Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology最新文献

{"title":"Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes.","authors":"Patrick P Edger,&nbsp;J Chris Pires","doi":"10.1007/s10577-009-9055-9","DOIUrl":"https://doi.org/10.1007/s10577-009-9055-9","url":null,"abstract":"<p><p>Whole genome duplications (WGDs) followed by diploidization, which includes gene loss, have been an important recurrent process in the evolution of higher eukaryotes. Gene retention is biased to specific functional gene categories during diploidization. Dosage-sensitive genes, which include transcription factors, are significantly over-retained following WGDs. By contrast, these same functional gene categories exhibit lower retention rates following smaller scale duplications (e.g., local and tandem duplicates, segmental duplicates, aneuploidy). In light of these recent observations, we review current theories that address the fate of nuclear genes following duplication events (i.e., Gain of Function Hypothesis, Subfunctionalization Hypothesis, Increased Gene Dosage Hypothesis, Functional Buffering Model, and the Gene Balance Hypothesis). We broadly review different mechanisms of dosage-compensation that have evolved to alleviate harmful dosage-imbalances. In addition, we examine a recently proposed extension of the Gene Balance Hypothesis to explain the shared single copy status for a specific functional class of genes across the flowering plants. We speculate that the preferential retention of dosage-sensitive genes (e.g., regulatory genes such as transcription factors) and gene loss following WGDs has played a significant role in the development of morphological complexity in eukaryotes and facilitating speciation, respectively. Lastly, we will review recent findings that suggest polyploid lineages had increased rates of survival and speciation following mass extinction events, including the Cretaceous-Tertiary (KT) extinction.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"699-717"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9055-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40055422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sumoylation precedes accumulation of phosphorylated H2AX on sex chromosomes during their meiotic inactivation.","authors":"Margarita Vigodner","doi":"10.1007/s10577-008-9006-x","DOIUrl":"https://doi.org/10.1007/s10577-008-9006-x","url":null,"abstract":"<p><p>During meiosis in male mammals, X and Y chromosomes undergo the process of meiotic sex chromosome inactivation (MSCI). A crucial role in MSCI has recently been reported for BRCA1, ATR kinase, and phosphorylated histone H2AX, but the exact mechanism remains to be determined. Small ubiquitin-like modifier (SUMO) proteins have recently been shown to localize to the sex body in mouse meiotic spermatocytes, but the role they play during MSCI is unknown. In this study, in order to better understand the molecular events of MSCI, we followed dynamic changes in gammaH2AX and SUMO localization patterns during MSCI. Using confocal laser scanning microscopy (CLSM) as an analytical tool for visualizing numerous spermatocytes from the same development stage and for consecutively following the meiotic progression, we were able to demonstrate a very early appearance of SUMO-1, which preceded gammaH2AX accumulation on the sex chromosomes during their meiotic inactivation. In contrast to SUMO-1, SUMO-2/3 was undetectable in zygotene spermatocytes, suggesting a possible specific role for SUMO-1 in the initiation of MSCI.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"37-45"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-008-9006-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27933927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dm nxf1/sbr gene affects the formation of meiotic spindle in female Drosophila melanogaster.","authors":"Elena V Golubkova,&nbsp;Ekaterina G Markova,&nbsp;Anton V Markov,&nbsp;Elina O Avanesyan,&nbsp;Seppo Nokkala,&nbsp;Ludmila A Mamon","doi":"10.1007/s10577-009-9046-x","DOIUrl":"https://doi.org/10.1007/s10577-009-9046-x","url":null,"abstract":"<p><p>The small bristles (sbr) gene of Drosophila melanogaster belongs to the family of nuclear export factor (NXF) genes that participate in mRNA nuclear export. During meiosis, females of Drosophila melanogaster that carry various combinations of mutant alleles of the Dm nxf1/sbr gene exhibit disruption of the division spindle and misalignment of chromosomes at the metaphase plate. Meiosis of sbr ( 5 ) /+ females is characterized by the formation of tripolar spindles during the first cell division. According to the sequencing results, the sbr ( 5 ) (l(1)K4) lethal allele is a deletion of 492 nucleotides. In SBR(5) protein, 57 of the 146 amino acids that have been lost by deletion belong to the NTF2-like domain.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"833-45"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9046-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40034831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis.","authors":"Rachael Thomas,&nbsp;Clare Rebbeck,&nbsp;Armand M Leroi,&nbsp;Austin Burt,&nbsp;Matthew Breen","doi":"10.1007/s10577-009-9080-8","DOIUrl":"https://doi.org/10.1007/s10577-009-9080-8","url":null,"abstract":"<p><p>Canine transmissible venereal tumor (CTVT) is an intriguing cancer that is transmitted naturally as an allograft by transplantation of viable tumor cells from affected to susceptible dogs. At least initially, the tumor is able to evade the host's immune response; thus, CTVT has potential to provide novel insights into tumor immunobiology. The nature of CTVT as a \"contagious\" cancer, originating from a common ancestral source of infection, has been demonstrated previously by a series of studies comparing geographically distinct tumors at the molecular level. While these studies have revealed that apparently unrelated tumors share a striking degree of karyotypic conservation, technological restraints have limited the ability to investigate the chromosome composition of CTVTs in any detail. We present characterization of a strategically selected panel of CTVT cases using microarray-based comparative genomic hybridization analysis at ~one-megabase resolution. These data show for the first time that the tumor presents with an extensive range of non-random chromosome copy number aberrations that are distributed widely throughout the dog genome. The majority of abnormalities detected were imbalances of small subchromosomal regions, often involving centromeric and telomeric sequences. All cases also showed the sex chromosome complement XO. There was remarkable conservation in the cytogenetic profiles of the tumors analyzed, with only minor variation observed between different cases. These data suggest that the CTVT genome demonstrates a vast degree of both structural and numerical reorganization that is maintained during transmission among the domestic dog population.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"927-34"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9080-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40050587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel, simple and rapid nondenaturing FISH (ND-FISH) technique for the detection of plant telomeres. Potential used and possible target structures detected.","authors":"Angeles Cuadrado,&nbsp;Hieronim Golczyk,&nbsp;Nicolás Jouve","doi":"10.1007/s10577-009-9060-z","DOIUrl":"https://doi.org/10.1007/s10577-009-9060-z","url":null,"abstract":"<p><p>We report a new technique-nondenaturing FISH (ND-FISH)-for the rapid detection of plant telomeres without the need for prior denaturation of the chromosomes. In its development, two modified, synthetic oligonucleotides, 21 nt in length, fluorescently labelled at their 5' and 3' ends and complementary to either the cytidine-rich (C(3)TA(3)) or guanosine-rich (T(3)AG(3)) telomeric DNA strands, were used as probes. The high binding affinity of these probes and the short hybridization time required allows the visualization of plant telomeres in less than an hour. In tests, both probes gave strong signals visualized as double spots at both chromosome ends; this was true of both the mitotic and meiotic chromosomes of barley, wheat, rye, maize, Brachypodium distachyon and Rhoeo spathacea. They were also able to detect telomere motifs at certain intercalary sites in the chromosomes of R. spathacea. To investigate the nature of the target structures detected, the chromosomes were treated with RNase A and single strand-specific nuclease S1 before ND-FISH experiments. Signal formation was resistant to standard enzymatic treatment, but sensitive when much higher enzyme concentrations were used. The results are discussed in relation to current knowledge of telomere structure.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"755-62"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9060-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40025202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The worm solution: a chromosome-full of condensin helps gene expression go down.","authors":"Györgyi Csankovszki, Emily L Petty, Karishma S Collette","doi":"10.1007/s10577-009-9061-y","DOIUrl":"10.1007/s10577-009-9061-y","url":null,"abstract":"<p><p>Dosage compensation in the nematode Caenorhabditis elegans is achieved by the binding of a condensin-like dosage compensation complex (DCC) to both X chromosomes in hermaphrodites to downregulate gene expression two-fold. Condensin I(DC), a sub-part of the DCC, differs from the mitotic condensin I complex by a single subunit, strengthening the connection between dosage compensation and mitotic chromosome condensation. The DCC is targeted to X chromosomes by initial binding to a number of recruiting elements, followed by dispersal or spreading to secondary sites. While the complex is greatly enriched on the X chromosomes, many sites on autosomes also bind the complex. DCC binding does not correlate with DCC-mediated repression, suggesting that the complex acts in a chromosome-wide manner, rather than on a gene-by-gene basis. Worm dosage compensation represents an excellent model system to study how condensin-mediated changes in higher order chromatin organization affect gene expression.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"621-35"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992697/pdf/nihms253753.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40055416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The paracentric inversion In(2Rh)PL alters the centromeric organization of chromosome 2 in Drosophila melanogaster.","authors":"Sarantis Chlamydas,&nbsp;Patrick Heun,&nbsp;Patrizio Dimitri,&nbsp;Roberta Moschetti,&nbsp;Paolo Barsanti,&nbsp;Ruggiero Caizzi","doi":"10.1007/s10577-008-9000-3","DOIUrl":"https://doi.org/10.1007/s10577-008-9000-3","url":null,"abstract":"<p><p>Centromeres are complex structures involved in an evolutionarily conserved function, the correct segregation of chromosomes and chromatids during meiosis and mitosis. The centromere is determined by epigenetic processes that result in a particular nucleosome organization (CEN chromatin) that differs from the rest of the chromatin including the heterochromatin that normally surrounds the centromere in higher organisms. Many of the current models of centromere origin and organization rely on the molecular and cytological characterization of minichromosomes and their derivatives, and on studies on the origin and maintenance of neocentromeres. Here, we describe the peculiar centromere organization observed in In(2Rh)PL, a paracentric D. melanogaster inversion in which the centromere is maintained in its natural context but is directly flanked by a euchromatic domain as a result of the rearrangement. We have identified the breakpoints of the inversion and show that the proximal one is within the centromere region. The data presented suggest that, notwithstanding the loss of all the pericentric 2Rh heterochromatin, the centromere of the In(2Rh)PL chromosome is still active but presents a nucleosomal organization quite different from the organization usually observed in the centromeric region.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"1-9"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-008-9000-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27918519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the evolutionary origins of X chromosome inactivation in mammals: insights from marsupials and monotremes.","authors":"Janine E Deakin,&nbsp;Julie Chaumeil,&nbsp;Timothy A Hore,&nbsp;Jennifer A Marshall Graves","doi":"10.1007/s10577-009-9058-6","DOIUrl":"https://doi.org/10.1007/s10577-009-9058-6","url":null,"abstract":"<p><p>Determining the evolutionary origin of X inactivation mechanisms in mammals requires knowledge of features of X inactivation across all three major mammal lineages; monotremes, marsupials and eutherians. In the past, research into X inactivation in marsupials and monotremes lagged far behind the major advances made in understanding the mechanisms of X inactivation in human and mouse. Fragmentary knowledge of the genic content and sequence of marsupial and monotreme X chromosomes has been alleviated by the recent release of genome sequences for two marsupials and one monotreme. This has lead to a number of important findings, among which is the absence of XIST in marsupials and monotremes, and the surprising finding that X-borne genes in platypus are subject to stochastic transcriptional inhibition rather than whole chromosome inactivation. Availability of sequence data, and new techniques for studying expression and chromatin modification, now make rapid advance possible.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"671-85"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9058-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40055420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantum dots as new-generation fluorochromes for FISH: an appraisal.","authors":"Dimitris Ioannou, Helen G Tempest, Benjamin M Skinner, Alan R Thornhill, Michael Ellis, Darren K Griffin","doi":"10.1007/s10577-009-9051-0","DOIUrl":"10.1007/s10577-009-9051-0","url":null,"abstract":"<p><p>In the field of nanotechnology, quantum dots (QDs) are a novel class of inorganic fluorochromes composed of nanometre-scale crystals made of a semiconductor material. Given the remarkable optical properties that they possess, they have been proposed as an ideal material for use in fluorescent in-situ hybridization (FISH). That is, they are resistant to photobleaching and they excite at a wide range of wavelengths but emit light in a very narrow band that can be controlled by particle size and thus have the potential for multiplexing experiments. The principal aim of this study was to compare the potential of QDs against traditional organic fluorochromes in both indirect (i.e. QD-conjugated streptavidin) and direct (i.e. synthesis of QD-labelled FISH probes) detection methods. In general, the indirect experiments met with a degree of success, with FISH applications demonstrated for chromosome painting, BAC mapping and use of oligonucleotide probes on human and avian chromosomes/nuclei. Many of the reported properties of QDs (e.g. brightness, 'blinking' and resistance to photobleaching) were observed. On the other hand, signals were more frequently observed where the chromatin was less condensed (e.g. around the periphery of the chromosome or in the interphase nucleus) and significant bleed-through to other filters was apparent (despite the reported narrow emission spectra). Most importantly, experimental success was intermittent (sometimes even in identical, parallel experiments) making attempts to improve reliability difficult. Experimentation with direct labelling showed evidence of the generation of QD-DNA constructs but no successful FISH experiments. We conclude that QDs are not, in their current form, suitable materials for FISH because of the lack of reproducibility of the experiments; we speculate why this might be the case and look forward to the possibility of nanotechnology forming the basis of future molecular cytogenetic applications.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"519-30"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40002116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The choanoflagellate Monosiga brevicollis karyotype revealed by the genome sequence: telomere-linked helicase genes resemble those of some fungi.","authors":"Hugh M Robertson","doi":"10.1007/s10577-009-9078-2","DOIUrl":"https://doi.org/10.1007/s10577-009-9078-2","url":null,"abstract":"<p><p>The approximately 42 Mbp assembled genome sequence for the choanoflagellate Monosiga brevicollis reveals that most of the large scaffolds of 300-2,600 kb represent entire chromosomes or chromosome arms. Telomeres are partially assembled at the termini of 37 scaffolds, while another 43 scaffolds end in telomere-associated regions containing distinctive gene sets. Potential centromeric regions were identified on 39 scaffolds. Together, these observations suggest a karyotype of approximately 40 metacentric and submetacentric chromosomes averaging 1 Mbp in size. Genes encoding RecQ family DNA helicases, along with ankyrin-domain proteins and serine/threonine kinases, are associated with most telomeres, a feature shared with some fungi. This telomere-linked helicase gene arrangement might be ancestral to both fungi and choanoflagellates in the super-kingdom Opisthokonta; however, the great lability of telomere architecture suggests that it could also be a convergent feature.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"873-82"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9078-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40043621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}