Chromosome Research最新文献

{"title":"Appearance of transient heteromorphic large chromosome in glyphosate-resistant Amaranthus tuberculatus.","authors":"Rajendran Sathishraj, Yoonha Ju, Bikram S Gill, Dal-Hoe Koo","doi":"10.1007/s10577-025-09768-0","DOIUrl":"10.1007/s10577-025-09768-0","url":null,"abstract":"<p><p>Glyphosate resistance in crop weeds is commonly attributed to rapid evolution through the amplification of the target gene, EPSPS (5-enolpyruvylshikimate-3-phosphate synthase). This amplification typically occurs through mechanisms such as unequal recombination, segmental duplications within the target chromosome, or the formation of ring chromosomes and extrachromosomal circular (ecc) DNA elements containing EPSPS. However, structural abnormalities in chromosomes not directly associated with EPSPS amplification have not been documented in the glyphosate-resistant weed population. Here, we describe the presence of a large chromosome found exclusively in the glyphosate-resistant Amaranthus tuberculatus (waterhemp) population but absent in susceptible counterparts. This large chromosome (~ 6 μm) is approximately twice the size of normal chromosomes (~ 2-3 μm) and is present in both male and female euploid plants (2n = 32) in a heteromorphic state. It aroses through pericentromeric heterochromatin expansion and duplications of the 5S rDNA locus but notably lacks the EPSPS gene. The large chromosome pairs with its normal homolog but was not transmitted to progeny in controlled greenhouse matings, suggesting a fitness cost in the absence of glyphosate selection pressure. This large chromosome offers a potential resource for the investigation of chromosome evolution of adaptive traits for glyphosate resistance in A. tuberculatus.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"9"},"PeriodicalIF":2.4,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Marking dad's centromeres: maintaining CENP-A in sperm.","authors":"Miriama Štiavnická, Rachel S Keegan, Elaine M Dunleavy","doi":"10.1007/s10577-025-09766-2","DOIUrl":"https://doi.org/10.1007/s10577-025-09766-2","url":null,"abstract":"<p><p>During spermiogenesis, histones are removed from most genomic loci and are replaced by protamines in mature sperm nuclei. Yet, centromeres appear resistant to this process. We review the experimental evidence that the centromeric histone CENP-A is maintained in mature sperm nuclei, comparing human, bovine, mouse and fly species. We also recall how the detection of centromeres in mature sperm nuclei in the 1990's contributed to the isolation of the CENP-A protein and the eventual cloning of the human CENP-A gene. Further, based on more recent genetic studies carried out in flies and in mice, we discuss the inheritance and functional importance of paternal CENP-A and how it is complemented by maternal CENP-A to give rise to a healthy embryo. Finally, we raise some unanswered questions regarding the exclusive maintenance of CENP-A on sperm, the organisation of sperm centromeric chromatin and its importance for fertility and early embryo development.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"8"},"PeriodicalIF":2.4,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12031959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-CISH: an in situ chromogenic DNA repeat detection system for research and life science education.","authors":"Bhanu Prakash Potlapalli, Fabian Dassau, Jörg Fuchs, Deboprio Roy Sushmoy, Andreas Houben","doi":"10.1007/s10577-025-09767-1","DOIUrl":"https://doi.org/10.1007/s10577-025-09767-1","url":null,"abstract":"<p><p>In situ hybridization is a technique to visualize specific DNA sequences within nuclei and chromosomes. Various DNA in situ fluorescent labeling methods have been developed, which typically involve global DNA denaturation prior to the probe hybridization and often require fluorescence microscopes for visualization. Here, we report the development of a CRISPR/dCas9-mediated chromogenic in situ DNA detection (CRISPR-CISH) method that combines chromogenic signal detection with CRISPR imaging. This non-fluorescent approach uses 3' biotin-labeled tracrRNA and target-specific crRNA to form mature gRNA, which activates dCas9 to bind to target sequences. The subsequent application of streptavidin alkaline phosphatase or horseradish peroxidase generates chromogenic, target-specific signals that can be analyzed using conventional bright-field microscopes. Additionally, chromatin counterstains were identified to aid in the interpretation of CRISPR-CISH-generated target signals. This advancement makes in situ DNA detection techniques more accessible to researchers, diagnostic applications, and educational institutions in resource-limited settings.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"7"},"PeriodicalIF":2.4,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12011966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae).","authors":"Fernanda Souza de Oliveira, Toby Brann, Ivan Rodrigo Wolf, Viviane Nogaroto, Cesar Martins, Anna Victoria Protasio, Marcelo Ricardo Vicari","doi":"10.1007/s10577-025-09765-3","DOIUrl":"10.1007/s10577-025-09765-3","url":null,"abstract":"<p><p>Transposable elements (TEs) are widely present in eukaryotic genomes, where they can contribute to genome size and functional modifications. As new genomes are sequenced and annotated, more studies can be conducted regarding TE content, distribution, and genome evolution. TEs are extensively diversified in fish genomes resulting in an important role in genome and chromosome evolution. However, curated TE libraries are still scarce in non-model organisms, making it difficult to evaluate TE's impact on genomic modifications thoroughly. Here, we aimed to obtain a curated TE library from the neotropical fish Apareiodon sp. genome. The prospection and curation of the TE library resulted in 244 families from 18 superfamilies of DNA transposons and retrotransposons, which comprise about 10% of the genome, with most insertions fitting in one or a few families. A greater diversity of retrotransposon families is present, especially for Ty3 superfamily. Despite the greater number of retrotransposon families, DNA transposons are the most abundant in the genome, with 37% of all TE insertions belonging to the Tc1-Mariner superfamily. Complete TE copies were observed for almost all superfamilies, with most of the sequences on the Tc1-Mariner group. DNA transposons and SINEs presented older insertions in the genome, followed by LINEs and LTR retrotransposons. TE genome density is highest in the cs25 scaffold, and enriched for Helitron elements. With these data, allied to previous studies on chromosome evolution, we suggest that cs25 bears the W chromosome specific region of the Apareiodon sp. genome, with the presence of significant amount of Helitron insertions.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"6"},"PeriodicalIF":2.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TOP2B is required for compartment strength changes upon retinoic acid treatment in SH-SY5Y cells.","authors":"Erica M Hildebrand, Ian G Cowell, Mushtaq M Khazeem, Snehal Sambare, Ozgun Uyan, Job Dekker, Caroline A Austin","doi":"10.1007/s10577-025-09764-4","DOIUrl":"10.1007/s10577-025-09764-4","url":null,"abstract":"<p><p>DNA topoisomerase II beta (TOP2B) is required for correct execution of certain developmental transcriptional programs and for signal-induced transcriptional activation, including transcriptional activation by nuclear hormone ligands such as retinoic acid. In addition, TOP2B is enriched at genomic locations occupied by CCCTC-Binding factor (CTCF) and cohesin (RAD21). suggesting a role in chromosome looping and/or establishing or maintaining aspects of chromosome 3D structure. This led us to investigate the effect of TOP2B inactivation on patterns of intra- and inter- chromosomal interaction that reflect the 3D architecture of the genome. Using the retinoic acid responsive SH-SY5Y neuroblastoma cell line model, we had previously demonstrated many gene expression changes upon retinoic acid treatment and upon deletion of TOP2B. We report here that these expression changes in TOP2B null versus WT cells are accompanied by surprisingly subtle changes in local chromosome organization. However, we do observe quantitative changes in chromosome organization on a megabase scale. First, lack of TOP2B did affect compartment strength changes that occur upon ATRA treatment. Second, we observe an excess of very long-range interactions, reminiscent of interactions seen in mitotic cells, suggesting the possibility that in the absence of TOP2B some mitotic interactions are retained. Third, we see quantitative changes in centromere-telomere interactions, again indicating global changes at the megabase and chromosome level. These data support the surprising conclusion that TOP2B has only a minor role in chromosome dynamics and organization.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"5"},"PeriodicalIF":2.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First prenatal case of jumping-like translocations: unraveling complex chromosomal rearrangements.","authors":"Kevin Cassinari, Anne Claire Brehin, Ferdi Kundul, Mathieu Castelain, Sophie Patrier-Sallebert, Alain Diguet, Eric Verspyck, Claude Houdayer, Géraldine Joly-Hélas, Pascal Chambon","doi":"10.1007/s10577-025-09763-5","DOIUrl":"10.1007/s10577-025-09763-5","url":null,"abstract":"<p><p>Jumping translocations and jumping-like translocations constitute a rare category of complex chromosomal rearrangements, which are primarily observed in hematologic disorders and solid tumors. This study outlines a complex structural mosaic rearrangement involving a single recipient chromosome and three distinct donor chromosomes, with varying patterns of mosaicism observed across different cell lines. The rearrangement was confirmed by karyotyping, FISH, and array-CGH. These analyses revealed significant chromosomal duplications and deletions, which may contribute to the observed phenotypic abnormalities. Following characterization via various cytogenetic techniques, this rearrangement appears to be the first reported instance of a jumping-like translocation in prenatal constitutional genetics. This finding enables the formulation of hypotheses regarding the mechanisms underlying such intricate structural variants and their detection via contemporary genetic methods.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"3"},"PeriodicalIF":2.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lampbrush chromosomes of Danio rerio.","authors":"D Dedukh, T Kulikova, M Dobrovolskaia, A Maslova, A Krasikova","doi":"10.1007/s10577-024-09761-z","DOIUrl":"10.1007/s10577-024-09761-z","url":null,"abstract":"<p><p>Danio rerio, commonly known as zebrafish, is an established model organism for the developmental and cell biology studies. Although significant progress has been made in the analysis of the D. rerio genome, cytogenetic studies face challenges due to the unclear identification of chromosomes. Here, we present a novel approach to the study of the D. rerio karyotype, focusing on the analysis of lampbrush chromosomes isolated from growing oocytes. Lampbrush chromosomes, existing during diplotene, serve as a powerful tool for high-resolution mapping and transcription analysis due to their profound decondensation and remarkable lateral loops decorated by RNA polymerases and ribonucleoprotein (RNP) matrix. In D. rerio, lampbrush chromosomes are about 20 times longer than corresponding metaphase chromosomes. We found that the lampbrush chromosome stage karyotype of D. rerio is generally undifferentiated, except for several bivalents bearing distinct marker structures, including loops with complex RNP matrix and locus-associated nuclear bodies. Locus-associated nuclear bodies were enriched for coilin and snRNAs; the loci where they formed presumably correspond to the histone gene clusters. Further, we observed the accumulation of splicing factors in giant terminal RNP aggregates on one bivalent. DAPI staining of Danio rerio lampbrush chromosomes revealed large and small chromomeres non-uniformly distributed along the axis. For example, D. rerio lampbrush chromosome 4, comprising the sex-determining region, is divided into two halves-with small chromomeres bearing long lateral loops and with large dense chromomeres bearing no or very tiny lateral loops. As centromeres were not distinguishable, we identified centromeric regions in all bivalents by FISH mapping of pericentromeric RFAL1, RFAL2, and RFAM tandem repeats. Through a combination of morphological analysis, immunostaining of marker structures, and centromere mapping, we developed cytological maps of D. rerio lampbrush chromosomes. Finally, by RNA FISH we revealed transcripts of pericentromeric and telomeric tandem repeats at the lampbrush chromosome stage.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"2"},"PeriodicalIF":2.4,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ipsilateral restriction of chromosome movement along a centrosome, and apical-basal axis during the cell cycle.","authors":"Pingping Cai, Christian J Casas, Gabriel Quintero Plancarte, Takashi Mikawa, Lisa L Hua","doi":"10.1007/s10577-024-09760-0","DOIUrl":"10.1007/s10577-024-09760-0","url":null,"abstract":"<p><p>Little is known about how distance between homologous chromosomes are controlled during the cell cycle. Here, we show that the distribution of centromere components display two discrete clusters placed to either side of the centrosome and apical/basal axis from prophase to G₁ interphase. 4-Dimensional live cell imaging analysis of centromere and centrosome tracking reveals that centromeres oscillate largely within one cluster, but do not cross over to the other cluster. We propose a model of an axis-dependent ipsilateral restriction of chromosome oscillations throughout mitosis.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"33 1","pages":"1"},"PeriodicalIF":2.4,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Varied chromosome distribution behaviours during meiosis in triploid Chinese chives contribute to the formation of viable pollen.","authors":"Peng-Qiang Yao, Li-Hua Xie, Mei-Yu Li, Si-Qian Jiao, Shuai-Zheng Qi, Zhe Wang, Shi-Ping Cheng","doi":"10.1007/s10577-024-09759-7","DOIUrl":"10.1007/s10577-024-09759-7","url":null,"abstract":"<p><p>Triploids play an important role in the polyploidization process and are considered a bridge between diploids and polyploids. To inform plant polyploidization research and polyploid breeding, it is important to explore chromosome behaviour during triploid pollen development, pollen fertility problems in triploids and the potential value of utilizing triploids. In this study, acetocarmine, carbol fuchsin and fluorescence staining methods were used to observe microsporogenesis and microspore development in fertile triploid Chinese chives. The results revealed that some of the pollen mother cells were able to undergo equal chromosome distributions (approximately 36%), whereas other pollen mother cells formed lagging chromosomes, chromosome bridges, micronuclei and early cytoplasmic divisions during microsporogenesis, resulting in microspores of different sizes. Regardless of whether an equal tetrad or an abnormal polyad was formed, microspores were released from callose in a normal manner and contained nuclei. During the process of microspore development, most of the microspore nuclei disappeared gradually and ultimately formed empty pollen cells that lacked nuclei. During the meiosis of pollen mother cells in triploid Chinese chives, a variety of chromosome distribution behaviours contribute to the formation of some viable pollen.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"32 4","pages":"15"},"PeriodicalIF":2.4,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative karyotype analysis provides cytogenetic evidence for the origin of sweetpotato.","authors":"Jianying Sun, Qian Zhang, Meiling Xu, Mengxiao Yan, Xingyu Liu, Jian Sun, Qinghe Cao, Hongxia Wang, Jun Yang, Zongyun Li, Yonghua Han","doi":"10.1007/s10577-024-09758-8","DOIUrl":"10.1007/s10577-024-09758-8","url":null,"abstract":"<p><p>The origin of hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] remains controversial. Comparative karyotype analysis is particularly useful in determining species relationships and the origin of polyploid species. In previous study, we developed a set of oligo probes and identified all chromosomes of Ipomoea nil, a model diploid Ipomoea species. Here, we found that this set of oligo probes could be used to identify all chromosomes of sweetpotato and its wild relatives with different ploidy. Karyotypes based on individually identified chromosomes were established and the number and position of 5S and 35S rDNA loci were determined for these Ipomoea species. Comparison of their karyotypes revealed distinct variations in the karyotypic parameters. Karyological relationships among these species were revealed by principal coordinate analysis (PCoA) based on six quantitative parameters (x, 2n, TCL, M_CA, CV_CL and CV_CI). These results show that I. trifida is the most closely related diploid species to sweetpotato, and other diploid species could be excluded from consideration as its possible diploid ancestor. In addition, our study also provides cytogenetic evidence for the segmental allopolyploid hypothesis of sweetpotato origin.</p>","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"32 4","pages":"14"},"PeriodicalIF":2.4,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}