Chromosoma最新文献_第4页

Centromeric and pericentric transcription and transcripts: their intricate relationships, regulation, and functions. 着丝粒和近心粒转录和转录本:它们的复杂关系、调控和功能。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-09-01 DOI: 10.1007/s00412-023-00801-x

Jing Zhu, Qiao Guo, Minjun Choi, Zhoubin Liang, Karen Wing Yee Yuen

{"title":"Centromeric and pericentric transcription and transcripts: their intricate relationships, regulation, and functions.","authors":"Jing Zhu, Qiao Guo, Minjun Choi, Zhoubin Liang, Karen Wing Yee Yuen","doi":"10.1007/s00412-023-00801-x","DOIUrl":"https://doi.org/10.1007/s00412-023-00801-x","url":null,"abstract":"Centromeres are no longer considered to be silent. Both centromeric and pericentric transcription have been discovered, and their RNA transcripts have been characterized and probed for functions in numerous monocentric model organisms recently. Here, we will discuss the challenges in centromere transcription studies due to the repetitive nature and sequence similarity in centromeric and pericentric regions. Various technological breakthroughs have helped to tackle these challenges and reveal unique features of the centromeres and pericentromeres. We will briefly introduce these techniques, including third-generation long-read DNA and RNA sequencing, protein-DNA and RNA-DNA interaction detection methods, and epigenomic and nucleosomal mapping techniques. Interestingly, some newly analyzed repeat-based holocentromeres also resemble the architecture and the transcription behavior of monocentromeres. We will summarize evidences that support the functions of the transcription process and stalling, and those that support the functions of the centromeric and pericentric RNAs. The processing of centromeric and pericentric RNAs into multiple variants and their diverse structures may also provide clues to their functions. How future studies may address the separation of functions of specific centromeric transcription steps, processing pathways, and the transcripts themselves will also be discussed.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 3","pages":"211-230"},"PeriodicalIF":1.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10356649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9868545","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: 2

Fluorescence-based super-resolution-microscopy strategies for chromatin studies. 基于荧光的超分辨率显微镜策略用于染色质研究。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-09-01 DOI: 10.1007/s00412-023-00792-9

Thomas C Q Burgers, Rifka Vlijm

{"title":"Fluorescence-based super-resolution-microscopy strategies for chromatin studies.","authors":"Thomas C Q Burgers, Rifka Vlijm","doi":"10.1007/s00412-023-00792-9","DOIUrl":"https://doi.org/10.1007/s00412-023-00792-9","url":null,"abstract":"Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 3","pages":"191-209"},"PeriodicalIF":1.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10356683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9921662","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: 2

Are extraordinary nucleosome structures more ordinary than we thought? 非凡的核小体结构比我们想象的更普通吗?

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-09-01 DOI: 10.1007/s00412-023-00791-w

Claris Y Y Chong, Lu Gan

引用次数: 2

Regulation of the epigenome through RNA modifications. 通过RNA修饰调控表观基因组。

IF 2.5 4区生物学

Chromosoma Pub Date : 2023-09-01 Epub Date: 2023-05-04 DOI: 10.1007/s00412-023-00794-7

Emmely A Patrasso, Sweta Raikundalia, Daniel Arango

{"title":"Regulation of the epigenome through RNA modifications.","authors":"Emmely A Patrasso, Sweta Raikundalia, Daniel Arango","doi":"10.1007/s00412-023-00794-7","DOIUrl":"10.1007/s00412-023-00794-7","url":null,"abstract":"Chemical modifications of nucleotides expand the complexity and functional properties of genomes and transcriptomes. A handful of modifications in DNA bases are part of the epigenome, wherein DNA methylation regulates chromatin structure, transcription, and co-transcriptional RNA processing. In contrast, more than 150 chemical modifications of RNA constitute the epitranscriptome. Ribonucleoside modifications comprise a diverse repertoire of chemical groups, including methylation, acetylation, deamination, isomerization, and oxidation. Such RNA modifications regulate all steps of RNA metabolism, including folding, processing, stability, transport, translation, and RNA's intermolecular interactions. Initially thought to influence all aspects of the post-transcriptional regulation of gene expression exclusively, recent findings uncovered a crosstalk between the epitranscriptome and the epigenome. In other words, RNA modifications feedback to the epigenome to transcriptionally regulate gene expression. The epitranscriptome achieves this feat by directly or indirectly affecting chromatin structure and nuclear organization. This review highlights how chemical modifications in chromatin-associated RNAs (caRNAs) and messenger RNAs (mRNAs) encoding factors involved in transcription, chromatin structure, histone modifications, and nuclear organization affect gene expression transcriptionally.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 3","pages":"231-246"},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10524150/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10244762","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

Establishment and inheritance of minichromosomes from Arabidopsis haploid induction. 拟南芥单倍体诱导小染色体的建立与遗传。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-06-01 DOI: 10.1007/s00412-023-00788-5

Ek Han Tan, Benny Ordoñez, Tejas Thondehaalmath, Danelle K Seymour, Julin N Maloof, Ravi Maruthachalam, Luca Comai

{"title":"Establishment and inheritance of minichromosomes from Arabidopsis haploid induction.","authors":"Ek Han Tan, Benny Ordoñez, Tejas Thondehaalmath, Danelle K Seymour, Julin N Maloof, Ravi Maruthachalam, Luca Comai","doi":"10.1007/s00412-023-00788-5","DOIUrl":"https://doi.org/10.1007/s00412-023-00788-5","url":null,"abstract":"Minichromosomes are small, sometimes circular, rearranged chromosomes consisting of one centromere and short chromosomal arms formed by treatments that break DNA, including plant transformation. Minichromosomes have the potential to serve as vectors to quickly move valuable genes across a wide range of germplasm, including into adapted crop varieties. To realize this potential, minichromosomes must be reliably generated, easily manipulated, and stably inherited. Here we show a reliable method for minichromosome formation in haploids resulting from CENH3-mediated genome elimination, a process that generates genome instability and karyotypic novelty specifically on one parental genome. First, we identified 2 out of 260 haploids, each containing a single-copy minichromosome originating from centromeric regions of chromosomes 1 and 3, respectively. The chromosome 1 minichromosome we characterized did not pair at meiosis but displayed consistent transmission over nine selfing generations. Next, we demonstrated that CENH3-based haploid induction can produce minichromosomes in a targeted manner. Haploid inducers carrying a selectable pericentromeric marker were used to isolate additional chromosome-specific minichromosomes, which occurred in 3 out of 163 haploids. Our findings document the formation of heritable, rearranged chromosomes, and we provide a method for convenient minichromosome production.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 2","pages":"105-115"},"PeriodicalIF":1.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10247564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9693868","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: 1

The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae. 卫星的发射:DNA重复序列作为细胞遗传学工具在发现野生小麦的染色体宇宙。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-06-01 DOI: 10.1007/s00412-023-00789-4

Pavel Yu Kroupin, Daniil S Ulyanov, Gennady I Karlov, Mikhail G Divashuk

{"title":"The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae.","authors":"Pavel Yu Kroupin, Daniil S Ulyanov, Gennady I Karlov, Mikhail G Divashuk","doi":"10.1007/s00412-023-00789-4","DOIUrl":"https://doi.org/10.1007/s00412-023-00789-4","url":null,"abstract":"Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for \"classical\" wheat probes (pSc119.2 and Afa family) and \"universal\" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 2","pages":"65-88"},"PeriodicalIF":1.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9689645","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

Replisome-cohesin interactions provided by the Tof1-Csm3 and Mrc1 cohesion establishment factors. Tof1-Csm3和Mrc1内聚建立因子提供的复制体-内聚素相互作用。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-06-01 Epub Date: 2023-05-11 DOI: 10.1007/s00412-023-00797-4

Sudikchya Shrestha, Masashi Minamino, Zhuo A Chen, Céline Bouchoux, Juri Rappsilber, Frank Uhlmann

{"title":"Replisome-cohesin interactions provided by the Tof1-Csm3 and Mrc1 cohesion establishment factors.","authors":"Sudikchya Shrestha, Masashi Minamino, Zhuo A Chen, Céline Bouchoux, Juri Rappsilber, Frank Uhlmann","doi":"10.1007/s00412-023-00797-4","DOIUrl":"10.1007/s00412-023-00797-4","url":null,"abstract":"The chromosomal cohesin complex establishes sister chromatid cohesion during S phase, which forms the basis for faithful segregation of DNA replication products during cell divisions. Cohesion establishment is defective in the absence of either of three non-essential Saccharomyces cerevisiae replication fork components Tof1-Csm3 and Mrc1. Here, we investigate how these conserved factors contribute to cohesion establishment. Tof1-Csm3 and Mrc1 serve known roles during DNA replication, including replication checkpoint signaling, securing replication fork speed, as well as recruiting topoisomerase I and the histone chaperone FACT. By modulating each of these functions independently, we rule out that one of these known replication roles explains the contribution of Tof1-Csm3 and Mrc1 to cohesion establishment. Instead, using purified components, we reveal direct and multipronged protein interactions of Tof1-Csm3 and Mrc1 with the cohesin complex. Our findings open the possibility that a series of physical interactions between replication fork components and cohesin facilitate successful establishment of sister chromatid cohesion during DNA replication.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 2","pages":"117-135"},"PeriodicalIF":1.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10247859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9744612","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

Chromosome stability @10! 染色体稳定性@10!

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-06-01 DOI: 10.1007/s00412-023-00795-6

K T Nishant, Kaustuv Sanyal

引用次数: 0

A cytological revisit on parthenogenetic Artemia and the deficiency of a meiosis-specific recombinase DMC1 in the possible transition from bisexuality to parthenogenesis. 单性生殖青蒿的细胞学回顾和减数分裂特异性重组酶DMC1在双性恋到单性生殖的可能转变中的缺乏。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-06-01 DOI: 10.1007/s00412-023-00790-x

Lian-Ying Xu, Wen-Tao Wu, Ning Bi, Zhi-Jun Yan, Fan Yang, Wei-Jun Yang, Jin-Shu Yang

{"title":"A cytological revisit on parthenogenetic Artemia and the deficiency of a meiosis-specific recombinase DMC1 in the possible transition from bisexuality to parthenogenesis.","authors":"Lian-Ying Xu, Wen-Tao Wu, Ning Bi, Zhi-Jun Yan, Fan Yang, Wei-Jun Yang, Jin-Shu Yang","doi":"10.1007/s00412-023-00790-x","DOIUrl":"https://doi.org/10.1007/s00412-023-00790-x","url":null,"abstract":"Although parthenogenesis is widespread in nature and known to have close relationships with bisexuality, the transitional mechanism is poorly understood. Artemia is an ideal model to address this issue because bisexuality and \"contagious\" obligate parthenogenesis independently exist in its congeneric members. In the present study, we first performed chromosome spreading and immunofluorescence to compare meiotic processes of Artemia adopting two distinct reproductive ways. The results showed that, unlike conventional meiosis in bisexual Artemia, meiosis II in parthenogenic Artemia is entirely absent and anaphase I is followed by a single mitosis-like equational division. Interspecific comparative transcriptomics showed that two central molecules in homologous recombination (HR), Dmc1 and Rad51, exhibited significantly higher expression in bisexual versus parthenogenetic Artemia. qRT-PCR indicated that the expression of both genes peaked at the early oogenesis and gradually decreased afterward. Knocking-down by RNAi of Dmc1 in unfertilized females of bisexual Artemia resulted in a severe deficiency of homologous chromosome pairing and produced univalents at the middle oogenesis stage, which was similar to that of parthenogenic Artemia, while in contrast, silencing Rad51 led to no significant chromosome morphological change. Our results indicated that Dmc1 is vital for HR in bisexual Artemia, and the deficiency of Dmc1 may be correlated with or even possibly one of core factors in the transition from bisexuality to parthenogenesis.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 2","pages":"89-103"},"PeriodicalIF":1.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10046892","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

A genome-wide RNAi screen for genes important for proliferation of cultured Drosophila cells at low temperature identifies the Ball/VRK protein kinase. 对低温培养果蝇细胞增殖重要基因的全基因组RNAi筛选鉴定出Ball/VRK蛋白激酶。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-03-01 DOI: 10.1007/s00412-023-00787-6

Anna Mendaluk, Emmanuel Caussinus, Michael Boutros, Christian F Lehner

{"title":"A genome-wide RNAi screen for genes important for proliferation of cultured Drosophila cells at low temperature identifies the Ball/VRK protein kinase.","authors":"Anna Mendaluk, Emmanuel Caussinus, Michael Boutros, Christian F Lehner","doi":"10.1007/s00412-023-00787-6","DOIUrl":"https://doi.org/10.1007/s00412-023-00787-6","url":null,"abstract":"A change in ambient temperature is predicted to disrupt cellular homeostasis by affecting all cellular processes in an albeit non-uniform manner. Diffusion is generally less temperature-sensitive than enzymes, for example, and each enzyme has a characteristic individual temperature profile. The actual effects of temperature variation on cells are still poorly understood at the molecular level. Towards an improved understanding, we have performed a genome-wide RNA interference screen with S2R + cells. This Drosophila cell line proliferates over a temperature range comparable to that tolerated by the parental ectothermic organism. Based on effects on cell counts and cell cycle profile after knockdown at 27 and 17 °C, respectively, genes were identified with an apparent greater physiological significance at one or the other temperature. While 27 °C is close to the temperature optimum, the substantially lower 17 °C was chosen to identify genes important at low temperatures, which have received less attention compared to the heat shock response. Among a substantial number of screen hits, we validated a set successfully in cell culture and selected ballchen for further evaluation in the organism. This gene encodes the conserved metazoan VRK protein kinase that is crucial for the release of chromosomes from the nuclear envelope during mitosis. Our analyses in early embryos and larval wing imaginal discs confirmed a higher requirement for ballchen function at temperatures below the optimum. Overall, our experiments validate the genome-wide screen as a basis for future characterizations of genes with increased physiological significance at the lower end of the readily tolerated temperature range.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":"132 1","pages":"31-53"},"PeriodicalIF":1.6,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9352289","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