cientifico e Tecnologico do Estado do Parana) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Sex chromosome differentiation is subject to independent evolutionary processes among different lineages. The accumulation of repetitive DNAs and consequent crossing-over restriction guide the origin of the heteromorphic sex chromosome region. Several Neotropical fish species have emerged as interesting models for understanding evolution and genome diversity, although knowledge of their genomes is scarce. Here, we investigate the content of repetitive DNAs between males and females of Apareiodon sp. based on large-scale genomic data focusing on W sex chromosome differentiation. In Apareiodon, females are the heterogametic sex (ZW) and males are the homogametic sex (ZZ). The genome size estimate for Apareiodon was 1.2 Gb (with similar to 42x and similar to 47x coverage for males and females, respectively). In Apareiodon sp., approximately 36% of the genome was composed of repetitive DNAs and transposable elements (TEs) were the most abundant class. Read coverage analysis revealed different amounts of repetitive DNAs in males and females. The female-enriched clusters were located on the W sex chromosome and were mostly composed of microsatellite expansions and DNA transposons. Landscape analysis of TE contents demonstrated two major waves of invasions of TEs in the Apareiodon genome. Estimation of TE insertion times correlated with in situ locations permitted the inference that helitron, Tc1-mariner, and CMC EnSpm DNA transposons accumulated repeated copies during W chromosome differentiation between 20 and 12 million years ago. DNA transposons and microsatellite expansions appeared to be major players in W chromosome differentiation and to guide modifications in the genome content of the heteromorphic sex chromosomes. Univ Estadual Ponta Grossa, Dept Biol Estrutural Mol & Genet, Av Carlos Cavalcanti 4748, BR-84030900 Ponta Grossa, Parana, Brazil Univ Fed Parana, Ctr Politecn, Programa Posgrad Genet, Caixa Postal 19071, BR-81531990 Curitiba, Parana, Brazil Univ Estadual Paulista, Inst Biociencias Botucatu, Dept Morfol, Dist Rubiao Jr S-N, BR-18618689 Botucatu, SP, Brazil Univ Fed Sao Carlos, Dept Genet & Evolucao, Rodovia Washington Luis,Km 235, BR-13565905 Sao Carlos, SP, Brazil Univ Estadual Paulista, Dept Bioproc & Biotecnol, Fazenda Lageado, Rua Jose Barbosa de Barros 1780, BR-18610307 Botucatu, SP, Brazil Univ Estadual Paulista, Inst Biociencias Botucatu, Dept Morfol, Dist Rubiao Jr S-N, BR-18618689 Botucatu, SP, Brazil Univ Estadual Paulista, Dept Bioproc & Biotecnol, Fazenda Lageado, Rua Jose Barbosa de Barros 1780, BR-18610307 Botucatu, SP, Brazil FAPESP: 2015/16661-1 CAPES: 001 CNPq: 304166/2016-2

Made available in DSpace on 2018-11-26T17:24:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-03-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) National Council for Scientific and Technological Development Sao Paulo State University Supernumerary chromosomes have been studied in many species of eukaryotes, including the cichlid fish, Astatotilapia latifasciata. However, there are many unanswered questions about the maintenance, inheritance, and functional aspects of supernumerary chromosomes. The cichlid family has been highlighted as a model for evolutionary studies, including those that focus on mechanisms of chromosome evolution. Individuals of A. latifasciata are known to carry up to two B heterochromatic isochromosomes that are enriched in repetitive DNA and contain few intact gene sequences. We isolated and characterized a transcriptionally active repeated DNA, called B chromosome noncoding DNA (BncDNA), highly represented across all B chromosomes of A. latifasciata. BncDNA transcripts are differentially processed among six different tissues, including the production of smaller transcripts, indicating transcriptional variation may be linked to B chromosome presence and sexual phenotype. The transcript lengths and lack of similarity with known protein/gene sequences indicate BncRNA might represent a novel long noncoding RNA family (lncRNA). The potential for interaction between BncRNA and known miRNAs were computationally predicted, resulting in the identification of possible binding of this sequence in upregulated miRNAs related to the presence of B chromosomes. In conclusion, Bnc is a transcriptionally active repetitive DNA enriched in B chromosomes with potential action over B chromosome maintenance in somatic cells and meiotic drive in gametic cells. Sao Paulo State Univ, Inst Biosci, Dept Morphol, BR-18618689 Botucatu, SP, Brazil Univ Connecticut, Allied Hlth Sci Dept, Storrs, CT 06269 USA Univ Connecticut, Inst Syst Genom, Storrs, CT 06269 USA Sao Paulo State Univ, Dept Biol, Inst Biosci, BR-13506900 Rio Claro, SP, Brazil Sao Paulo State Univ, Dept Biostat, Inst Biosci, BR-18618689 Botucatu, SP, Brazil Univ Connecticut, Dept Mol & Cell Biol, Storrs, CT 06269 USA Sao Paulo State Univ, Inst Biosci, Dept Morphol, BR-18618689 Botucatu, SP, Brazil Sao Paulo State Univ, Dept Biol, Inst Biosci, BR-13506900 Rio Claro, SP, Brazil Sao Paulo State Univ, Dept Biostat, Inst Biosci, BR-18618689 Botucatu, SP, Brazil FAPESP: 13/04533-3 FAPESP: 10/17212-2 FAPESP: 12/20959-8 FAPESP: 13/016886 National Council for Scientific and Technological Development: 474684/2013-0 National Council for Scientific and Technological Development: 301728/2011-9 Sao Paulo State University: 0045/021/13-PROPe/CDC

Molecular cytogenetics is a promising field of biomedical research that has recently revolutionized our thinking on genome structure and behavior. This is in part due to discoveries of human genomic variations and their contribution to biodiversity and disease. Since these studies were primarily targeted at variation of the genome structure, it appears apposite to cover them by molecular cytogenomics. Human brain diseases, which encompass pathogenic conditions from severe neurodegenerative diseases and major psychiatric disorders to brain tumors, are a heavy burden for the patients and their relatives. It has been suggested that most of them, if not all, are of genetic nature and several recent studies have supported the hypothesis assuming them to be associated with genomic instabilities (i.e. single-gene mutations, gross and subtle chromosome imbalances, aneuploidy). The present review is focused on the intriguing relationship between genomic instability and human brain diseases. Looking through the data, we were able to conclude that both interindividual and intercellular genomic variations could be pathogenic representing, therefore, a possible mechanism for human brain malfunctioning. Nevertheless, there are still numerous gaps in our knowledge concerning the link between genomic variations and brain diseases, which, hopefully, will be filled by forthcoming studies. In this light, the present review considers perspectives of this dynamically developing field of neurogenetics and genomics.

One of the most important breakthroughs in the history of genetics and plant breeding was the development of plant cytology and experimental mutagenesis, which later brought about plant cytogenetics and mutation breeding and now they have entered in functional biology era with the unprecedented development of plant molecular cytogenetics, genetics, and functional genomics. Application of cell biology particularly chromosome biology in the fields of plant genome structure and function has ushered the development of plant cytogenomics. Development of advanced technology like DNA base-specific fluorescence banding, GISH, and FISH-based chromosome painting has greatly facilitated the identification, localization, and mapping of chromosome-specific markers in plants, which is of high importance in plant molecular systematics, species identification, detection of hybrid nature, alien chromosomes and chromosomal aberrations, analysis of somaclonal variations, and diversity analysis. The dynamism of chromatin architecture and cell cycle, representing chromosome functional biology, is another important part of plant cytogenomics. On the other hand, mutagenomics is defined as applied mutation breeding, in which genomic information and tools are utilized in the designing of breeding strategies, screening, selection and verification/authentication of natural and induced mutants, and the utilization of desirable mutations in the breeding processes. Considerable progress has been made in recent times in breeding of cereals, legumes, oil seeds, vegetables, horticultural crops, spices and condiments, fiber-yielding plants, and medicinal and aromatic plants for diverse types of desirable agronomic and functional traits including disease and abiotic stress resistance/tolerance; herbicide resistance; lowering of anti-nutritional factors; enhancement of proteins, minerals, vitamins, essential amino acids, flavonoids, antioxidants, and dietary fibers; enrichment of soil nutrition; enhancement of ornamental, medicinal, and aromatic values; and development of functional and therapeutic foods and other diverse traits related to nutritional quality and high yield. This can be found in a mutant population which carries variant forms of potentially each and every gene present in a particular genome. The functionality of mutagenomics is greatly enhanced due to integration of classical mutagenesis with modern “omics” technology through the development of desirable diploid mutants, recombinant inbred lines, and aneuploid and polyploid lines as effective cytogenetic tools, utilizable in genome mapping and analysis. Functional sets of aneuploid tools are now available in different edible plants, through which several morphological, biochemical, and molecular traits/markers have been assigned on definite chromosomes to construct linkage maps. Recently, induced mutations showing alterations in antioxidant defense response have been identified and tested against diverse types of abiotic stresses to reveal intrinsic cellular and metabolic events toward sensitivity of seed plants to salinity, drought, metal toxicity, and other stresses. These mutations are giving vital inputs, which can be used in formulating effective breeding strategies in different agroclimatic conditions. Mutagenized population has revealed altered pattern of genome response and can also be exploited in enhancing production of natural plant products like antioxidants and flavonoids. Furthermore, these large mutant populations have the potential in reverse genetics approach by employing various techniques, particularly “Targeting Induced Local Lesions in Genomics (TILLING)” technology to better understand gene functions through high-throughput mutation screening, and have been successfully used in major crop plants along with model plant Arabidopsis. The development of mutagenomic approach, thus, provides a cost-effective, clean, and easy-to-use functional tool to increase the genetic diversity and in utilization of this diversity in plant molecular mutation breeding through modern genomic methods.