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

{"title":"Karyotypic stability of Fragaria (strawberry) species revealed by cross-species chromosome painting.","authors":"Manman Qu,&nbsp;Luyue Zhang,&nbsp;Kunpeng Li,&nbsp;Jianying Sun,&nbsp;Zongyun Li,&nbsp;Yonghua Han","doi":"10.1007/s10577-021-09666-1","DOIUrl":"https://doi.org/10.1007/s10577-021-09666-1","url":null,"abstract":"<p><p>Chromosome karyotyping analysis is particularly useful in determining species relationships and the origin of polyploid species. Identification of individual chromosomes is the foundation for karyotype development. For Fragaria (strawberry) species, definitive identification of the individual chromosomes is extremely difficult because of their small size and similar shape. Here, we identified all chromosomes for 11 representative Fragaria species with different ploidy using a set of oligonucleotide-based probes developed in Fragaria vesca. Comprehensive molecular cytogenetic karyotypes were established based on the individually identified chromosomes. In addition, we used oligo probes to assign the 5S and 45S rDNA loci to specific chromosomes in 16 Fragaria species. We found that these Fragaria species maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements at the cytological level were observed in any of the chromosomes among these species. Despite karyotypic stability and similarity, variations in the signal intensity of oligo probes were observed among the homologous chromosomes in several polyploid species. Moreover, most Fragaria species also showed differences in the distribution patterns of 45S and 5S rDNA. These data provide new insights into the origins of several polyploid Fragaria species.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"285-300"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09666-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39252065","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 r-X1 deletion induces terminal deficiencies in the maize B chromosome.","authors":"Yen-Hua Huang,&nbsp;Tzu-Che Lin,&nbsp;Wan-Yi Chiou,&nbsp;Ya-Ming Cheng","doi":"10.1007/s10577-021-09671-4","DOIUrl":"https://doi.org/10.1007/s10577-021-09671-4","url":null,"abstract":"<p><p>In addition to causing the nondisjunction of maize B and normal A chromosomes at the second megaspore division during embryo sac development, the r-X1 deletion results in terminal deficiencies (TDs) in various A chromosomal arms, but whether the r-X1 deletion also induces TDs of the maize B chromosome remains unknown. To answer this question, the chromosomal composition in the r-X1-containing progeny of r-X1/R-r female parents carrying two standard B chromosomes was determined. Nine of 104 (8.7%) examined kernels contained a smaller telocentric B chromosome, and one of these (designated Bdef-1) was further identified as a TD with a breakpoint in the third distal heterochromatic region of the B chromosome. Thus, the results indicated that the r-X1 deletion could also induce TDs of the maize B chromosome during megaspore divisions. The Bdef-1 chromosome lacked nondisjunctional behavior, and this behavior was restored by the presence of the B chromosome in the cell. A transmission analysis of the Bdef-1 chromosome revealed that loss of the distal portion of the B chromosome reduced female but not male transmission of the B chromosome. Furthermore, the Bdef-1 chromosome was used to more finely map B-derived miRNA genes on the B chromosome. Our results indicate that the r-X1 deletion results in TDs of the B chromosome in maize, and the r-X1 deletion system can thus be used to generate a series of terminally truncated B chromosomes that may be used to map features of the B chromosome, including genes and properties related to B chromosome functions.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"351-360"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39382316","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":"Analysis of the Robertsonian (1;29) fusion in Bovinae reveals a common mechanism: insights into its clinical occurrence and chromosomal evolution.","authors":"A Escudeiro,&nbsp;F Adega,&nbsp;T J Robinson,&nbsp;J S Heslop-Harrison,&nbsp;R Chaves","doi":"10.1007/s10577-021-09667-0","DOIUrl":"https://doi.org/10.1007/s10577-021-09667-0","url":null,"abstract":"<p><p>The interest in Robertsonian fusion chromosomes (Rb fusions), sometimes referred to as Robertsonian translocations, derives from their impact on mammalian karyotype evolution, as well from their influence on fertility and disease. The formation of a Rb chromosome necessitates the occurrence of double strand breaks in the pericentromeric regions of two chromosomes in the satellite DNA (satDNA) sequences. Here, we report on the fine-scale molecular analysis of the centromeric satDNA families in the Rb(1;29) translocation of domestic cattle and six antelope species of the subfamily Bovinae. We do so from two perspectives: its occurrence as a chromosomal abnormality in cattle and, secondly, as a fixed evolutionarily rearrangement in spiral-horned antelope (Tragelaphini). By analysing the reorganization of satDNAs in the centromeric regions of translocated chromosomes, we show that Rb fusions are multistep, complex rearrangements which entail the precise elimination and reorganization of specific (peri)centromeric satDNA sequences. Importantly, these structural changes do not influence the centromeric activity of the satellite DNAs that provide segregation stability to the translocated chromosome. Our results suggest a common mechanism for Rb fusions in these bovids and, more widely, for mammals in general.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"301-312"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-021-09667-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39261932","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":"Effectiveness of Create ML in microscopy image classifications: a simple and inexpensive deep learning pipeline for non-data scientists.","authors":"Kiyotaka Nagaki,&nbsp;Tomoyuki Furuta,&nbsp;Naoki Yamaji,&nbsp;Daichi Kuniyoshi,&nbsp;Megumi Ishihara,&nbsp;Yuji Kishima,&nbsp;Minoru Murata,&nbsp;Atsushi Hoshino,&nbsp;Hirotomo Takatsuka","doi":"10.1007/s10577-021-09676-z","DOIUrl":"https://doi.org/10.1007/s10577-021-09676-z","url":null,"abstract":"<p><p>Observing chromosomes is a time-consuming and labor-intensive process, and chromosomes have been analyzed manually for many years. In the last decade, automated acquisition systems for microscopic images have advanced dramatically due to advances in their controlling computer systems, and nowadays, it is possible to automatically acquire sets of tiling-images consisting of large number, more than 1000, of images from large areas of specimens. However, there has been no simple and inexpensive system to efficiently select images containing mitotic cells among these images. In this paper, a classification system of chromosomal images by deep learning artificial intelligence (AI) that can be easily handled by non-data scientists was applied. With this system, models suitable for our own samples could be easily built on a Macintosh computer with Create ML. As examples, models constructed by learning using chromosome images derived from various plant species were able to classify images containing mitotic cells among samples from plant species not used for learning in addition to samples from the species used. The system also worked for cells in tissue sections and tetrads. Since this system is inexpensive and can be easily trained via deep learning using scientists' own samples, it can be used not only for chromosomal image analysis but also for analysis of other biology-related images.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"361-371"},"PeriodicalIF":2.6,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39518334","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":"Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma.","authors":"Rachael Thomas,&nbsp;Luke Borst,&nbsp;Daniel Rotroff,&nbsp;Alison Motsinger-Reif,&nbsp;Kerstin Lindblad-Toh,&nbsp;Jaime F Modiano,&nbsp;Matthew Breen","doi":"10.1007/s10577-014-9406-z","DOIUrl":"https://doi.org/10.1007/s10577-014-9406-z","url":null,"abstract":"<p><p>Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"305-19"},"PeriodicalIF":2.6,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-014-9406-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40287213","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":"Comparative cytogenomics of poultry: mapping of single gene and repeat loci in the Japanese quail (Coturnix japonica).","authors":"Marla C McPherson,&nbsp;Charmaine M Robinson,&nbsp;Lida P Gehlen,&nbsp;Mary E Delany","doi":"10.1007/s10577-014-9411-2","DOIUrl":"https://doi.org/10.1007/s10577-014-9411-2","url":null,"abstract":"<p><p>Well-characterized molecular and cytogenetic maps are yet to be established in Japanese quail (Coturnix japonica). The aim of the current study was to cytogenetically map and determine linkage of specific genes and gene complexes in Japanese quail through the use of chicken (Gallus gallus) and turkey (Meleagris gallopavo) genomic DNA probes and conduct a comparative study among the three genomes. Chicken and turkey clones were used as probes on mitotic metaphase and meiotic pachytene stage chromosomes of the three species for the purpose of high-resolution fluorescence in situ hybridization (FISH). The genes and complexes studied included telomerase RNA (TR), telomerase reverse transcriptase (TERT), 5S rDNA, 18S-5.8S-28S rDNA (i.e., nucleolus organizer region (NOR)), and the major histocompatibility complex (MHC). The telomeric profile of Japanese quail was investigated through the use of FISH with a TTAGGG-PNA probe. A range of telomeric array sizes were confirmed as found for the other poultry species. Three NOR loci were identified in Japanese quail, and single loci each for TR, TERT, 5S rDNA and the MHC-B. The MHC-B and one NOR locus were linked on a microchromosome in Japanese quail. We confirmed physical linkage of 5S rDNA and the TR gene on an intermediate-sized chromosome in quail, similar to both chicken and turkey. TERT localized to CJA 2 in quail and the orthologous chromosome region in chicken (GGA 2) and in turkey (MGA 3). The cytogenetic profile of Japanese quail was further developed by this study and synteny was identified among the three poultry species. </p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"71-83"},"PeriodicalIF":2.6,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-014-9411-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40287995","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":"Avian sex, sex chromosomes, and dosage compensation in the age of genomics.","authors":"Jennifer A Marshall Graves","doi":"10.1007/s10577-014-9409-9","DOIUrl":"https://doi.org/10.1007/s10577-014-9409-9","url":null,"abstract":"<p><p>Comparisons of the sex chromosome systems in birds and mammals are widening our view and deepening our understanding of vertebrate sex chromosome organization, function, and evolution. Birds have a very conserved ZW system of sex determination in which males have two copies of a large, gene-rich Z chromosome, and females have a single Z and a female-specific W chromosome. The avian ZW system is quite the reverse of the well-studied mammalian XY chromosome system, and evolved independently from different autosomal blocs. Despite the different gene content of mammal and bird sex chromosomes, there are many parallels. Genes on the bird Z and the mammal X have both undergone selection for male-advantage functions, and there has been amplification of male-advantage genes and accumulation of LINEs. The bird W and mammal Y have both undergone extensive degradation, but some birds retain early stages and some mammals terminal stages of the process, suggesting that the process is more advanced in mammals. Different sex-determining genes, DMRT1 and SRY, define the ZW and XY systems, but DMRT1 is involved in downstream events in mammals. Birds show strong cell autonomous specification of somatic sex differences in ZZ and ZW tissue, but there is growing evidence for direct X chromosome effects on sexual phenotype in mammals. Dosage compensation in birds appears to be phenotypically and molecularly quite different from X inactivation, being partial and gene-specific, but both systems use tools from the same molecular toolbox and there are some signs that galliform birds represent an early stage in the evolution of a coordinated system. </p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"45-57"},"PeriodicalIF":2.6,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-014-9409-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40287214","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":"Boosting transcription by transcription: enhancer-associated transcripts.","authors":"Emily M Darrow,&nbsp;Brian P Chadwick","doi":"10.1007/s10577-013-9384-6","DOIUrl":"https://doi.org/10.1007/s10577-013-9384-6","url":null,"abstract":"<p><p>Enhancers are traditionally viewed as DNA sequences located some distance from a promoter that act in cis and in an orientation-independent fashion to increase utilization of specific promoters and thereby regulate gene expression. Much progress has been made over the last decade toward understanding how these distant elements interact with target promoters, but how transcription is enhanced remains an object of active inquiry. Recent reports convey the prevalence and diversity of enhancer transcription and transcripts and support both as key factors with mechanistically distinct, but not mutually exclusive roles in enhancer function. Decoupling the causes and effects of transcription on the local chromatin landscape and understanding the role of enhancer transcripts in the context of long-range interactions are challenges that require additional attention. In this review, we focus on the possible functions of enhancer transcription by highlighting several recent enhancer RNA papers and, within the context of other enhancer studies, speculate on the role of enhancer transcription in regulating differential gene expression. </p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"713-24"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9384-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31823648","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":"A multitasking Argonaute: exploring the many facets of C. elegans CSR-1.","authors":"Christopher J Wedeles,&nbsp;Monica Z Wu,&nbsp;Julie M Claycomb","doi":"10.1007/s10577-013-9383-7","DOIUrl":"https://doi.org/10.1007/s10577-013-9383-7","url":null,"abstract":"<p><p>While initial studies of small RNA-mediated gene regulatory pathways focused on the cytoplasmic functions of such pathways, identifying roles for Argonaute/small RNA pathways in modulating chromatin and organizing the genome has become a topic of intense research in recent years. Nuclear regulatory mechanisms for Argonaute/small RNA pathways appear to be widespread, in organisms ranging from plants to fission yeast, Caenorhabditis elegans to humans. As the effectors of small RNA-mediated gene regulatory pathways, Argonaute proteins guide the chromatin-directed activities of these pathways. Of particular interest is the C. elegans Argonaute, chromosome segregation and RNAi deficient (CSR-1), which has been implicated in such diverse functions as organizing the holocentromeres of worm chromosomes, modulating germline chromatin, protecting the genome from foreign nucleic acid, regulating histone levels, executing RNAi, and inhibiting translation in conjunction with Pumilio proteins. CSR-1 interacts with small RNAs known as 22G-RNAs, which have complementarity to 25 % of the protein coding genes. This peculiar Argonaute is the only essential C. elegans Argonaute out of 24 family members in total. Here, we summarize the current understanding of CSR-1 functions in the worm, with emphasis on the chromatin-directed activities of this ever-intriguing Argonaute. </p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"573-86"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9383-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31823647","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":"RNAi function, diversity, and loss in the fungal kingdom.","authors":"R Blake Billmyre,&nbsp;Silvia Calo,&nbsp;Marianna Feretzaki,&nbsp;Xuying Wang,&nbsp;Joseph Heitman","doi":"10.1007/s10577-013-9388-2","DOIUrl":"https://doi.org/10.1007/s10577-013-9388-2","url":null,"abstract":"<p><p>RNAi is conserved and has been studied in a broad cross-section of the fungal kingdom, including Neurospora crassa, Schizosaccharomyces pombe, Cryptococcus neoformans, and Mucor circinelloides. And yet well known species, including the model yeast Saccharomyces cerevisiae and the plant pathogen Ustilago maydis, have lost RNAi, providing insights and opportunities to illuminate benefits conferred both by the presence of RNAi and its loss. Some of the earliest studies of RNAi were conducted in Neurospora, contemporaneously with the elucidation of RNAi in Caenorhabditis elegans. RNAi is a key epigenetic mechanism for maintaining genomic stability and integrity, as well as to defend against viruses, and given its ubiquity was likely present in the last eukaryotic common ancestor. In this review, we describe the diversity of RNAi mechanisms found in the fungi, highlighting recent work in Neurospora, S. pombe, and Cryptococcus. Finally, we consider frequent, independent losses of RNAi in diverse fungal lineages and both review and speculate on evolutionary forces that may drive the losses or result therefrom.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"561-72"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9388-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40278709","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}