Chromosoma最新文献_第3页

Karyotypes of water frogs from the Pelophylax esculentus complex: results of cross-species chromosomal painting. 水蛙复合体的核型:跨种染色体绘制的结果。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-11-01 Epub Date: 2023-11-25 DOI: 10.1007/s00412-023-00812-8

Dmitrij Dedukh, Antonina Maslova, Ahmed Al-Rikabi, Niklas Padutsch, Thomas Liehr, Alla Krasikova

{"title":"Karyotypes of water frogs from the Pelophylax esculentus complex: results of cross-species chromosomal painting.","authors":"Dmitrij Dedukh, Antonina Maslova, Ahmed Al-Rikabi, Niklas Padutsch, Thomas Liehr, Alla Krasikova","doi":"10.1007/s00412-023-00812-8","DOIUrl":"10.1007/s00412-023-00812-8","url":null,"abstract":"Amphibian species have the largest genome size enriched with repetitive sequences and relatively similar karyotypes. Moreover, many amphibian species frequently hybridize causing nuclear and mitochondrial genome introgressions. In addition, hybridization in some amphibian species may lead to clonality and polyploidization. All such events were found in water frogs from the genus Pelophylax. Among the species within the genus Pelophylax, P. esculentus complex is the most widely distributed and well-studied. This complex includes two parental species, P. ridibundus and P. lessonae, and their hybrids, P. esculentus, reproducing hemiclonally. Parental species and their hybrids have similar but slightly polymorphic karyotypes, so their precise identification is still required. Here, we have developed a complete set of 13 chromosome painting probes for two parental species allowing the precise identification of all chromosomes. Applying chromosomal painting, we identified homologous chromosomes in both parental species and orthologous chromosomes in their diploid hemiclonal hybrids. Comparative painting did not reveal interchromosomal exchanges between the studied water frog species and their hybrids. Using cross-specific chromosome painting, we detected unequal distribution of the signals along chromosomes suggesting the presence of species-specific tandem repeats. Application of chromosomal paints to the karyotypes of hybrids revealed differences in the intensity of staining for P. ridibundus and P. lessonae chromosomes. Thus, both parental genomes have a divergence in unique sequences. Obtained chromosome probes may serve as a powerful tool to unravel chromosomal evolution in phylogenetically related species, identify individual chromosomes in different cell types, and investigate the elimination of chromosomes in hybrid water frogs.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138433514","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

The regulation of Tfh cell differentiation by β-hydroxybutyrylation modification of transcription factor Bcl6. 转录因子 Bcl6 的β-羟基丁酰化修饰对 Tfh 细胞分化的调控。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-11-01 Epub Date: 2023-05-25 DOI: 10.1007/s00412-023-00799-2

Jingtian Guo, Yimeng Wang, Lei Tang, Tiejun Tang, Zhuolan Li, Mengyuan Li, Liming Wang, Aizhong Zeng, Yuxiao Ma, Shihao Huang, Xiaomeng Jiang, Wei Guo

{"title":"The regulation of Tfh cell differentiation by β-hydroxybutyrylation modification of transcription factor Bcl6.","authors":"Jingtian Guo, Yimeng Wang, Lei Tang, Tiejun Tang, Zhuolan Li, Mengyuan Li, Liming Wang, Aizhong Zeng, Yuxiao Ma, Shihao Huang, Xiaomeng Jiang, Wei Guo","doi":"10.1007/s00412-023-00799-2","DOIUrl":"10.1007/s00412-023-00799-2","url":null,"abstract":"Transcriptional repressor B cell lymphoma 6 (Bcl6) is a major transcription factor involved in Tfh cell differentiation and germinal center response, which is regulated by a variety of biological processes. However, the functional impact of post-translational modifications, particularly lysine β-hydroxybutyrylation (Kbhb), on Bcl6 remains elusive. In this study, we revealed that Bcl6 is modified by Kbhb to affect Tfh cell differentiation, resulting in the decrease of cell population and cytokine IL-21. Furthermore, the modification sites are identified from enzymatic reactions to be lysine residues at positions 376, 377, and 379 by mass spectrometry, which is confirmed by site-directed mutagenesis and functional analyses. Collectively, our present study provides evidence on the Kbhb modification of Bcl6 and also generates new insights into the regulation of Tfh cell differentiation, which is a starting point for a thorough understanding of the functional involvement of Kbhb modification in the differentiations of Tfh and other T cells.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9895388","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

Modeling of covalent modifications of histones to estimate the binding affinity. 建立组蛋白共价修饰模型，估算结合亲和力。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-11-01 Epub Date: 2023-05-20 DOI: 10.1007/s00412-023-00798-3

Ali Aslhashemi, Mahdi Rezaei Karamati, Hossein Motavalli, Milad Bastami

{"title":"Modeling of covalent modifications of histones to estimate the binding affinity.","authors":"Ali Aslhashemi, Mahdi Rezaei Karamati, Hossein Motavalli, Milad Bastami","doi":"10.1007/s00412-023-00798-3","DOIUrl":"10.1007/s00412-023-00798-3","url":null,"abstract":"Covalent histone modifications such as methylation, acetylation, phosphorylation, and other epigenetic modifications of the chromatin play an essential role in regulating eukaryotic cells of which most of these reactions are catalyzed by the enzymes. The binding energy of enzymes is often determined by experimental data via mathematical and statistical models due to specific modifications. Many theoretical models have been introduced to study histone modifications and reprogramming experiments in mammalian cells, in which all efforts in determining the affinity binding are essential part of the work. Here, we introduce a one-dimensional statistical Potts model to accurately determine the enzyme's binding free energy using the experimental data for various types of cells. We study the methylation of lysine 4 and 27 on histone H3 and suppose that each histone has one modification site with one of the seven states: H3K27me3, H3K27me2, H3K27me1, unmodified, H3K4me1, H3K4me2, and H3K4me3. Based on this model, the histone covalent modification is described. Moreover, by using simulation data, the histone's binding free energy and the energy of chromatin states are determined, when they are subject to changes from unmodified to active or repressive states, by finding the probability of the transition.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9495996","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

Increased genome size is caused by heterochromatin addition in two non-related bat species, Hesperoptenus doriae and Philetor brachypterus (Vespertilionidae, Chiroptera, Mammalia). 两种非亲缘关系的蝙蝠--Hesperoptenus doriae和Philetor brachypterus（蝙蝠科，翼手目，哺乳纲）--的异染色质增加导致基因组体积增大。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-11-01 Epub Date: 2023-06-16 DOI: 10.1007/s00412-023-00802-w

Marianne Volleth, Johann Greilhuber, Klaus-Gerhard Heller, Stefan Müller, Hoi-Sen Yong, Josef Loidl

{"title":"Increased genome size is caused by heterochromatin addition in two non-related bat species, Hesperoptenus doriae and Philetor brachypterus (Vespertilionidae, Chiroptera, Mammalia).","authors":"Marianne Volleth, Johann Greilhuber, Klaus-Gerhard Heller, Stefan Müller, Hoi-Sen Yong, Josef Loidl","doi":"10.1007/s00412-023-00802-w","DOIUrl":"10.1007/s00412-023-00802-w","url":null,"abstract":"The average genome size (GS) of bats, which are the only mammals capable of powered flight, is approximately 18% smaller than that of closely related mammalian orders. The low nuclear DNA content of Chiroptera is comparable to that of birds, which are also characterized by a high metabolic rate. Only a few chiropteran taxa possess notable amounts of constitutive heterochromatin. Here, we studied the karyotypes of two non-related vesper bat species with unusually high amounts of constitutive heterochromatin: Hesperoptenus doriae and Philetor brachypterus. Conventional staining methods and whole-chromosome painting with probes derived from Myotis myotis (2n = 44), showing a karyotype close to that of the presumed ancestor of Vespertilionidae, revealed Robertsonian fusions as the main type of rearrangement leading to the exceptionally reduced diploid chromosome number of 2n = 26 in both species. Moreover, both karyotypes are characterized by large blocks of pericentromeric heterochromatin composed of CMA-positive and DA-DAPI-positive segments. In H. doriae, the heterochromatin accumulation has resulted in a genome size of 3.22 pg (1C), which is 40% greater than the mean genome size for the family. For P. brachypterus, a genome size of 2.94 pg was determined, representing an increase of about 28%. Most notably, in H. doriae, the presence of additional constitutive heterochromatin correlates with an extended mitotic cell cycle duration in vitro. A reduction in diploid chromosome number to 30 or lower is discussed as a possible cause of the accumulation of pericentromeric heterochromatin in Vespertilionidae.","PeriodicalId":10248,"journal":{"name":"Chromosoma","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10012073","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

Casting histone variants during mammalian reproduction. 在哺乳动物繁殖过程中铸造组蛋白变异。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-09-01 DOI: 10.1007/s00412-023-00803-9

Germaine Karam, Antoine Molaro

引用次数: 0

Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation. 利用合成DNA文库研究染色质和基因调控。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-09-01 Epub Date: 2023-05-15 DOI: 10.1007/s00412-023-00796-5

Holly Kleinschmidt, Cheng Xu, Lu Bai

引用次数: 0

New voices in epigenetics. 表观遗传学的新声音。

IF 1.6 4区生物学

Chromosoma Pub Date : 2023-09-01 DOI: 10.1007/s00412-023-00805-7

Genevieve Almouzni, Tom Misteli, Yamini Dalal

引用次数: 0

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":null,"pages":null},"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":null,"pages":null},"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