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TP63–TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancer Epigenet. Chromatin (IF 3.9) Pub Date : 2024-03-14 R. Sultanov, A. Mulyukina, O. Zubkova, A. Fedoseeva, A. Bogomazova, K. Klimina, A. Larin, T. Zatsepin, T. Prikazchikova, M. Lukina, M. Bogomiakova, E. Sharova, E. Generozov, M. Lagarkova, G. Arapidi
Prostate adenocarcinoma (PRAD) is the second leading cause of cancer-related deaths in men. High variability in DNA methylation and a high rate of large genomic rearrangements are often observed in PRAD. To investigate the reasons for such high variance, we integrated DNA methylation, RNA-seq, and copy number alterations datasets from The Cancer Genome Atlas (TCGA), focusing on PRAD, and employed weighted
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Intrafamily heterooligomerization as an emerging mechanism of methyltransferase regulation Epigenet. Chromatin (IF 3.9) Pub Date : 2024-03-01 Haley V. Hobble, Christine E. Schaner Tooley
Protein and nucleic acid methylation are important biochemical modifications. In addition to their well-established roles in gene regulation, they also regulate cell signaling, metabolism, and translation. Despite this high biological relevance, little is known about the general regulation of methyltransferase function. Methyltransferases are divided into superfamilies based on structural similarities
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Research progress of SWI/SNF complex in breast cancer Epigenet. Chromatin (IF 3.9) Pub Date : 2024-02-17 Kexuan Li, Baocai Wang, Haolin Hu
In the past decade, numerous epigenetic mechanisms have been discovered to be associated with cancer. The mammalian SWI/SNF complex is an ATP-dependent chromatin remodeling complex whose mutations are associated with various malignancies including breast cancer. As the SWI/SNF complex has become one of the most commonly mutated complexes in cancer, targeting epigenetic mutations acquired during breast
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A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin Epigenet. Chromatin (IF 3.9) Pub Date : 2024-02-10 Janith A. Seneviratne, William W. H. Ho, Eleanor Glancy, Melanie A. Eckersley-Maslin
Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome occurs predominantly at promoters that are poised for future transcriptional upregulation or terminal silencing. We know little of the dynamics, resolution, and regulation of this chromatin state outside
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Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells Epigenet. Chromatin (IF 3.9) Pub Date : 2024-01-23 Alexander Calderon, Tamara Mestvirishvili, Francesco Boccalatte, Kelly V. Ruggles, Gregory David
Blood homeostasis requires the daily production of millions of terminally differentiated effector cells that all originate from hematopoietic stem cells (HSCs). HSCs are rare and exhibit unique self-renewal and multipotent properties, which depend on their ability to maintain quiescence through ill-defined processes. Defective control of cell cycle progression can eventually lead to bone marrow failure
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Role of sex in immune response and epigenetic mechanisms Epigenet. Chromatin (IF 3.9) Pub Date : 2024-01-22 Sombodhi Bhattacharya, Debasmita Sadhukhan, Radha Saraswathy
The functioning of the human immune system is highly dependent on the sex of the individual, which comes by virtue of sex chromosomes and hormonal differences. Epigenetic mechanisms such as X chromosome inactivation, mosaicism, skewing, and dimorphism in X chromosome genes and Y chromosome regulatory genes create a sex-based variance in the immune response between males and females. This leads to differential
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Folate deficiency reduced aberrant level of DOT1L-mediated histone H3K79 methylation causes disruptive SHH gene expression involved in neural tube defects Epigenet. Chromatin (IF 3.9) Pub Date : 2023-12-14 Xue Li, Pei Pei, Jinying Shen, Juan Yu, Fang Wang, Lei Wang, Changyun Liu, Shan Wang
Neural tube defects (NTDs) are one of the most severe congenital abnormalities characterized by failures of the neural tube to close during early embryogenesis. Maternal folate deficiency could impact the occurrence of NTDs, however, the mechanisms involved in the cause of NTDs are poorly defined. Here, we report that histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression
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O-GlcNAcylation: the sweet side of epigenetics Epigenet. Chromatin (IF 3.9) Pub Date : 2023-12-14 Thomas Dupas, Benjamin Lauzier, Serge McGraw
Histones display a wide variety of post-translational modifications, including acetylation, methylation, and phosphorylation. These epigenetic modifications can influence chromatin structure and function without altering the DNA sequence. Histones can also undergo post-translational O-GlcNAcylation, a rather understudied modification that plays critical roles in almost all biological processes and
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Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease Epigenet. Chromatin (IF 3.9) Pub Date : 2023-12-11 Gridina Maria, Popov Andrey, Shadskiy Artem, Torgunakov Nikita, Kechin Andrey, Khrapov Evgeny, Ryzhkova Oxana, Filipenko Maxim, Fishman Veniamin
This study presents a novel approach for mapping global chromatin interactions using S1 nuclease, a sequence-agnostic enzyme. We develop and outline a protocol that leverages S1 nuclease's ability to effectively introduce breaks into both open and closed chromatin regions, allowing for comprehensive profiling of chromatin properties. Our S1 Hi–C method enables the preparation of high-quality Hi–C libraries
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The functions of SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) in biological process and disease Epigenet. Chromatin (IF 3.9) Pub Date : 2023-12-07 Hanshen Luo, Xingliang Wu, Xue-Hai Zhu, Xin Yi, Dunfeng Du, Ding-Sheng Jiang
Histone methyltransferase SETDB1 (SET domain bifurcated histone lysine methyltransferase 1, also known as ESET or KMT1E) is known to be involved in the deposition of the di- and tri-methyl marks on H3K9 (H3K9me2 and H3K9me3), which are associated with transcription repression. SETDB1 exerts an essential role in the silencing of endogenous retroviruses (ERVs) in embryonic stem cells (mESCs) by tri-methylating
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Chromatin balances cell redox and energy homeostasis Epigenet. Chromatin (IF 3.9) Pub Date : 2023-11-28 Tamaki Suganuma, Jerry L. Workman
Chromatin plays a central role in the conversion of energy in cells: alteration of chromatin structure to make DNA accessible consumes energy, and compaction of chromatin preserves energy. Alteration of chromatin structure uses energy sources derived from carbon metabolism such as ATP and acetyl-CoA; conversely, chromatin compaction and epigenetic modification feedback to metabolism and energy homeostasis
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Differential usage of DNA modifications in neurons, astrocytes, and microglia Epigenet. Chromatin (IF 3.9) Pub Date : 2023-11-13 Kyla B. Tooley, Ana J. Chucair-Elliott, Sarah R. Ocañas, Adeline H. Machalinski, Kevin D. Pham, Walker Hoolehan, Adam M. Kulpa, David R. Stanford, Willard M. Freeman
Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used
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Estimating genome-wide DNA methylation heterogeneity with methylation patterns Epigenet. Chromatin (IF 3.9) Pub Date : 2023-11-09 Pei-Yu Lin, Ya-Ting Chang, Yu-Chun Huang, Pao-Yang Chen
In a heterogeneous population of cells, individual cells can behave differently and respond variably to the environment. This cellular diversity can be assessed by measuring DNA methylation patterns. The loci with variable methylation patterns are informative of cellular heterogeneity and may serve as biomarkers of diseases and developmental progression. Cell-to-cell methylation heterogeneity can be
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Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents Epigenet. Chromatin (IF 3.9) Pub Date : 2023-11-04 Lirik Behluli, Alyssa M. Fontanilla, Laura Andessner-Angleitner, Nikolas Tolar, Julia M. Molina, Lenka Gahurova
During early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells, oocyte and embryo. The first wave of de novo DNA methylation establishment occurs in oocytes. Its molecular mechanisms have been studied in mouse, a classical mammalian model. Current model describes DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3L as two essential
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EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter Epigenet. Chromatin (IF 3.9) Pub Date : 2023-10-26 Can Bora Yildiz, Tathagata Kundu, Julia Gehrmann, Jannis Koesling, Amin Ravaei, Philip Wolff, Florian Kraft, Tiago Maié, Mira Jakovcevski, Daniel Pensold, Olav Zimmermann, Giulia Rossetti, Ivan G. Costa, Geraldine Zimmer-Bensch
Cell–cell communication is mediated by membrane receptors and their ligands, such as the Eph/ephrin system, orchestrating cell migration during development and in diverse cancer types. Epigenetic mechanisms are key for integrating external “signals”, e.g., from neighboring cells, into the transcriptome in health and disease. Previously, we reported ephrinA5 to trigger transcriptional changes of lncRNAs
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Development of super-specific epigenome editing by targeted allele-specific DNA methylation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-10-21 Nivethika Rajaram, Alexandra G. Kouroukli, Susanne Bens, Pavel Bashtrykov, Albert Jeltsch
Epigenome editing refers to the targeted reprogramming of genomic loci using an EpiEditor which may consist of an sgRNA/dCas9 complex that recruits DNMT3A/3L to the target locus. Methylation of the locus can lead to a modulation of gene expression. Allele-specific DNA methylation (ASM) refers to the targeted methylation delivery only to one allele of a locus. In the context of diseases caused by a
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Analyses of POL30 (PCNA) reveal positional effects in transient repression or bi-modal active/silent state at the sub-telomeres of S. cerevisiae Epigenet. Chromatin (IF 3.9) Pub Date : 2023-10-19 Safia Mahabub Sauty, Krassimir Yankulov
Classical studies on position effect variegation in Drosophila have demonstrated the existence of bi-modal Active/Silent state of the genes juxtaposed to heterochromatin. Later studies with irreversible methods for the detection of gene repression have revealed a similar phenomenon at the telomeres of Saccharomyces cerevisiae and other species. In this study, we used dual reporter constructs and a
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Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-10-16 Kevin C. L. Cheng, Jennifer M. Frost, Francisco J. Sánchez-Luque, Marta García-Canãdas, Darren Taylor, Wan R. Yang, Branavy Irayanar, Swetha Sampath, Hemalvi Patani, Karl Agger, Kristian Helin, Gabriella Ficz, Kathleen H. Burns, Adam Ewing, José L. García-Pérez, Miguel R. Branco
Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the
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Knockout tales: the versatile roles of histone H3.3 in development and disease Epigenet. Chromatin (IF 3.9) Pub Date : 2023-10-10 Rachel H. Klein, Paul S. Knoepfler
Histone variant H3.3 plays novel roles in development as compared to canonical H3 proteins and is the most commonly mutated histone protein of any kind in human disease. Here we discuss how gene targeting studies of the two H3.3-coding genes H3f3a and H3f3b have provided important insights into H3.3 functions including in gametes as well as brain and lung development. Knockouts have also provided insights
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The application of epiphenotyping approaches to DNA methylation array studies of the human placenta Epigenet. Chromatin (IF 3.9) Pub Date : 2023-10-04 A. Khan, A. M. Inkster, M. S. Peñaherrera, S. King, S. Kildea, T. F. Oberlander, D. M. Olson, C. Vaillancourt, U. Brain, E. O. Beraldo, A. G. Beristain, V. L. Clifton, G. F. Del Gobbo, W. L. Lam, G. A. S. Metz, J. W. Y. Ng, E. M. Price, J. M. Schuetz, V. Yuan, É. Portales-Casamar, W. P. Robinson
Genome-wide DNA methylation (DNAme) profiling of the placenta with Illumina Infinium Methylation bead arrays is often used to explore the connections between in utero exposures, placental pathology, and fetal development. However, many technical and biological factors can lead to signals of DNAme variation between samples and between cohorts, and understanding and accounting for these factors is essential
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Nucleophosmin 1 cooperates with the methyltransferase DOT1L to preserve peri-nucleolar heterochromatin organization by regulating H3K27me3 levels and DNA repeats expression Epigenet. Chromatin (IF 3.9) Pub Date : 2023-09-28 Annalisa Izzo, Ipek Akol, Alejandro Villarreal, Shannon Lebel, Marta Garcia-Miralles, Arquimedes Cheffer, Patrick Bovio, Stefanie Heidrich, Tanja Vogel
NPM1 is a phosphoprotein highly abundant in the nucleolus. However, additional nuclear functions have been attributed to NPM1, probably through interaction with other nuclear factors. DOT1L is one interaction partner of NPM1 that catalyzes methylation of histone H3 at lysine 79 (H3K79). DOT1L, playing functional roles in several biological processes, is known for its capability to organize and regulate
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Histone crotonylation of peripheral blood mononuclear cells is a potential biomarker for diagnosis of colorectal cancer Epigenet. Chromatin (IF 3.9) Pub Date : 2023-09-26 Jia-Yi Hou, Ning Li, Jie Wang, Li-Juan Gao, Jia-Song Chang, Ji-Min Cao
Blood-based tests have public appeal in screening cancers due to their minimally invasive nature, ability to integrate with other routine blood tests, and high compliance. This study aimed to investigate whether certain epigenetic modulation of peripheral blood mononuclear cells (PBMCs) could be a biomarker of colorectal cancer (CRC). Western blotting of histones in the PBMCs from 40 colorectal cancer
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Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data Epigenet. Chromatin (IF 3.9) Pub Date : 2023-09-25 Zhaonan Zou, Yuka Yoshimura, Yoshihiro Yamanishi, Shinya Oki
Despite well-documented effects on human health, the action modes of environmental pollutants are incompletely understood. Although transcriptome-based approaches are widely used to predict associations between chemicals and disorders, the molecular cues regulating pollutant-derived gene expression changes remain unclear. Therefore, we developed a data-mining approach, termed “DAR-ChIPEA,” to identify
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Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer Epigenet. Chromatin (IF 3.9) Pub Date : 2023-09-23 Jun Wang, Yanqin Niu, Ming Yang, Lirong Shu, Hongxian Wang, Xiaoqian Wu, Yaqin He, Peng Chen, Guocheng Zhong, Zhixiong Tang, Shasha Zhang, Qianwen Guo, Yun Wang, Li Yu, Deming Gou
Breast cancer, the most common malignancy in women worldwide, has been proven to have both altered plasma cell-free DNA (cfDNA) methylation and fragmentation profiles. Nevertheless, simultaneously detecting both of them for breast cancer diagnosis has never been reported. Moreover, although fragmentation pattern of cfDNA is determined by nuclease digestion of chromatin, structure of which may be affected
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Co-effects of m6A and chromatin accessibility dynamics in the regulation of cardiomyocyte differentiation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-08-11 Xue-Hong Liu, Zhun Liu, Ze-Hui Ren, Hong-Xuan Chen, Ying Zhang, Zhang Zhang, Nan Cao, Guan-Zheng Luo
Cardiomyocyte growth and differentiation rely on precise gene expression regulation, with epigenetic modifications emerging as key players in this intricate process. Among these modifications, N6-methyladenosine (m6A) stands out as one of the most prevalent modifications on mRNA, exerting influence over mRNA metabolism and gene expression. However, the specific function of m6A in cardiomyocyte differentiation
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Promoter hypermethylation of neural-related genes is compatible with stemness in solid cancers Epigenet. Chromatin (IF 3.9) Pub Date : 2023-08-03 Musa Idris, Louis Coussement, Maria M. Alves, Tim De Meyer, Veerle Melotte
DNA hypermethylation is an epigenetic feature that modulates gene expression, and its deregulation is observed in cancer. Previously, we identified a neural-related DNA hypermethylation fingerprint in colon cancer, where most of the top hypermethylated and downregulated genes have known functions in the nervous system. To evaluate the presence of this signature and its relevance to carcinogenesis in
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Alterations in the hepatocyte epigenetic landscape in steatosis Epigenet. Chromatin (IF 3.9) Pub Date : 2023-07-06 Ranjan Kumar Maji, Beate Czepukojc, Michael Scherer, Sascha Tierling, Cristina Cadenas, Kathrin Gianmoena, Nina Gasparoni, Karl Nordström, Gilles Gasparoni, Stephan Laggai, Xinyi Yang, Anupam Sinha, Peter Ebert, Maren Falk-Paulsen, Sarah Kinkley, Jessica Hoppstädter, Ho-Ryun Chung, Philip Rosenstiel, Jan G. Hengstler, Jörn Walter, Marcel H. Schulz, Sonja M. Kessler, Alexandra K. Kiemer
Fatty liver disease or the accumulation of fat in the liver, has been reported to affect the global population. This comes with an increased risk for the development of fibrosis, cirrhosis, and hepatocellular carcinoma. Yet, little is known about the effects of a diet containing high fat and alcohol towards epigenetic aging, with respect to changes in transcriptional and epigenomic profiles. In this
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Etiology of super-enhancer reprogramming and activation in cancer Epigenet. Chromatin (IF 3.9) Pub Date : 2023-07-06 Royce W. Zhou, Ramon E. Parsons
Super-enhancers are large, densely concentrated swaths of enhancers that regulate genes critical for cell identity. Tumorigenesis is accompanied by changes in the super-enhancer landscape. These aberrant super-enhancers commonly form to activate proto-oncogenes, or other genes upon which cancer cells depend, that initiate tumorigenesis, promote tumor proliferation, and increase the fitness of cancer
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The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus Epigenet. Chromatin (IF 3.9) Pub Date : 2023-07-01 Christopher B. Cunningham, Emily A. Shelby, Elizabeth C. McKinney, Robert J. Schmitz, Allen J. Moore, Patricia J. Moore
The function of DNA methyltransferase genes of insects is a puzzle, because an association between gene expression and methylation is not universal for insects. If the genes normally involved in cytosine methylation are not influencing gene expression, what might be their role? We previously demonstrated that gametogenesis of Oncopeltus fasciatus is interrupted at meiosis following knockdown of DNA
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Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics Epigenet. Chromatin (IF 3.9) Pub Date : 2023-06-23 Jente van Staalduinen, Thomas van Staveren, Frank Grosveld, Kerstin S. Wendt
Our understanding of the organization of the chromatin fiber within the cell nucleus has made great progress in the last few years. High-resolution techniques based on next-generation sequencing as well as optical imaging that can investigate chromatin conformations down to the single cell level have revealed that chromatin structure is highly heterogeneous at the level of the individual allele. While
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PARP-dependent and NAT10-independent acetylation of N4-cytidine in RNA appears in UV-damaged chromatin Epigenet. Chromatin (IF 3.9) Pub Date : 2023-06-15 Alena Svobodová Kovaříková, Lenka Stixová, Aleš Kovařík, Eva Bártová
RNA modifications have been known for many years, but their function has not been fully elucidated yet. For instance, the regulatory role of acetylation on N4-cytidine (ac4C) in RNA can be explored not only in terms of RNA stability and mRNA translation but also in DNA repair. Here, we observe a high level of ac4C RNA at DNA lesions in interphase cells and irradiated cells in telophase. Ac4C RNA appears
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Histone modification analysis reveals common regulators of gene expression in liver and blood stage merozoites of Plasmodium parasites Epigenet. Chromatin (IF 3.9) Pub Date : 2023-06-15 Ashley B. Reers, Rodriel Bautista, James McLellan, Beatriz Morales, Rolando Garza, Sebastiaan Bol, Kirsten K. Hanson, Evelien M. Bunnik
Gene expression in malaria parasites is subject to various layers of regulation, including histone post-translational modifications (PTMs). Gene regulatory mechanisms have been extensively studied during the main developmental stages of Plasmodium parasites inside erythrocytes, from the ring stage following invasion to the schizont stage leading up to egress. However, gene regulation in merozoites
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Assignment of the somatic A/B compartments to chromatin domains in giant transcriptionally active lampbrush chromosomes Epigenet. Chromatin (IF 3.9) Pub Date : 2023-06-15 Alla Krasikova, Tatiana Kulikova, Juan Sebastian Rodriguez Ramos, Antonina Maslova
The three-dimensional configuration of the eukaryotic genome is an emerging area of research. Chromosome conformation capture outlined genome segregation into large scale A and B compartments corresponding mainly to transcriptionally active and repressive chromatin. It remains unknown how the compartmentalization of the genome changes in growing oocytes of animals with hypertranscriptional type of
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Var∣Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data Epigenet. Chromatin (IF 3.9) Pub Date : 2023-06-14 Mohammad Salma, Elina Alaterre, Jérôme Moreaux, Eric Soler
High-throughput sequencing (HTS) offers unprecedented opportunities for the discovery of causative gene variants in multiple human disorders including cancers, and has revolutionized clinical diagnostics. However, despite more than a decade of use of HTS-based assays, extracting relevant functional information from whole-exome sequencing (WES) data remains challenging, especially for non-specialists
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Correction: Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi‑C, Micro‑C, and promoter capture Micro‑C Epigenet. Chromatin (IF 3.9) Pub Date : 2023-06-07 Beoung Hun Lee, Zexun Wu, Suhn K. Rhie
Correction: Epigenetics & Chromatin (2022) 15:41 https://doi.org/10.1186/s13072-022-00473-4 The original version of this article [1], unfortunately contained a mistake. The presentation of Fig. 5D has been published incorrectly without Y-axis label. The correct Fig. 5 is provided. Fig. 5 Promoter capture Micro-C data analysis. A An overview of promoter capture Micro-C experimental procedure, including
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Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin Epigenet. Chromatin (IF 3.9) Pub Date : 2023-05-30 Igor S. Tolokh, Nicholas Allen Kinney, Igor V. Sharakhov, Alexey V. Onufriev
Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult. We have developed a coarse-grained dynamical model of
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CpG DNA methylation changes during epididymal sperm maturation in bulls Epigenet. Chromatin (IF 3.9) Pub Date : 2023-05-30 Emanuele Capra, F. Turri, B. Lazzari, S. Biffani, A. Lange Consiglio, P. Ajmone Marsan, A. Stella, F. Pizzi
During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and
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Premature ovarian insufficiency is associated with global alterations in the regulatory landscape and gene expression in balanced X-autosome translocations Epigenet. Chromatin (IF 3.9) Pub Date : 2023-05-19 Adriana Di-Battista, Bianca Pereira Favilla, Malú Zamariolli, Natália Nunes, Alexandre Defelicibus, Lucia Armelin-Correa, Israel Tojal da Silva, Alexandre Reymond, Mariana Moyses-Oliveira, Maria Isabel Melaragno
Patients with balanced X-autosome translocations and premature ovarian insufficiency (POI) constitute an interesting paradigm to study the effect of chromosome repositioning. Their breakpoints are clustered within cytobands Xq13–Xq21, 80% of them in Xq21, and usually, no gene disruption can be associated with POI phenotype. As deletions within Xq21 do not cause POI, and since different breakpoints
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The pattern of histone H3 epigenetic posttranslational modifications is regulated by the VRK1 chromatin kinase Epigenet. Chromatin (IF 3.9) Pub Date : 2023-05-13 Eva Monte-Serrano, Patricia Morejón-García, Ignacio Campillo-Marcos, Aurora Campos-Díaz, Elena Navarro-Carrasco, Pedro A. Lazo
Dynamic chromatin remodeling is associated with changes in the epigenetic pattern of histone acetylations and methylations required for processes based on dynamic chromatin remodeling and implicated in different nuclear functions. These histone epigenetic modifications need to be coordinated, a role that may be mediated by chromatin kinases such as VRK1, which phosphorylates histones H3 and H2A. The
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Loss of CpG island immunity to DNA methylation induced by mutation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-05-11 Bernhard Horsthemke, Adrian Bird
The inheritance of acquired traits in mammals is a highly controversial topic in biology. Recently, Takahashi et al. (Cell 186:715–731, 2023) have reported that insertion of CpG-free DNA into a CpG island (CGI) can induce DNA methylation of the CGI and that this aberrant methylation pattern can be transmitted across generations, even after removal of the foreign DNA. These results were interpreted
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The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes Epigenet. Chromatin (IF 3.9) Pub Date : 2023-05-10 Benjamin H. Weekley, Judd C. Rice
Proteolysis of the histone H3 N-terminal tail (H3NT) is an evolutionarily conserved epigenomic feature of nearly all eukaryotes, generating a cleaved H3 product that is retained in ~ 5–10% of the genome. Although H3NT proteolysis within chromatin was first reported over 60 years ago, the genomic sites targeted for H3NT proteolysis and the impact of this histone modification on chromatin structure and
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Caf1 regulates the histone methyltransferase activity of Ash1 by sensing unmodified histone H3 Epigenet. Chromatin (IF 3.9) Pub Date : 2023-04-29 Eojin Yoon, Ji-Joon Song
Histone modifications are one of the many key mechanisms that regulate gene expression. Ash1 is a histone H3K36 methyltransferase and is involved in gene activation. Ash1 forms a large complex with Mrg15 and Caf1/p55/Nurf55/RbAp48 (AMC complex). The Ash1 subunit alone exhibits very low activity due to the autoinhibition, and the binding of Mrg15 releases the autoinhibition. Caf1 is a scaffolding protein
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An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies Epigenet. Chromatin (IF 3.9) Pub Date : 2023-04-28 Betelehem Solomon Bera, Taylor V. Thompson, Eric Sosa, Hiroko Nomaru, David Reynolds, Robert A. Dubin, Shahina B. Maqbool, Deyou Zheng, Bernice E. Morrow, John M. Greally, Masako Suzuki
Single-cell technologies to analyze transcription and chromatin structure have been widely used in many research areas to reveal the functions and molecular properties of cells at single-cell resolution. Sample multiplexing techniques are valuable when performing single-cell analysis, reducing technical variation and permitting cost efficiencies. Several commercially available methods have been used
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Partial erosion on under-methylated regions and chromatin reprogramming contribute to oncogene activation in IDH mutant gliomas Epigenet. Chromatin (IF 3.9) Pub Date : 2023-04-28 Xinyu Wang, Lijun Dai, Yang Liu, Chenghao Li, Dandan Fan, Yue Zhou, Pengcheng Li, Qingran Kong, Jianzhong Su
IDH1/2 hotspot mutations are well known to drive oncogenic mutations in gliomas and are well-defined in the WHO 2021 classification of central nervous system tumors. Specifically, IDH mutations lead to aberrant hypermethylation of under-methylated regions (UMRs) in normal tissues through the disruption of TET enzymes. However, the chromatin reprogramming and transcriptional changes induced by IDH-related
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Epigenetic modifier alpha-ketoglutarate modulates aberrant gene body methylation and hydroxymethylation marks in diabetic heart Epigenet. Chromatin (IF 3.9) Pub Date : 2023-04-27 Rohini Dhat, Dattatray Mongad, Sivarupa Raji, Silpa Arkat, Nitish R. Mahapatra, Nishant Singhal, Sandhya L. Sitasawad
Diabetic cardiomyopathy (DCM) is a leading cause of death in diabetic patients. Hyperglycemic myocardial microenvironment significantly alters chromatin architecture and the transcriptome, resulting in aberrant activation of signaling pathways in a diabetic heart. Epigenetic marks play vital roles in transcriptional reprogramming during the development of DCM. The current study is aimed to profile
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Ovulatory signal-triggered chromatin remodeling in ovarian granulosa cells by HDAC2 phosphorylation activation-mediated histone deacetylation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-04-19 Jiamin Jin, Peipei Ren, Xiang Li, Yinyi Zhang, Weijie Yang, Yerong Ma, Mengru Lai, Chao Yu, Songying Zhang, Yin-Li Zhang
Epigenetic reprogramming is involved in luteinizing hormone (LH)-induced ovulation; however, the underlying mechanisms are largely unknown. We here observed a rapid histone deacetylation process between two waves of active transcription mediated by the follicle-stimulating hormone (FSH) and the LH congener human chorionic gonadotropin (hCG), respectively. Analysis of the genome-wide H3K27Ac distribution
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Multilevel interrogation of H3.3 reveals a primordial role in transcription regulation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-04-07 Syed Nabeel-Shah, Jyoti Garg, Kanwal Ashraf, Renu Jeyapala, Hyunmin Lee, Alexandra Petrova, James D. Burns, Shuye Pu, Zhaolei Zhang, Jack F. Greenblatt, Ronald E. Pearlman, Jean-Philippe Lambert, Jeffrey Fillingham
Eukaryotic cells can rapidly adjust their transcriptional profile in response to molecular needs. Such dynamic regulation is, in part, achieved through epigenetic modifications and selective incorporation of histone variants into chromatin. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. Although H3.3 has been well studied in metazoans, information
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PCGF6/MAX/KDM5D facilitates MAZ/CDK4 axis expression and pRCC progression by hypomethylation of the DNA promoter Epigenet. Chromatin (IF 3.9) Pub Date : 2023-03-09 Meng Zhu, Ruo-Nan Zhang, Hong Zhang, Chang-bao Qu, Xiao-chong Zhang, Li-Xin Ren, Zhan Yang, Jun-Fei Gu
Polycomb group RING finger protein 6 (PCGF6) plays an important role as a regulator of transcription in a variety of cellular processes, including tumorigenesis. However, the function and expression of PCGF6 in papillary RCC (pRCC) remain unclear. In the present study, we found that PCGF6 expression was significantly elevated in pRCC tissues, and high expression of PCGF6 was associated with poor survival
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Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5 Epigenet. Chromatin (IF 3.9) Pub Date : 2023-02-18 Matanel Yheskel, Simone Sidoli, Julie Secombe
KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription
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The transgenic IG-DMR sequence of the mouse Dlk1-Dio3 domain acquired imprinted DNA methylation during the post-fertilization period Epigenet. Chromatin (IF 3.9) Pub Date : 2023-02-17 Hitomi Matsuzaki, Shokichi Sugihara, Keiji Tanimoto
Allele-specific methylation of the imprinting control region (ICR) is the molecular basis for the genomic imprinting phenomenon that is unique to placental mammals. We previously showed that the ICR at the mouse H19 gene locus (H19 ICR) was unexpectedly established after fertilization and not during spermatogenesis in transgenic mice (TgM), and that the same activity was essential for the maintenance
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The SAGA histone acetyltransferase module targets SMC5/6 to specific genes Epigenet. Chromatin (IF 3.9) Pub Date : 2023-02-16 L. Mahrik, B. Stefanovie, A. Maresova, J. Princova, P. Kolesar, E. Lelkes, C. Faux, D. Helmlinger, M. Prevorovsky, J. J. Palecek
Structural Maintenance of Chromosomes (SMC) complexes are molecular machines driving chromatin organization at higher levels. In eukaryotes, three SMC complexes (cohesin, condensin and SMC5/6) play key roles in cohesion, condensation, replication, transcription and DNA repair. Their physical binding to DNA requires accessible chromatin. We performed a genetic screen in fission yeast to identify novel
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The impact of spatial correlation on methylation entropy with application to mouse brain methylome Epigenet. Chromatin (IF 3.9) Pub Date : 2023-02-04 Xiaowei Wu, Joung Min Choi
With the advance of bisulfite sequencing technologies, massive amount of methylation data have been generated, which provide unprecedented opportunities to study the epigenetic mechanism and its relationship to other biological processes. A commonly seen feature of the methylation data is the correlation between nearby CpG sites. Although such a spatial correlation was utilized in several epigenetic
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Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation Epigenet. Chromatin (IF 3.9) Pub Date : 2023-01-25 William Chang, Yilin Zhao, Danielle Rayêe, Qing Xie, Masako Suzuki, Deyou Zheng, Ales Cvekl
Cellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels. DNA methylation represents a universal mechanism to control chromatin organization and its accessibility. Cytosine methylation of CpG dinucleotides regulates binding of methylation-sensitive DNA-binding transcription factors within regulatory regions of transcription, including promoters
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Phthalates impact on the epigenetic factors contributed specifically by the father at fertilization Epigenet. Chromatin (IF 3.9) Pub Date : 2023-01-24 G. M. Swanson, F. L. Nassan, J. B. Ford, R. Hauser, J. R. Pilsner, S. A. Krawetz
Preconception exposure to phthalates such as the anti-androgenic dibutyl-phthalate (DBP) impacts both male and female reproduction, yet how this occurs largely remains unknown. Previously we defined a series of RNAs expressly provided by sperm at fertilization and separately, and in parallel, those that responded to high DBP exposure. Utilizing both populations of RNAs, we now begin to unravel the
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ATAC-seq and RNA-seq analysis unravel the mechanism of sex differentiation and infertility in sex reversal chicken Epigenet. Chromatin (IF 3.9) Pub Date : 2023-01-09 Zhang, Xiuan, Li, Jianbo, Wang, Xiqiong, Jie, Yuchen, Sun, Congjiao, Zheng, Jiangxia, Li, Junying, Yang, Ning, Chen, Sirui
Sex determination and differentiation are complex and delicate processes. In female chickens, the process of sex differentiation is sensitive and prone to be affected by the administration of aromatase inhibitors, which result in chicken sex reversal and infertility. However, the molecular mechanisms underlying sex differentiation and infertility in chicken sex reversal remain unclear. Therefore, we
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Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data Epigenet. Chromatin (IF 3.9) Pub Date : 2023-01-07 Inkster, Amy M., Wong, Martin T., Matthews, Allison M., Brown, Carolyn J., Robinson, Wendy P.
Many human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into analyses vital. Unfortunately, X and Y chromosome data are frequently excluded from large-scale analyses of the human genome and epigenome due to analytical complexity associated with sex chromosome dosage differences between XX and XY individuals, and the impact
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Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C Epigenet. Chromatin (IF 3.9) Pub Date : 2022-12-21 Lee, Beoung Hun, Wu, Zexun, Rhie, Suhn K.
Regulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin interactions of regulatory elements, 3C-derived methods such as Hi-C and Micro-C are developed. Here, we generated and analyzed Hi-C, Micro-C, and promoter capture Micro-C datasets with different sequencing depths to study chromatin interactions of regulatory elements
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Efficient generation of epigenetic disease model mice by epigenome editing using the piggyBac transposon system Epigenet. Chromatin (IF 3.9) Pub Date : 2022-12-16 Horii, Takuro, Morita, Sumiyo, Kimura, Mika, Hatada, Izuho
Epigenome-edited animal models enable direct demonstration of disease causing epigenetic mutations. Transgenic (TG) mice stably expressing epigenome-editing factors exhibit dramatic and stable changes in target epigenome modifications. Successful germline transmission of a transgene from founder mice to offspring will yield a sufficient number of epigenome-edited mice for phenotypic analysis; however
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Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain Epigenet. Chromatin (IF 3.9) Pub Date : 2022-12-03 Farley, Sean J., Grishok, Alla, Zeldich, Ella
Intellectual disability is a well-known hallmark of Down Syndrome (DS) that results from the triplication of the critical region of human chromosome 21 (HSA21). Major studies were conducted in recent years to gain an understanding about the contribution of individual triplicated genes to DS-related brain pathology. Global transcriptomic alterations and widespread changes in the establishment of neural
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Manipulating chromatin architecture in C. elegans Epigenet. Chromatin (IF 3.9) Pub Date : 2022-11-29 Carter, John L., Kempton, Colton E., Hales, Emily D. S., Johnson, Steven M.
Nucleosome-mediated chromatin compaction has a direct effect on the accessibility of trans-acting activators and repressors to DNA targets and serves as a primary regulatory agent of genetic expression. Understanding the nature and dynamics of chromatin is fundamental to elucidating the mechanisms and factors that epigenetically regulate gene expression. Previous work has shown that there are three