Chromosoma最新文献_第4页

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":" ","pages":"247-256"},"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":" ","pages":"269-288"},"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":"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