Review
Biochemistry & Molecular Biology
Jun Ueda, Taiga Yamazaki, Hiroshi Funakoshi
Summary: The advancement in epigenetics research has potential applications in the treatment of various diseases through epigenome editing. Efforts are being made to improve target specificity, enzymatic activity, and drug delivery for successful in vivo application of epigenome editing. This review discusses the latest findings, current limitations, and future challenges in the practical application of epigenome editing for disease therapy, and introduces important factors to consider, such as chromatin plasticity, for a more effective therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Dakota L. Jones, Grey F. Hallstroem, Xi Jiang, Ryan C. Locke, Mary Kate Evans, Edward D. Bonnevie, Anjana Srikumar, Thomas P. Leahy, Madhura P. Nijsure, Joel D. Boerckel, Robert L. Mauck, Nathaniel A. Dyment
Summary: Cells integrate mechanical cues to maintain tissue function and homeostasis, but the underlying mechanisms are not well understood. This study shows that loss of tensile cues changes nuclear morphology, positioning, and gene expression, resulting in weakening of tendons.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Dermatology
Ramile Dilshat, Hong Nhung Vu, Eirikur Steingrimsson
Summary: Melanocytes originate in the neural crest, migrate and proliferate before differentiating into pigment-producing cells, determining color and protecting against UV radiation; their lineage is regulated by transcription factors and signaling pathways, with epigenetic modifiers and replacement histones playing key roles in this process.
EXPERIMENTAL DERMATOLOGY
(2021)
Article
Multidisciplinary Sciences
Aydan Bulut-Karslioglu, Hu Jin, Yun-Kyo Kim, Brandon Cho, Marcela Guzman-Ayala, Andrew J. K. Williamson, Miroslav Hejna, Maximilian Stoetzel, Anthony D. Whetton, Jun S. Song, Miguel Ramalho-Santos
Summary: Chd1 in ES cells mediates hypertranscription and protects genome integrity by preventing DNA break accumulation, interacting with DNA repair factors. Genes prone to DNA breaks in Chd1 KO ES cells have specific characteristics, revealing the vulnerability of stem cells to endogenous DNA break accumulation.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Alfonso Carlos Barragan-Rosillo, Carlos Alberto Peralta-Alvarez, Jonathan Odilon Ojeda-Rivera, Rodrigo G. Arzate-Mejia, Felix Recillas-Targa, Luis Herrera-Estrella
Summary: Plants have evolved strategies to cope with phosphorus scarcity, with genetic approaches identifying key regulators like PHR1 and PHL2 in the transcriptional response to phosphate starvation. Chromatin accessibility undergoes genome-wide remodeling in root cells during Pi starvation, with PHR1 and PHL2 playing a crucial role in this process. These transcription factors directly activate a second wave of epigenetic changes needed for the transcriptional activation of low-Pi-responsive genes in Pi-starved root cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Martin Filipovski, Jelly H. M. Soffers, Seychelle M. Vos, Lucas Farnung
Summary: This study reports the structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex and reveals the direct role of Pol II and transcription elongation factors in nucleosome retention, explaining how nucleosomes are retained to maintain the chromatin structure of actively transcribed genes.
Article
Biochemistry & Molecular Biology
Alexander Munden, Mary Lauren Benton, John A. Capra, Jared T. Nordman
Summary: R-loops play important roles in various biological processes. This study reveals that R-loop abundance and genome localization change during Drosophila embryogenesis and that RNaseH1 activity is crucial for embryonic development. The findings also demonstrate the developmental plasticity of R-loops in gene formation and their relative positioning.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Cell Biology
Frederic Berger, Kathrin Muegge, Eric J. Richards
Summary: Different variants of the histone H2A are found in distinct locations in the genome, but the mechanisms responsible for depositing specific H2A variants are not well understood. However, there are exceptions, such as chromatin remodelers that control H2A.Z dynamics at promoters. This review focuses on the identification of a specific class of chromatin remodelers (LSH and DDM1) that deposit the variants macroH2A in mammals and H2A.W in plants, respectively, and discusses their function in heterochromatin and genome stability.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Developmental Biology
Howard Cedar, Ofra Sabag, Yitzhak Reizel
Summary: DNA methylation plays a crucial role in gene regulation during development. The establishment of methylation patterns in the early embryo maintains a genome-wide network of gene regulatory elements by organizing an inaccessible chromatin structure. Programmed demethylation in each cell type allows for the maintenance of select elements in an open structure, enabling interaction with a wide range of transcription factors to regulate cell identity defining gene expression profiles.
Article
Biochemistry & Molecular Biology
Ryota Yamamoto, Genki Sato, Takamitsu Amai, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: In this study, a novel technology for inducing chromatin loosening in target regions of Saccharomyces cerevisiae was established through nucleosomal histone acetylation. The system successfully increased euchromatic DNA at the target locus, suggesting the potential of inducing euchromatic state in a target locus using this developed method.
Article
Biochemistry & Molecular Biology
Divya Reddy, Saikat Bhattacharya, Sanket Shah, Mudasir Rashid, Sanjay Gupta
Summary: The study demonstrates the downregulation of histone H3 variant H3.3 and the upregulation of H3.2 in HCC, leading to alterations in histone modifications associated with active transcription. Specific histone chaperones CAF-1 and HIRA may play a role in regulating H3.3 and H3.2 levels. Inhibition of DNA methylation and histone deacetylation could potentially restore histone H3 variant expression in tumor cells.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Editorial Material
Cardiac & Cardiovascular Systems
Emma Louise Robinson, Chukwuemeka George Anene-Nzelu, Manuel Rosa-Garrido, Roger S. Y. Foo
Summary: Epigenetic regulation is crucial for the homeostasis of every tissue and organ, especially in the cardiovascular system. Understanding the signaling from the cardiac epigenome is essential for unraveling the molecular underpinnings of cardiovascular disease and development.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2021)
Review
Multidisciplinary Sciences
Jason H. Brickner
Summary: This article discusses the mechanisms by which histone modifications can be inherited and relates them to the phenomenon of epigenetic transcriptional memory. Recent studies have found that the histone H3 lysine 4 dimethylation associated with this memory plays a critical role in sustaining memory and can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism involves a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1(-) COMPASS. This is the first example of chromatin-mediated inheritance of a mark that promotes transcription.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Multidisciplinary Sciences
Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A. Doudna
Summary: The fusion of PRDM9 and Cas9 in CRISPR-Cas genome editing can increase the efficiency of homology-directed repair (HDR) and avoid off-target editing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Malte Thodberg, Axel Thieffry, Jette Bornholdt, Mette Boyd, Christian Holmberg, Ajuna Azad, Christopher T. Workman, Yun Chen, Karl Ekwall, Olaf Nielsen, Albin Sandelin
NUCLEIC ACIDS RESEARCH
(2019)
Article
Genetics & Heredity
Viviane Page, Jennifer J. Chen, Mickael Durand-Dubief, David Grabowski, Eriko Oya, Miriam Sanso, Ryan D. Martin, Terence E. Hebert, Robert P. Fisher, Karl Ekwall, Jason C. Tanny
Article
Genetics & Heredity
Eriko Oya, Mickael Durand-Dubief, Adiel Cohen, Vladimir Maksimov, Catherine Schurra, Jun-ichi Nakayama, Ronit Weisman, Benoit Arcangioli, Karl Ekwall
EPIGENETICS & CHROMATIN
(2019)
Article
Biochemistry & Molecular Biology
Eriko Oya, Reiko Nakagawa, Yuriko Yoshimura, Mayo Tanaka, Gohei Nishibuchi, Shinichi Machida, Atsuko Shirai, Karl Ekwall, Hitoshi Kurumizaka, Hideaki Tagami, Jun-ichi Nakayama
Article
Biochemistry & Molecular Biology
Farzaneh Shahin Varnoosfaderani, Anna Palau, Wenbo Dong, Jenna Persson, Mickael Durand-Dubief, J. Peter Svensson, Andreas Lennartsson
Article
Biology
Adrien Birot, Marta Tormos-Perez, Sabine Vaur, Amelie Feytout, Julien Jaegy, Dacil Alonso Gil, Stephanie Vazquez, Karl Ekwall, Jean-Paul Javerzat
Article
Hematology
Huthayfa Mujahed, Sophia Miliara, Anne Neddermeyer, Sofia Bengtzen, Christer Nilsson, Stefan Deneberg, Lina Cordeddu, Karl Ekwall, Andreas Lennartsson, Soren Lehmann
Article
Multidisciplinary Sciences
Wenbo Dong, Eriko Oya, Yasaman Zahedi, Punit Prasad, J. Peter Svensson, Andreas Lennartsson, Karl Ekwall, Mickael Durand-Dubief
SCIENTIFIC REPORTS
(2020)
Article
Oncology
Chatarina Larsson, Lina Cordeddu, Lee Siggens, Tatjana Pandzic, Snehangshu Kundu, Liqun He, Muhammad Akhtar Ali, Nusa Pristovsek, Karin Hartman, Karl Ekwall, Tobias Sjoblom
CLINICAL EPIGENETICS
(2020)
Article
Biochemistry & Molecular Biology
Yasaman Zahedi, Mickael Durand-Dubief, Karl Ekwall
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Wenbo Dong, Punit Prasad, Andreas Lennartsson, Karl Ekwall
Summary: The study investigated the role of non-ATPase domains of Hrp3 using in vitro methods, and found that deletion of all non-ATPase domains led to reduced ATP hydrolyzing activities in vitro. Deletion of the coupling region stimulated ATPase activity moderately with the nucleosome, while deletion of SANT and coupling regions completely loss interactions with the nucleosomes. Overall, the enzymatic activity of Hrp3 is fine-tuned by unique contributions of all four non-catalytic domains in association with nucleosomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Muhammad Shoaib, Qinming Chen, Xiangyan Shi, Nidhi Nair, Chinmayi Prasanna, Renliang Yang, David Walter, Klaus S. Frederiksen, Hjorleifur Einarsson, J. Peter Svensson, Chuan Fa Liu, Karl Ekwall, Mads Lerdrup, Lars Nordenskiold, Claus S. Sorensen
Summary: The study demonstrates that H4K20 methylation can directly promote chromatin openness by disrupting chromatin folding, particularly at highly transcribed genes. H4K20me1 changes the conformational state of H4 and leads to more dynamic H4-tails, maintaining chromatin accessibility throughout the cell cycle.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yasaman Zahedi, Shengyuan Zeng, Karl Ekwall
Summary: Cellular quiescence is a vital physiological state that occurs at the G(0) stage in both single-celled and multicellular eukaryotes. The chromatin remodeling complex Ino80C has been found to play a crucial role in the survival of quiescent cells. In this study, we demonstrate that Ino80C is involved in the regulation of gene expression in G(0) cells. Null mutants for certain Ino80C subunits, the histone variant H2A.Z, and Inositol kinase Asp1 exhibit similar phenotypes in quiescence, including reduced genome-wide transcription and failure to activate quiescence genes, particularly those localized to subtelomeric regions. Our findings suggest that Ino80C evicts H2A.Z from chromatin in quiescent cells, leading to the inactivation of subtelomeric boundary element and the activation of genes necessary for survival in quiescence.
CHROMOSOME RESEARCH
(2023)
Article
Genetics & Heredity
Nele Brusselaers, Karl Ekwall, Mickael Durand-Dubief
Article
Biology
Anissia Ait-Saada, Olga Khorosjutina, Jiang Chen, Karol Kramarz, Vladimir Maksimov, J. Peter Svensson, Sarah Lambert, Karl Ekwall
LIFE SCIENCE ALLIANCE
(2019)