Article
Multidisciplinary Sciences
Kenneth Wu, Namrita Dhillon, Kelvin Du, Rohinton T. Kamakaka
Summary: Gene silencing in budding yeast is maintained by unacetylated nucleosomes and requires 50% to 75% acetylation for activation. The Sir4 gene is a key component in maintaining gene silencing, with even a two-fold reduction in acetyltransferases potentially leading to transcriptional silence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Sarah Lensch, Michael H. Herschl, Connor H. Ludwig, Joydeb Sinha, Michaela M. Hinks, Adi Mukund, Taihei Fujimori, Lacramioara Bintu
Summary: This study systematically investigates gene coupling in mammalian cells and finds that gene silencing and reactivation can act at a distance, involving histone modification and chromatin regulator recruitment. The configuration of insulator elements also plays a role in this process.
Review
Developmental Biology
Andrew Keniry, Marnie E. Blewitt
Summary: This article discusses the silencing process of the second X chromosome in females in mammals, and the crucial role of chromatin features in establishing and maintaining the silent state. It also explores the possibility of learning from this process to potentially treat X-linked diseases in females.
Article
Biochemistry & Molecular Biology
Catarine Markus, Ales Pecinka, Aldo Merotto
Summary: The study reveals that herbicide treatment impacts transcriptional gene silencing pathways, and misregulation of these pathways results in increased sensitivity of Arabidopsis plants to herbicide treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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)
Article
Biology
Samuel N. Bogan, Marie E. Strader, Gretchen E. Hofmann
Summary: This study investigates the effects of DNA methylation on gene expression and splicing in the larvae of the purple sea urchin. It finds that differential gene body methylation has stronger effects on gene expression among genes with poorly accessible transcriptional start sites, and the baseline transcript abundance influences the direction of this effect. Considering the interactions between methylation and chromatin accessibility, the transcriptional responses to maternal conditioning are significantly increased, suggesting that the relationship between methylation and gene regulation is partially explained by chromatin state.
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
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)
Article
Multidisciplinary Sciences
Gabriel K. Griffin, Jingyi Wu, Arvin Iracheta-Vellve, James C. Patti, Jeffrey Hsu, Thomas Davis, Deborah Dele-Oni, Peter P. Du, Aya G. Halawi, Jeffrey J. Ishizuka, Sarah Y. Kim, Susan Klaeger, Nelson H. Knudsen, Brian C. Miller, Tung H. Nguyen, Kira E. Olander, Malvina Papanastasiou, Suzanna Rachimi, Emily J. Robitschek, Emily M. Schneider, Mitchell D. Yeary, Margaret D. Zimmer, Jacob D. Jaffe, Steven A. Carr, John G. Doench, W. Nicholas Haining, Kathleen B. Yates, Robert T. Manguso, Bradley E. Bernstein
Summary: A CRISPR-Cas9 screen in mouse tumour models treated with immune checkpoint blockade identified SETDB1 as an epigenetic checkpoint protein that suppresses tumour-intrinsic immunogenicity. Loss of SETDB1 leads to derepression of immune-stimulating genes and triggers TE-specific cytotoxic T cell responses, suggesting it as a potential target for immunotherapy in cancer treatment.
Article
Microbiology
Suffian Azizan, Shamista A. Selvarajah, Jingyi Tang, Myriam D. Jeninga, Danae Schulz, Kapil Pareek, Tamara Herr, Karen P. Day, Tania F. De Koning-Ward, Michaela Petter, Michael F. Duffy
Summary: The alternative histones Pf H2A.Z and Pf H2B.Z in Plasmodium falciparum are enriched in intergenic euchromatin and play critical roles in gene expression and chromatin structure. The acetylated forms of these histones are dynamically associated with gene expression at promoters and are antagonized by histone deacetylases at heterochromatin boundaries. These findings suggest that acetylated Pf H2A.Z and Pf H2B.Z contribute to the maintenance of chromatin structure and enable rapid adaptation to altered host environments.
Article
Biochemistry & Molecular Biology
Bhavana Kayyar, Anjhana C. Ravikkumar, Utsa Bhaduri, M. R. S. Rao
Summary: Sox8 is a crucial transcription factor that plays an important role in sex maintenance and fertility of adult mice. It is regulated by the lncRNA Mrhl in a p68-dependent manner under the control of the Wnt signaling pathway. The downregulation of Mrhl leads to the meiotic commitment of the spermatogonial cells through Sox8 dependence. The involvement of architectural proteins CTCF and cohesin in mediating a chromatin loop, as well as the interaction between lncRNA Mrhl and the Sox8 locus through a DNA:DNA:RNA triplex, are important for the regulation of Sox8 expression.
MOLECULAR AND CELLULAR BIOLOGY
(2022)
Review
Cell Biology
Arianna Mangiavacchi, Gabriele Morelli, Valerio Orlando
Summary: Non-coding DNA makes up about 98.5% of the human genome and has been re-evaluated to reveal its importance in cell regulation through the presence of non-coding RNAs (ncRNAs). This review focuses on the relationship between chromatin-interacting RNAs, such as long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), circular RNA (circRNA), and the epigenome, highlighting their role in regulating gene expression and their impact on human diseases, particularly cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Review
Cell Biology
Angeliki Ntorla, Joseph Robert Burgoyne
Summary: Histone crotonylation is a newly identified epigenetic modification that regulates gene expression and is functionally distinct from histone acetylation, potentially regulating cellular metabolic status through competition for modification sites. It plays diverse functional roles within the cell, including signal-dependent gene activation, spermatogenesis, and tissue injury.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Cezary Krasnodebski, Agnieszka Sawula, Urszula Kazmierczak, Magdalena Zuk
Summary: Oligo technology is a cost-effective and easy-to-implement method for manipulating gene activity. It can be used in both animal and plant cells. The mechanism of action involves direct interaction with nucleic acids and indirect regulation of gene expression through cellular processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Genetics & Heredity
Anne E. Dodson, Jasper Rine
Article
Multidisciplinary Sciences
Gavin Schlissel, Marek K. Krzyzanowski, Fabrice Caudron, Yves Barral, Jasper Rine
Article
Genetics & Heredity
Kathryn J. Sieverman, Jasper Rine
Article
Multidisciplinary Sciences
Ryan Janke, Grant A. King, Martin Kupiec, Jasper Rine
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Genetics & Heredity
Kathryn J. Sieverman, Jasper Rine
Article
Genetics & Heredity
Laura Kasak, Constantina Bakolitsa, Zhiqiang Hu, Changhua Yu, Jasper Rine, Dago F. Dimster-Denk, Gaurav Pandey, Greet De Baets, Yana Bromberg, Chen Cao, Emidio Capriotti, Rita Casadio, Joost Van Durme, Manuel Giollo, Rachel Karchin, Panagiotis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Pier Luigi Martelli, David Masica, Sean D. Mooney, Ayodeji Olatubosun, Predrag Radivojac, Frederic Rousseau, Lipika R. Pal, Castrense Savojardo, Joost Schymkowitz, Janita Thusberg, Silvio C. E. Tosatto, Mauno Vihinen, Jouni Valiaho, Susanna Repo, John Moult, Steven E. Brenner, Iddo Friedberg
Article
Genetics & Heredity
Molly Brothers, Jasper Rine
Article
Multidisciplinary Sciences
Gavin Schlissel, Jasper Rine
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biology
Daniel S. Saxton, Jasper Rine
Article
Biology
Davis Goodnight, Jasper Rine
Article
Biology
Ryan Janke, Anthony T. Iavarone, Jasper Rine