Epigenomes最新文献_第10页

R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage. 减数分裂中r环的形成:在减数分裂转录相关DNA损伤中的作用。

IF 2.5

Epigenomes Pub Date : 2022-08-24 DOI: 10.3390/epigenomes6030026

Yasuhiro Fujiwara, Mary Ann Handel, Yuki Okada

引用次数: 1

De Novo Polycomb Recruitment and Repressive Domain Formation. 新多聚核糖招募和抑制域的形成

IF 2.5

Epigenomes Pub Date : 2022-08-22 DOI: 10.3390/epigenomes6030025

Itzel Alejandra Hernández-Romero, Victor Julian Valdes

{"title":"De Novo Polycomb Recruitment and Repressive Domain Formation.","authors":"Itzel Alejandra Hernández-Romero, Victor Julian Valdes","doi":"10.3390/epigenomes6030025","DOIUrl":"10.3390/epigenomes6030025","url":null,"abstract":"Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Experimental and Computational Approaches for Non-CpG Methylation Analysis. 非cpg甲基化分析的实验和计算方法。

IF 2.5

Epigenomes Pub Date : 2022-08-16 DOI: 10.3390/epigenomes6030024

Deepa Ramasamy, Arunagiri Kuha Deva Magendhra Rao, Thangarajan Rajkumar, Samson Mani

{"title":"Experimental and Computational Approaches for Non-CpG Methylation Analysis.","authors":"Deepa Ramasamy, Arunagiri Kuha Deva Magendhra Rao, Thangarajan Rajkumar, Samson Mani","doi":"10.3390/epigenomes6030024","DOIUrl":"https://doi.org/10.3390/epigenomes6030024","url":null,"abstract":"Cytosine methylation adjacent to adenine, thymine, and cytosine residues but not guanine of the DNA is distinctively known as non-CpG methylation. This CA/CT/CC methylation accounts for 15% of the total cytosine methylation and varies among different cell and tissue types. The abundance of CpG methylation has largely concealed the role of non-CpG methylation. Limitations in the early detection methods could not distinguish CpG methylation from non-CpG methylation. Recent advancements in enrichment strategies and high throughput sequencing technologies have enabled the detection of non-CpG methylation. This review discusses the advanced experimental and computational approaches to detect and describe the genomic distribution and function of non-CpG methylation. We present different approaches such as enzyme-based and antibody-based enrichment, which, when coupled, can also improve the sensitivity and specificity of non-CpG detection. We also describe the current bioinformatics pipelines and their specific application in computing and visualizing the imbalance of CpG and non-CpG methylation. Enrichment modes and the computational suites need to be further developed to ease the challenges of understanding the functional role of non-CpG methylation.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Role of Polycomb Proteins in Cell Lineage Commitment and Embryonic Development. 多梳蛋白在细胞谱系承诺和胚胎发育中的作用。

IF 2.5

Epigenomes Pub Date : 2022-08-12 DOI: 10.3390/epigenomes6030023

Chet H Loh, Gert Jan C Veenstra

{"title":"The Role of Polycomb Proteins in Cell Lineage Commitment and Embryonic Development.","authors":"Chet H Loh, Gert Jan C Veenstra","doi":"10.3390/epigenomes6030023","DOIUrl":"https://doi.org/10.3390/epigenomes6030023","url":null,"abstract":"Embryonic development is a highly intricate and complex process. Different regulatory mechanisms cooperatively dictate the fate of cells as they progress from pluripotent stem cells to terminally differentiated cell types in tissues. A crucial regulator of these processes is the Polycomb Repressive Complex 2 (PRC2). By catalyzing the mono-, di-, and tri-methylation of lysine residues on histone H3 tails (H3K27me3), PRC2 compacts chromatin by cooperating with Polycomb Repressive Complex 1 (PRC1) and represses transcription of target genes. Proteomic and biochemical studies have revealed two variant complexes of PRC2, namely PRC2.1 which consists of the core proteins (EZH2, SUZ12, EED, and RBBP4/7) interacting with one of the Polycomb-like proteins (MTF2, PHF1, PHF19), and EPOP or PALI1/2, and PRC2.2 which contains JARID2 and AEBP2 proteins. MTF2 and JARID2 have been discovered to have crucial roles in directing and recruiting PRC2 to target genes for repression in embryonic stem cells (ESCs). Following these findings, recent work in the field has begun to explore the roles of different PRC2 variant complexes during different stages of embryonic development, by examining molecular phenotypes of PRC2 mutants in both in vitro (2D and 3D differentiation) and in vivo (knock-out mice) assays, analyzed with modern single-cell omics and biochemical assays. In this review, we discuss the latest findings that uncovered the roles of different PRC2 proteins during cell-fate and lineage specification and extrapolate these findings to define a developmental roadmap for different flavors of PRC2 regulation during mammalian embryonic development.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses. 由高度差异组蛋白构建的核小体结构：寄生虫和巨型 DNA 病毒。

IF 2.5

Epigenomes Pub Date : 2022-08-02 DOI: 10.3390/epigenomes6030022

Shoko Sato, Mariko Dacher, Hitoshi Kurumizaka

{"title":"Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses.","authors":"Shoko Sato, Mariko Dacher, Hitoshi Kurumizaka","doi":"10.3390/epigenomes6030022","DOIUrl":"10.3390/epigenomes6030022","url":null,"abstract":"In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9396995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40649118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epigenomic Approaches for the Diagnosis of Rare Diseases. 用于诊断罕见疾病的表观基因组学方法。

IF 2.5

Epigenomes Pub Date : 2022-07-27 DOI: 10.3390/epigenomes6030021

Beatriz Martinez-Delgado, Maria J Barrero

引用次数: 0

Making Mitotic Chromosomes in a Test Tube. 在试管中制作有丝分裂染色体

IF 2.5

Epigenomes Pub Date : 2022-07-20 DOI: 10.3390/epigenomes6030020

Keishi Shintomi

引用次数: 0

Clinical Epigenetics on the Baltic Coast. 波罗的海沿岸的临床表观遗传学。

IF 2.5

Epigenomes Pub Date : 2022-07-20 DOI: 10.3390/epigenomes6030019

Ryszard Maleszka

引用次数: 0

DNA Hypomethylation May Contribute to Metabolic Recovery of Frozen Wood Frog Brains. DNA低甲基化可能有助于冷冻林蛙大脑的代谢恢复。

IF 2.5

Epigenomes Pub Date : 2022-07-12 DOI: 10.3390/epigenomes6030017

Tighe Bloskie, Kenneth B Storey

{"title":"DNA Hypomethylation May Contribute to Metabolic Recovery of Frozen Wood Frog Brains.","authors":"Tighe Bloskie, Kenneth B Storey","doi":"10.3390/epigenomes6030017","DOIUrl":"https://doi.org/10.3390/epigenomes6030017","url":null,"abstract":"Transcriptional suppression is characteristic of extreme stress responses, speculated to preserve energetic resources in the maintenance of hypometabolism. In recent years, epigenetic regulation has become heavily implicated in stress adaptation of many animals, including supporting freeze tolerance of the wood frog (Rana sylvatica). However, nervous tissues are frequently lacking in these multi-tissue analyses which warrants investigation. The present study examines the role of DNA methylation, a core epigenetic mechanism, in the response of wood frog brains to freezing. We use immunoblot analysis to track the relative expression of DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins and ten-eleven-translocation (TET) demethylases across the freeze-thaw cycle in R. sylvatica brain, including selected comparisons to freeze-associated sub-stresses (anoxia and dehydration). Global methyltransferase activities and 5-hmC content were also assessed. The data show coordinated evidence for DNA hypomethylation in wood frog brains during freeze-recovery through the combined roles of depressed DNMT3A/3L expression driving lowered DNMT activity and increased TET2/3 levels leading to elevated 5-hmC genomic content (p < 0.05). Raised levels of DNMT1 during high dehydration were also noteworthy. The above suggest that alleviation of transcriptionally repressive 5-mC DNA methylation is a necessary component of the wood frog freeze-thaw cycle, potentially facilitating the resumption of a normoxic transcriptional state as frogs thaw and resume normal metabolic activities.","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9419109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epidrugs: Toward Understanding and Treating Diverse Diseases. 外源性药物:了解和治疗多种疾病。

IF 2.5

Epigenomes Pub Date : 2022-07-12 DOI: 10.3390/epigenomes6030018

Takashi Umehara

引用次数: 2