Epigenetics & Chromatin最新文献

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Transcriptional silencing in Saccharomyces cerevisiae: known unknowns 酿酒酵母中的转录沉默:已知的未知数
IF 3.9 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-09-14 DOI: 10.1186/s13072-024-00553-7
Namrita Dhillon, Rohinton T. Kamakaka
{"title":"Transcriptional silencing in Saccharomyces cerevisiae: known unknowns","authors":"Namrita Dhillon, Rohinton T. Kamakaka","doi":"10.1186/s13072-024-00553-7","DOIUrl":"https://doi.org/10.1186/s13072-024-00553-7","url":null,"abstract":"Transcriptional silencing in Saccharomyces cerevisiae is a persistent and highly stable form of gene repression. It involves DNA silencers and repressor proteins that bind nucleosomes. The silenced state is influenced by numerous factors including the concentration of repressors, nature of activators, architecture of regulatory elements, modifying enzymes and the dynamics of chromatin.Silencers function to increase the residence time of repressor Sir proteins at silenced domains while clustering of silenced domains enables increased concentrations of repressors and helps facilitate long-range interactions. The presence of an accessible NDR at the regulatory regions of silenced genes, the cycling of chromatin configurations at regulatory sites, the mobility of Sir proteins, and the non-uniform distribution of the Sir proteins across the silenced domain, all result in silenced chromatin that only stably silences weak promoters and enhancers via changes in transcription burst duration and frequency.These data collectively suggest that silencing is probabilistic and the robustness of silencing is achieved through sub-optimization of many different nodes of action such that a stable expression state is generated and maintained even though individual constituents are in constant flux.","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"47 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142262071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 role of hexokinases in epigenetic regulation: altered hexokinase expression and chromatin stability in yeast. 己糖激酶在表观遗传调控中的作用:酵母中己糖激酶表达和染色质稳定性的改变。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-08-27 DOI: 10.1186/s13072-024-00551-9
Srinivasu Karri, Quinn Dickinson, Jing Jia, Yi Yang, Haiyun Gan, Zhiquan Wang, Yibin Deng, Chuanhe Yu
{"title":"The role of hexokinases in epigenetic regulation: altered hexokinase expression and chromatin stability in yeast.","authors":"Srinivasu Karri, Quinn Dickinson, Jing Jia, Yi Yang, Haiyun Gan, Zhiquan Wang, Yibin Deng, Chuanhe Yu","doi":"10.1186/s13072-024-00551-9","DOIUrl":"10.1186/s13072-024-00551-9","url":null,"abstract":"<p><strong>Background: </strong>Human hexokinase 2 (HK2) plays an important role in regulating Warburg effect, which metabolizes glucose to lactate acid even in the presence of ample oxygen and provides intermediate metabolites to support cancer cell proliferation and tumor growth. HK2 overexpression has been observed in various types of cancers and targeting HK2-driven Warburg effect has been suggested as a potential cancer therapeutic strategy. Given that epigenetic enzymes utilize metabolic intermediates as substrates or co-factors to carry out post-translational modification of histones and nucleic acids modifications in cells, we hypothesized that altering HK2 expression could impact the epigenome and, consequently, chromatin stability in yeast. To test this hypothesis, we established genetic models with different yeast hexokinase 2 (HXK2) expression in Saccharomyces cerevisiae yeast cells and investigated the effect of HXK2-dependent metabolism on parental nucleosome transfer, a key DNA replication-coupled epigenetic inheritance process, and chromatin stability.</p><p><strong>Results: </strong>By comparing the growth of mutant yeast cells carrying single deletion of hxk1Δ, hxk2Δ, or double-loss of hxk1Δ hxk2Δ to wild-type cells, we firstly confirmed that HXK2 is the dominant HXK in yeast cell growth. Surprisingly, manipulating HXK2 expression in yeast, whether through overexpression or deletion, had only a marginal impact on parental nucleosome assembly, but a noticeable trend with decrease chromatin instability. However, targeting yeast cells with 2-deoxy-D-glucose (2-DG), a clinical glycolysis inhibitor that has been proposed as an anti-cancer treatment, significantly increased chromatin instability.</p><p><strong>Conclusion: </strong>Our findings suggest that in yeast cells lacking HXK2, alternative HXKs such as HXK1 or glucokinase 1 (GLK1) play a role in supporting glycolysis at a level that adequately maintains epigenomic stability. While our study demonstrated an increase in epigenetic instability with 2-DG treatment, the observed effect seemed to occur dependent on non-glycolytic function of Hxk2. Thus, additional research is needed to identify the molecular mechanism through which 2-DG influences chromatin stability.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"27"},"PeriodicalIF":4.2,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
DNA methylation correlates of chronological age in diverse human tissue types. 不同人体组织类型中与计时年龄相关的 DNA 甲基化。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-08-08 DOI: 10.1186/s13072-024-00546-6
Niyati Jain, James L Li, Lin Tong, Farzana Jasmine, Muhammad G Kibriya, Kathryn Demanelis, Meritxell Oliva, Lin S Chen, Brandon L Pierce
{"title":"DNA methylation correlates of chronological age in diverse human tissue types.","authors":"Niyati Jain, James L Li, Lin Tong, Farzana Jasmine, Muhammad G Kibriya, Kathryn Demanelis, Meritxell Oliva, Lin S Chen, Brandon L Pierce","doi":"10.1186/s13072-024-00546-6","DOIUrl":"10.1186/s13072-024-00546-6","url":null,"abstract":"<p><strong>Background: </strong>While the association of chronological age with DNA methylation (DNAm) in whole blood has been extensively studied, the tissue-specificity of age-related DNAm changes remains an active area of research. Studies investigating the association of age with DNAm in tissues such as brain, skin, immune cells, fat, and liver have identified tissue-specific and non-specific effects, thus, motivating additional studies of diverse human tissue and cell types.</p><p><strong>Results: </strong>Here, we performed an epigenome-wide association study, leveraging DNAm data (Illumina EPIC array) from 961 tissue samples representing 9 tissue types (breast, lung, colon, ovary, prostate, skeletal muscle, testis, whole blood, and kidney) from the Genotype-Tissue Expression (GTEx) project. We identified age-associated CpG sites (false discovery rate < 0.05) in 8 tissues (all except skeletal muscle, n = 47). This included 162,002 unique hypermethylated and 90,626 hypomethylated CpG sites across all tissue types, with 130,137 (80%) hypermethylated CpGs and 74,703 (82%) hypomethylated CpG sites observed in a single tissue type. While the majority of age-associated CpG sites appeared tissue-specific, the patterns of enrichment among genomic features, such as chromatin states and CpG islands, were similar across most tissues, suggesting common mechanisms underlying cellular aging. Consistent with previous findings, we observed that hypermethylated CpG sites are enriched in regions with repressed polycomb signatures and CpG islands, while hypomethylated CpG sites preferentially occurred in non-CpG islands and enhancers. To gain insights into the functional effects of age-related DNAm changes, we assessed the correlation between DNAm and local gene expression changes to identify age-related expression quantitative trait methylation (age-eQTMs). We identified several age-eQTMs present in multiple tissue-types, including in the CDKN2A, HENMT1, and VCWE regions.</p><p><strong>Conclusion: </strong>Overall, our findings will aid future efforts to develop biomarkers of aging and understand mechanisms of aging in diverse human tissue types.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"25"},"PeriodicalIF":4.2,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11308253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Transcriptional regulation mechanism of PARP1 and its application in disease treatment. PARP1 的转录调控机制及其在疾病治疗中的应用。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-08-08 DOI: 10.1186/s13072-024-00550-w
Yu Lu, Wenliang Fu, Weiwei Xing, Haowei Wu, Chao Zhang, Donggang Xu
{"title":"Transcriptional regulation mechanism of PARP1 and its application in disease treatment.","authors":"Yu Lu, Wenliang Fu, Weiwei Xing, Haowei Wu, Chao Zhang, Donggang Xu","doi":"10.1186/s13072-024-00550-w","DOIUrl":"10.1186/s13072-024-00550-w","url":null,"abstract":"<p><p>Poly (ADP-ribose) polymerase 1 (PARP1) is a multifunctional nuclear enzyme that catalyzes poly-ADP ribosylation in eukaryotic cells. In addition to maintaining genomic integrity, this nuclear enzyme is also involved in transcriptional regulation. PARP1 can trigger and maintain changes in the chromatin structure and directly recruit transcription factors. PARP1 also prevents DNA methylation. However, most previous reviews on PARP1 have focused on its involvement in maintaining genome integrity, with less focus on its transcriptional regulatory function. This article comprehensively reviews the transcriptional regulatory function of PARP1 and its application in disease treatment, providing new ideas for targeting PARP1 for the treatment of diseases other than cancer.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"26"},"PeriodicalIF":4.2,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11308664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Long-term exposure to diesel exhaust particles induces concordant changes in DNA methylation and transcriptome in human adenocarcinoma alveolar basal epithelial cells. 长期暴露于柴油废气颗粒会诱导人类腺癌肺泡基底上皮细胞的 DNA 甲基化和转录组发生一致的变化。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-08-05 DOI: 10.1186/s13072-024-00549-3
Alexandra Lukyanchuk, Naomi Muraki, Tomoko Kawai, Takehiro Sato, Kenichiro Hata, Tsuyoshi Ito, Atsushi Tajima
{"title":"Long-term exposure to diesel exhaust particles induces concordant changes in DNA methylation and transcriptome in human adenocarcinoma alveolar basal epithelial cells.","authors":"Alexandra Lukyanchuk, Naomi Muraki, Tomoko Kawai, Takehiro Sato, Kenichiro Hata, Tsuyoshi Ito, Atsushi Tajima","doi":"10.1186/s13072-024-00549-3","DOIUrl":"10.1186/s13072-024-00549-3","url":null,"abstract":"<p><strong>Background: </strong>Diesel exhaust particles (DEP), which contain hazardous compounds, are emitted during the combustion of diesel. As approximately one-third of the vehicles worldwide use diesel, there are growing concerns about the risks posed by DEP to human health. Long-term exposure to DEP is associated with airway hyperresponsiveness, pulmonary fibrosis, and inflammation; however, the molecular mechanisms behind the effects of DEP on the respiratory tract are poorly understood. Such mechanisms can be addressed by examining transcriptional and DNA methylation changes. Although several studies have focused on the effects of short-term DEP exposure on gene expression, research on the transcriptional effects and genome-wide DNA methylation changes caused by long-term DEP exposure is lacking. Hence, in this study, we investigated transcriptional and DNA methylation changes in human adenocarcinoma alveolar basal epithelial A549 cells caused by prolonged exposure to DEP and determined whether these changes are concordant.</p><p><strong>Results: </strong>DNA methylation analysis using the Illumina Infinium MethylationEPIC BeadChips showed that the methylation levels of DEP-affected CpG sites in A549 cells changed in a dose-dependent manner; the extent of change increased with increasing dose reaching the statistical significance only in samples exposed to 30 µg/ml DEP. Four-week exposure to 30 µg/ml of DEP significantly induced DNA hypomethylation at 24,464 CpG sites, which were significantly enriched for DNase hypersensitive sites, genomic regions marked by H3K4me1 and H3K27ac, and several transcription factor binding sites. In contrast, 9,436 CpG sites with increased DNA methylation levels were significantly overrepresented in genomic regions marked by H3K27me3 as well as H3K4me1 and H3K27ac. In parallel, gene expression profiling by RNA sequencing demonstrated that long-term exposure to DEP altered the expression levels of 2,410 genes, enriching 16 gene sets including Xenobiotic metabolism, Inflammatory response, and Senescence. In silico analysis revealed that the expression levels of 854 genes correlated with the methylation levels of the DEP-affected cis-CpG sites.</p><p><strong>Conclusions: </strong>To our knowledge, this is the first report of genome-wide transcriptional and DNA methylation changes and their associations in A549 cells following long-term exposure to DEP.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"24"},"PeriodicalIF":4.2,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
The role of ribosomal DNA methylation in embryonic development, aging and diseases. 核糖体 DNA 甲基化在胚胎发育、衰老和疾病中的作用。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-07-31 DOI: 10.1186/s13072-024-00548-4
Fei Yang, Xutong Guo, Yiming Bao, Rujiao Li
{"title":"The role of ribosomal DNA methylation in embryonic development, aging and diseases.","authors":"Fei Yang, Xutong Guo, Yiming Bao, Rujiao Li","doi":"10.1186/s13072-024-00548-4","DOIUrl":"10.1186/s13072-024-00548-4","url":null,"abstract":"<p><p>The ribosomal DNA (rDNA) constitutes a remarkably conserved DNA sequence within species, located in the area of the nucleolus, and responsible for coding three major types of rRNAs (18S, 5.8S and 28S). While historical investigations into rDNA focused on its structure and coding capabilities, recent research has turned to explore its functional roles in various biological processes. In this review, we summarize the main findings of rDNA methylation with embryonic development, aging and diseases in multiple species, including epigenetic alterations, related biological processes and potential applications of rDNA methylation. We present an overview of current related research and identify gaps in this field.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"23"},"PeriodicalIF":4.2,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11290161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration. 将 CUT&Tag 应用于斑马鱼成体尾鳍,可发现再生过程中胚胎期 H3K4me3 模式的回归。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-07-20 DOI: 10.1186/s13072-024-00547-5
Phu Duong, Anjelica Rodriguez-Parks, Junsu Kang, Patrick J Murphy
{"title":"CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration.","authors":"Phu Duong, Anjelica Rodriguez-Parks, Junsu Kang, Patrick J Murphy","doi":"10.1186/s13072-024-00547-5","DOIUrl":"10.1186/s13072-024-00547-5","url":null,"abstract":"<p><p>Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of changes in chromatin modifications during adult fin regeneration in zebrafish. Our protocol generates data that recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and genes which lose H3K4me3 become silenced. Interestingly, these reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-h old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"22"},"PeriodicalIF":4.2,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11264793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues. CREdb:顺式调控元件及其在人体细胞和组织中的活性的综合数据库。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-07-16 DOI: 10.1186/s13072-024-00545-7
Chris Hartl, Jiali Zhuang, Aaron Tyler, Bing Zhou, Emily Wong, David Merberg, Brad Farrell, Chris DeBoever, Julie Bryant, Dorothée Diogo
{"title":"CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.","authors":"Chris Hartl, Jiali Zhuang, Aaron Tyler, Bing Zhou, Emily Wong, David Merberg, Brad Farrell, Chris DeBoever, Julie Bryant, Dorothée Diogo","doi":"10.1186/s13072-024-00545-7","DOIUrl":"10.1186/s13072-024-00545-7","url":null,"abstract":"<p><strong>Background: </strong>Cis-regulatory elements (CREs) play a pivotal role in gene expression regulation, allowing cells to serve diverse functions and respond to external stimuli. Understanding CREs is essential for personalized medicine and disease research, as an increasing number of genetic variants associated with phenotypes and diseases overlap with CREs. However, existing databases often focus on subsets of regulatory elements and present each identified instance of element individually, confounding the effort to obtain a comprehensive view. To address this gap, we have created CREdb, a comprehensive database with over 10 million human regulatory elements across 1,058 cell types and 315 tissues harmonized from different data sources. We curated and aligned the cell types and tissues to standard ontologies for efficient data query.</p><p><strong>Results: </strong>Data from 11 sources were curated and mapped to standard ontological terms. 11,223,434 combined elements are present in the final database, and these were merged into 5,666,240 consensus elements representing the combined ranges of the individual elements informed by their overlap. Each consensus element contains curated metadata including the number of elements supporting it and a hash linking to the source databases. The inferred activity of each consensus element in various cell-type and tissue context is also provided. Examples presented here show the potential utility of CREdb in annotating non-coding genetic variants and informing chromatin accessibility profiling analysis.</p><p><strong>Conclusions: </strong>We developed CREdb, a comprehensive database of CREs, to simplify the analysis of CREs by providing a unified framework for researchers. CREdb compiles consensus ranges for each element by integrating the information from all instances identified across various source databases. This unified database facilitates the functional annotation of non-coding genetic variants and complements chromatin accessibility profiling analysis. CREdb will serve as an important resource in expanding our knowledge of the epigenome and its role in human diseases.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"21"},"PeriodicalIF":4.2,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141628156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso 在没有 Kaiso 的情况下,体内 H19 ICR 的印迹 DNA 甲基化得以建立和维持
IF 3.9 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-06-05 DOI: 10.1186/s13072-024-00544-8
Hitomi Matsuzaki, Minami Kimura, Mizuki Morihashi, Keiji Tanimoto
{"title":"Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso","authors":"Hitomi Matsuzaki, Minami Kimura, Mizuki Morihashi, Keiji Tanimoto","doi":"10.1186/s13072-024-00544-8","DOIUrl":"https://doi.org/10.1186/s13072-024-00544-8","url":null,"abstract":"Paternal allele-specific DNA methylation of the imprinting control region (H19 ICR) controls genomic imprinting at the Igf2/H19 locus. We previously demonstrated that the mouse H19 ICR transgene acquires imprinted DNA methylation in preimplantation mouse embryos. This activity is also present in the endogenous H19 ICR and protects it from genome-wide reprogramming after fertilization. We also identified a 118-bp sequence within the H19 ICR that is responsible for post-fertilization imprinted methylation. Two mutations, one in the five RCTG motifs and the other a 36-bp deletion both in the 118-bp segment, caused complete and partial loss, respectively, of methylation following paternal transmission in each transgenic mouse. Interestingly, these mutations overlap with the binding site for the transcription factor Kaiso, which is reportedly involved in maintaining paternal methylation at the human H19 ICR (IC1) in cultured cells. In this study, we investigated if Kaiso regulates imprinted DNA methylation of the H19 ICR in vivo. Neither Kaiso deletion nor mutation of Kaiso binding sites in the 118-bp region affected DNA methylation of the mouse H19 ICR transgene. The endogenous mouse H19 ICR was methylated in a wild-type manner in Kaiso-null mutant mice. Additionally, the human IC1 transgene acquired imprinted DNA methylation after fertilization in the absence of Kaiso. Our results indicate that Kaiso is not essential for either post-fertilization imprinted DNA methylation of the transgenic H19 ICR in mouse or for methylation imprinting of the endogenous mouse H19 ICR.","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141259000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Native and tagged CENP-A histones are functionally inequivalent. 原生组蛋白和标记的 CENP-A 组蛋白在功能上是不等同的。
IF 4.2 2区 生物学
Epigenetics & Chromatin Pub Date : 2024-06-02 DOI: 10.1186/s13072-024-00543-9
Minh Bui, Songjoon Baek, Reda S Bentahar, Daniël P Melters, Yamini Dalal
{"title":"Native and tagged CENP-A histones are functionally inequivalent.","authors":"Minh Bui, Songjoon Baek, Reda S Bentahar, Daniël P Melters, Yamini Dalal","doi":"10.1186/s13072-024-00543-9","DOIUrl":"10.1186/s13072-024-00543-9","url":null,"abstract":"<p><strong>Background: </strong>Over the past several decades, the use of biochemical and fluorescent tags has elucidated mechanistic and cytological processes that would otherwise be impossible. The challenging nature of certain nuclear proteins includes low abundancy, poor antibody recognition, and transient dynamics. One approach to get around those issues is the addition of a peptide or larger protein tag to the target protein to improve enrichment, purification, and visualization. However, many of these studies were done under the assumption that tagged proteins can fully recapitulate native protein function.</p><p><strong>Results: </strong>We report that when C-terminally TAP-tagged CENP-A histone variant is introduced, it undergoes altered kinetochore protein binding, differs in post-translational modifications (PTMs), utilizes histone chaperones that differ from that of native CENP-A, and can partially displace native CENP-A in human cells. Additionally, these tagged CENP-A-containing nucleosomes have reduced centromeric incorporation at early G1 phase and poorly associates with linker histone H1.5 compared to native CENP-A nucleosomes.</p><p><strong>Conclusions: </strong>These data suggest expressing tagged versions of histone variant CENP-A may result in unexpected utilization of non-native pathways, thereby altering the biological function of the histone variant.</p>","PeriodicalId":49253,"journal":{"name":"Epigenetics & Chromatin","volume":"17 1","pages":"19"},"PeriodicalIF":4.2,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11145777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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