One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics
Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches ... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - December 11, 2021 Category: Genetics & Stem Cells Authors: Udayakumar S. Vishnu, Pierre-Olivier Est ève, Hang Gyeong Chin and Sriharsa Pradhan Tags: Methodology Source Type: research
Risk-focused differences in molecular processes implicated in SARS-CoV-2 infection: corollaries in DNA methylation and gene expression
Understanding the molecular basis of susceptibility factors to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global health imperative. It is well-established that males are mo... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - December 11, 2021 Category: Genetics & Stem Cells Authors: Chaini Konwar, Rebecca Asiimwe, Amy M. Inkster, Sarah M. Merrill, Gian L. Negri, Maria J. Aristizabal, Christopher F. Rider, Julie L. MacIsaac, Christopher Carlsten and Michael S. Kobor Tags: Research Source Type: research
Ethionine-mediated reduction of S-adenosylmethionine is responsible for the neural tube defects in the developing mouse embryo-mediated m6A modification and is involved in neural tube defects via modulating Wnt/ β-catenin signaling pathway
Neural tube defects (NTDs) remain one of the most life-threatening birth defects affecting infants. Most patients with NTDs eventually develop lifelong disability, which cause significant morbidity and mortali... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - December 4, 2021 Category: Genetics & Stem Cells Authors: Li Zhang, Rui Cao, Dandan Li, Yuqing Sun, Juan Zhang, Xiuwei Wang, Ajab Khan, Zhizhen Liu, Bo Niu, Jun Xu and Jun Xie Tags: Research Source Type: research
Revealing RCOR2 as a regulatory component of nuclear speckles
Nuclear processes such as transcription and RNA maturation can be impacted by subnuclear compartmentalization in condensates and nuclear bodies. Here, we characterize the nature of nuclear granules formed by R... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - November 24, 2021 Category: Genetics & Stem Cells Authors: Carlos Rivera, Daniel Verbel-Vergara, Duxan Arancibia, Anna Lappala, Marcela Gonz ález, Fabián Guzmán, Gianluca Merello, Jeannie T. Lee and María Estela Andrés Tags: Research Source Type: research
The solid and liquid states of chromatin
The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chr... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - October 30, 2021 Category: Genetics & Stem Cells Authors: Jeffrey C. Hansen, Kazuhiro Maeshima and Michael J. Hendzel Tags: Review Source Type: research
The role of MORC3 in silencing transposable elements in mouse embryonic stem cells
Microrchidia proteins (MORCs) are involved in epigenetic gene silencing in a variety of eukaryotic organisms. Deletion of MORCs result in several developmental abnormalities and their dysregulation has been im... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - October 27, 2021 Category: Genetics & Stem Cells Authors: Varsha P. Desai, Jihed Chouaref, Haoyu Wu, William A. Pastor, Ryan L. Kan, Harald M. Oey, Zheng Li, Jamie Ho, Kelly K. D. Vonk, David San Leon Granado, Michael A. Christopher, Amander T. Clark, Steven E. Jacobsen and Lucia Daxinger Tags: Research Source Type: research
The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor
5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - October 26, 2021 Category: Genetics & Stem Cells Authors: Nelia Luviano, Marie Lopez, Fleur Gawehns, Cristian Chaparro, Paola B. Arimondo, Slavica Ivanovic, Patrice David, Koen Verhoeven, C éline Cosseau and Christoph Grunau Tags: Research Source Type: research
Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse
Trimethylation of histone H3 on lysine 9 (H3K9me3) at satellite DNA sequences has been primarily studied at (peri)centromeric regions, where its level shows differences associated with various processes such a... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - October 18, 2021 Category: Genetics & Stem Cells Authors: Tanja Vojvoda Zeljko, Đurđica Ugarković and Željka Pezer Tags: Research Source Type: research
Telomere-specific chromatin capture using a pyrrole –imidazole polyamide probe for the identification of proteins and non-coding RNAs
Knowing chromatin components at a DNA regulatory element at any given time is essential for understanding how the element works during cellular proliferation, differentiation and development. A region-specific... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - October 9, 2021 Category: Genetics & Stem Cells Authors: Satoru Ide, Asuka Sasaki, Yusuke Kawamoto, Toshikazu Bando, Hiroshi Sugiyama and Kazuhiro Maeshima Tags: Methodology Source Type: research
High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs
It is established that protein-coding exons are preferentially localized in nucleosomes. To examine whether the same is true for non-coding exons, we analysed nucleosome occupancy in and adjacent to internal e... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - September 27, 2021 Category: Genetics & Stem Cells Authors: Pinki Dey and John S. Mattick Tags: Research Source Type: research
Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for det... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - September 16, 2021 Category: Genetics & Stem Cells Authors: Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana Shashkova, Marion Arnoux, Edouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul A. Lyons, Michel Georges and J örn Walter Tags: Research Source Type: research
Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation
Cell types in ventral midbrain are involved in diseases with variable genetic susceptibility, such as Parkinson ’s disease and schizophrenia. Many genetic variants affect regulatory regions and alter gene expre... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - September 9, 2021 Category: Genetics & Stem Cells Authors: Yujuan Gui, Kamil Grzyb, M élanie H. Thomas, Jochen Ohnmacht, Pierre Garcia, Manuel Buttini, Alexander Skupin, Thomas Sauter and Lasse Sinkkonen Tags: Research Source Type: research
Developmental programming of DNA methylation and gene expression patterns is associated with extreme cardiovascular tolerance to anoxia in the common snapping turtle
Environmental fluctuation during embryonic and fetal development can permanently alter an organism ’s morphology, physiology, and behaviour. This phenomenon, known as developmental plasticity, is particularly r... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - September 6, 2021 Category: Genetics & Stem Cells Authors: Ilan Ruhr, Jacob Bierstedt, Turk Rhen, Debojyoti Das, Sunil Kumar Singh, Soleille Miller, Dane A. Crossley II and Gina L. J. Galli Tags: Research Source Type: research
Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensio... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - August 28, 2021 Category: Genetics & Stem Cells Authors: Ning Liu, Wai Yee Low, Hamid Alinejad-Rokny, Stephen Pederson, Timothy Sadlon, Simon Barry and James Breen Tags: Review Source Type: research
Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure
Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In most conventional sequencing studi... (Source: Epigenetics and Chromatin)
Source: Epigenetics and Chromatin - August 23, 2021 Category: Genetics & Stem Cells Authors: Weitian Chen, Zhe Weng, Zhe Xie, Yeming Xie, Chen Zhang, Zhichao Chen, Fengying Ruan, Juan Wang, Yuxin Sun, Yitong Fang, Mei Guo, Yiqin Tong, Yaning Li and Chong Tang Tags: Research Source Type: research
