IF 2.5 4区生物学

Chromosoma Pub Date : 2024-12-10 DOI: 10.1007/s00412-024-00827-9

Ana Mattioli Laborne, Dora Yovana Barrios-Leal, John S Heslop-Harrison, Maura Helena Manfrin, Gustavo C S Kuhn

{"title":"Genome location, evolution and centromeric contribution of satellite DNAs shared between the two closely related species Drosophila serido and D. antonietae (repleta group, buzzatii cluster).","authors":"Ana Mattioli Laborne, Dora Yovana Barrios-Leal, John S Heslop-Harrison, Maura Helena Manfrin, Gustavo C S Kuhn","doi":"10.1007/s00412-024-00827-9","DOIUrl":"https://doi.org/10.1007/s00412-024-00827-9","url":null,"abstract":"Satellite DNAs are highly repetitive, tandemly arranged sequences, typically making up large portions (> 20%) of the eukaryotic genome. Most satDNAs are fast evolving and changes in their abundance and nucleotide composition may be related to genetic incompatibilities between species. Here, we used Illumina paired-end sequencing raw data and graph-based read-clustering with the TAREAN bioinformatic tool to study the satDNAs in two cactophilic neotropical cryptic species of Drosophila from the buzzatii cluster (repleta group), D. serido and D. antonietae, from five localities in Brazil. Both species share the same four families of satDNAs: pBuM, DBC-150, CDSTR138 and CDSTR230. They represent less than 4% of the genomic DNA and there are no large differences in the abundance of each satDNA between species. Despite not being the most abundant satDNA, CDSTR138 was found to be associated with most centromeres. All four satDNAs showed instances where repeats are more homogeneous within than between species, a phenomenon known as concerted evolution. On the other hand, there was no evidence for concerted evolution at the population level. Thus, these satDNAs may also be useful as potential markers for species identification. The low levels of satDNA differentiation (both quantitatively as qualitatively) between the two species might be among the reasons that allowed the establishment of a hybrid zone between the two species in the southern coast of Brazil.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"134 1","pages":"1"},"PeriodicalIF":2.5,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799181","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}

引用次数: 0

Multifaceted role of CTCF in X-chromosome inactivation. CTCF 在 X 染色体失活中的多方面作用

IF 2.5 4区生物学

Chromosoma Pub Date : 2024-10-01 Epub Date: 2024-10-21 DOI: 10.1007/s00412-024-00826-w

Lakshmi Sowjanya Bammidi, Srimonta Gayen

引用次数: 0

The passing of the last oracle: Adelaide Carpenter and Drosophila meiosis. 最后一个神谕的逝去阿德莱德-卡彭特与果蝇的减数分裂

IF 2.5 4区生物学

Chromosoma Pub Date : 2024-10-01 DOI: 10.1007/s00412-024-00825-x

R Scott Hawley, Helen K Salz, Kim S McKim, Jeff Sekelsky

引用次数: 0

Novel centromeric repetitive DNA elements reveal karyotype dynamics in polyploid sainfoin (Onobrychis viciifolia) 新的中心粒重复DNA元件揭示了多倍体红豆杉（Onobrychis viciifolia）核型的动态变化

IF 1.6 4区生物学

Chromosoma Pub Date : 2024-09-13 DOI: 10.1007/s00412-024-00824-y

Sevim D. Kara Öztürk, Ahmet L. Tek

{"title":"Novel centromeric repetitive DNA elements reveal karyotype dynamics in polyploid sainfoin (Onobrychis viciifolia)","authors":"Sevim D. Kara Öztürk, Ahmet L. Tek","doi":"10.1007/s00412-024-00824-y","DOIUrl":"https://doi.org/10.1007/s00412-024-00824-y","url":null,"abstract":"Polyploidy is a common feature in eukaryotes with one of paramount consequences leading to better environmental adaptation. Heterochromatin is often located at telomeres and centromeres and contains repetitive DNA sequences. Sainfoin (Onobrychis viciifolia) is an important perennial forage legume for sustainable agriculture. However, there are only a few studies on the sainfoin genome and chromosomes. In this study, novel tandem repetitive DNA sequences of the sainfoin genome (OnVi180, OnVi169, OnVi176 and OnVidimer) were characterized using bioinformatics, molecular and cytogenetic approaches. The OnVi180 and OnVi169 elements colocalized within functional centromeres. The OnVi176 and OnVidimer elements were localized in centromeric, subtelomeric and interstitial regions. We constructed a sainfoin karyotype that distinguishes the seven basic chromosome groups. Our study provides the first detailed description of heterochromatin and chromosome structure of sainfoin and proposes an origin of heterozygous ancestral genomes, possibly from the same ancestral diploid species, not necessarily from different species, or for chromosome rearrangements after polyploidy. Overall, we discuss our novel and complementary findings in a polyploid crop with unique and complex chromosomal features.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"70 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203257","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}

引用次数: 0

Vertebrate centromere architecture: from chromatin threads to functional structures. 脊椎动物的中心粒结构：从染色质线到功能结构。

IF 2.5 4区生物学

Chromosoma Pub Date : 2024-07-01 Epub Date: 2024-06-10 DOI: 10.1007/s00412-024-00823-z

Lorena Andrade Ruiz, Geert J P L Kops, Carlos Sacristan

{"title":"Vertebrate centromere architecture: from chromatin threads to functional structures.","authors":"Lorena Andrade Ruiz, Geert J P L Kops, Carlos Sacristan","doi":"10.1007/s00412-024-00823-z","DOIUrl":"10.1007/s00412-024-00823-z","url":null,"abstract":"Centromeres are chromatin structures specialized in sister chromatid cohesion, kinetochore assembly, and microtubule attachment during chromosome segregation. The regional centromere of vertebrates consists of long regions of highly repetitive sequences occupied by the Histone H3 variant CENP-A, and which are flanked by pericentromeres. The three-dimensional organization of centromeric chromatin is paramount for its functionality and its ability to withstand spindle forces. Alongside CENP-A, key contributors to the folding of this structure include components of the Constitutive Centromere-Associated Network (CCAN), the protein CENP-B, and condensin and cohesin complexes. Despite its importance, the intricate architecture of the regional centromere of vertebrates remains largely unknown. Recent advancements in long-read sequencing, super-resolution and cryo-electron microscopy, and chromosome conformation capture techniques have significantly improved our understanding of this structure at various levels, from the linear arrangement of centromeric sequences and their epigenetic landscape to their higher-order compaction. In this review, we discuss the latest insights on centromere organization and place them in the context of recent findings describing a bipartite higher-order organization of the centromere.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":" ","pages":"169-181"},"PeriodicalIF":2.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141295694","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}

引用次数: 0

CTCF is essential for proper mitotic spindle structure and anaphase segregation. CTCF对于正确的有丝分裂纺锤体结构和后期分离是必不可少的。

IF 2.5 4区生物学

Chromosoma Pub Date : 2024-07-01 Epub Date: 2023-09-20 DOI: 10.1007/s00412-023-00810-w

Katherine Chiu, Yasmin Berrada, Nebiyat Eskndir, Dasol Song, Claire Fong, Sarah Naughton, Tina Chen, Savanna Moy, Sarah Gyurmey, Liam James, Chimere Ezeiruaku, Caroline Capistran, Daniel Lowey, Vedang Diwanji, Samantha Peterson, Harshini Parakh, Ayanna R Burgess, Cassandra Probert, Annie Zhu, Bryn Anderson, Nehora Levi, Gabi Gerlitz, Mary C Packard, Katherine A Dorfman, Michael Seifu Bahiru, Andrew D Stephens

{"title":"CTCF is essential for proper mitotic spindle structure and anaphase segregation.","authors":"Katherine Chiu, Yasmin Berrada, Nebiyat Eskndir, Dasol Song, Claire Fong, Sarah Naughton, Tina Chen, Savanna Moy, Sarah Gyurmey, Liam James, Chimere Ezeiruaku, Caroline Capistran, Daniel Lowey, Vedang Diwanji, Samantha Peterson, Harshini Parakh, Ayanna R Burgess, Cassandra Probert, Annie Zhu, Bryn Anderson, Nehora Levi, Gabi Gerlitz, Mary C Packard, Katherine A Dorfman, Michael Seifu Bahiru, Andrew D Stephens","doi":"10.1007/s00412-023-00810-w","DOIUrl":"10.1007/s00412-023-00810-w","url":null,"abstract":"Mitosis is an essential process in which the duplicated genome is segregated equally into two daughter cells. CTCF has been reported to be present in mitosis and has a role in localizing CENP-E, but its importance for mitotic fidelity remains to be determined. To evaluate the importance of CTCF in mitosis, we tracked mitotic behaviors in wild-type and two different CTCF CRISPR-based genetic knockdowns. We find that knockdown of CTCF results in prolonged mitoses and failed anaphase segregation via time-lapse imaging of SiR-DNA. CTCF knockdown did not alter cell cycling or the mitotic checkpoint, which was activated upon nocodazole treatment. Immunofluorescence imaging of the mitotic spindle in CTCF knockdowns revealed disorganization via tri/tetrapolar spindles and chromosomes behind the spindle pole. Imaging of interphase nuclei showed that nuclear size increased drastically, consistent with failure to divide the duplicated genome in anaphase. Long-term inhibition of CNEP-E via GSK923295 recapitulates CTCF knockdown abnormal mitotic spindles with polar chromosomes and increased nuclear sizes. Population measurements of nuclear shape in CTCF knockdowns do not display decreased circularity or increased nuclear blebbing relative to wild-type. However, failed mitoses do display abnormal nuclear morphologies relative to successful mitoses, suggesting that population images do not capture individual behaviors. Thus, CTCF is important for both proper metaphase organization and anaphase segregation which impacts the size and shape of the interphase nucleus likely through its known role in recruiting CENP-E.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":" ","pages":"183-194"},"PeriodicalIF":2.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41112066","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}

引用次数: 0

CCAAT Promoter element regulates transgenerational expression of the MHC class I gene. CCAAT 启动子元件调控 MHC I 类基因的转代表达。

IF 2.5 4区生物学

Chromosoma Pub Date : 2024-07-01 Epub Date: 2024-06-26 DOI: 10.1007/s00412-024-00820-2

Jocelyn D Weissman, Aparna Kotekar, Zohar Barbash, Jie Mu, Dinah S Singer

{"title":"CCAAT Promoter element regulates transgenerational expression of the MHC class I gene.","authors":"Jocelyn D Weissman, Aparna Kotekar, Zohar Barbash, Jie Mu, Dinah S Singer","doi":"10.1007/s00412-024-00820-2","DOIUrl":"10.1007/s00412-024-00820-2","url":null,"abstract":"Transgenerational gene expression depends on both underlying DNA sequences and epigenetic modifications. The latter, which can result in transmission of variegated gene expression patterns across multiple generations without DNA alterations, has been termed epigenetic inheritance and has been documented in plants, worms, flies and mammals. Whereas transcription factors binding to cognate DNA sequence elements regulate gene expression, the molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. Here we report that mutation of the CCAAT box promoter element abrogates NF-Y binding and disrupts the stable transgenerational expression of an MHC class I transgene. Transgenic mice with a mutated CCAAT box in the MHC class I transgene display variegated expression of the transgene among littermates and progeny in multiple independently derived transgenic lines. After 4 generations, CCAAT mutant transgenic lines derived from a single founder stably displayed distinct patterns of expression. Histone modifications and RNA polymerase II binding correlate with expression of CCAAT mutant transgenic lines, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box also results in changes to CTCF binding and DNA looping patterns across the transgene that correlate with expression status. These studies identify the CCAAT promoter element as a regulator of stable transgenerational gene expression such that mutation of the CCAAT box results in variegated transgenerational inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study provides insights into how fidelity of gene expression patterns is maintained through multiple generations.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":" ","pages":"203-216"},"PeriodicalIF":2.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449856","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}

引用次数: 0

Chromatin organization and behavior in HRAS-transformed mouse fibroblasts. HRAS转化小鼠成纤维细胞的染色质组织与行为

IF 1.6 4区生物学

Chromosoma Pub Date : 2024-04-01 Epub Date: 2024-02-24 DOI: 10.1007/s00412-024-00817-x

Aoi Otsuka, Katsuhiko Minami, Koichi Higashi, Akane Kawaguchi, Sachiko Tamura, Satoru Ide, Michael J Hendzel, Ken Kurokawa, Kazuhiro Maeshima

{"title":"Chromatin organization and behavior in HRAS-transformed mouse fibroblasts.","authors":"Aoi Otsuka, Katsuhiko Minami, Koichi Higashi, Akane Kawaguchi, Sachiko Tamura, Satoru Ide, Michael J Hendzel, Ken Kurokawa, Kazuhiro Maeshima","doi":"10.1007/s00412-024-00817-x","DOIUrl":"10.1007/s00412-024-00817-x","url":null,"abstract":"In higher eukaryotic cells, a string of nucleosomes, where long genomic DNA is wrapped around core histones, are rather irregularly folded into a number of condensed chromatin domains, which have been revealed by super-resolution imaging and Hi-C technologies. Inside these domains, nucleosomes fluctuate and locally behave like a liquid. The behavior of chromatin may be highly related to DNA transaction activities such as transcription and repair, which are often upregulated in cancer cells. To investigate chromatin behavior in cancer cells and compare those of cancer and non-cancer cells, we focused on oncogenic-HRAS (Gly12Val)-transformed mouse fibroblasts CIRAS-3 cells and their parental 10T1/2 cells. CIRAS-3 cells are tumorigenic and highly metastatic. First, we found that HRAS-induced transformation altered not only chromosome structure, but also nuclear morphology in the cell. Using single-nucleosome imaging/tracking in live cells, we demonstrated that nucleosomes are locally more constrained in CIRAS-3 cells than in 10T1/2 cells. Consistently, heterochromatin marked with H3K27me3 was upregulated in CIRAS-3 cells. Finally, Hi-C analysis showed enriched interactions of the B-B compartment in CIRAS-3 cells, which likely represents transcriptionally inactive chromatin. Increased heterochromatin may play an important role in cell migration, as they have been reported to increase during metastasis. Our study also suggests that single-nucleosome imaging provides new insights into how local chromatin is structured in living cells.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":" ","pages":"135-148"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139943885","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}

引用次数: 0

Dicentric chromosomes are resolved through breakage and repair at their centromeres. 双心染色体是通过中心粒的断裂和修复来解决的。

IF 1.6 4区生物学

Chromosoma Pub Date : 2024-04-01 Epub Date: 2024-01-02 DOI: 10.1007/s00412-023-00814-6

Diana Cook, Stanislav G Kozmin, Elaine Yeh, Thomas D Petes, Kerry Bloom

{"title":"Dicentric chromosomes are resolved through breakage and repair at their centromeres.","authors":"Diana Cook, Stanislav G Kozmin, Elaine Yeh, Thomas D Petes, Kerry Bloom","doi":"10.1007/s00412-023-00814-6","DOIUrl":"10.1007/s00412-023-00814-6","url":null,"abstract":"Chromosomes with two centromeres provide a unique opportunity to study chromosome breakage and DNA repair using completely endogenous cellular machinery. Using a conditional transcriptional promoter to control the second centromere, we are able to activate the dicentric chromosome and follow the appearance of DNA repair products. We find that the rate of appearance of DNA repair products resulting from homology-based mechanisms exceeds the expected rate based on their limited centromere homology (340 bp) and distance from one another (up to 46.3 kb). In order to identify whether DNA breaks originate in the centromere, we introduced 12 single-nucleotide polymorphisms (SNPs) into one of the centromeres. Analysis of the distribution of SNPs in the recombinant centromeres reveals that recombination was initiated with about equal frequency within the conserved centromere DNA elements CDEII and CDEIII of the two centromeres. The conversion tracts range from about 50 bp to the full length of the homology between the two centromeres (340 bp). Breakage and repair events within and between the centromeres can account for the efficiency and distribution of DNA repair products. We propose that in addition to providing a site for kinetochore assembly, the centromere may be a point of stress relief in the face of genomic perturbations.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":" ","pages":"117-134"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11180013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139073493","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}

引用次数: 0

Meiosis through three centuries. 三个世纪的减数分裂

IF 2.5 4区生物学

Chromosoma Pub Date : 2024-04-01 DOI: 10.1007/s00412-024-00822-0

Gareth Jones, Nancy Kleckner, Denise Zickler

引用次数: 0

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