Article
Biochemistry & Molecular Biology
Pengying Hao, David J. Waxman
Summary: In this study, it was found that the absence of STAT5 in mouse liver led to a significant loss of sex bias in gene expression, with male-biased genes being downregulated and female-biased genes being derepressed. The loss of STAT5 binding was directly associated with the downregulation of male-biased genes, while an indirect mechanism was observed for the derepression of female-biased genes.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Article
Cell Biology
Susanne Leidescher, Johannes Ribisel, Simon Ullrich, Yana Feodorova, Erica Hildebrand, Alexandra Galitsyna, Sebastian Bultmann, Stephanie Link, Katharina Thanisch, Christopher Mulholland, Job Dekker, Heinrich Leonhardt, Leonid Mirny, Irina Solovei
Summary: Despite limited understanding of the spatial organization of the genome, this study demonstrates that highly expressed long genes form open-ended transcription loops with RNA polymerases moving along them. The extension and shape of these loops suggest intrinsic stiffness and could represent a general mechanism underlying eukaryotic transcription.
NATURE CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Calvin Shun Yu Lo, Marvin van Toorn, Vincent Gaggioli, Mariana Paes Dias, Yifan Zhu, Eleni Maria Manolika, Wei Zhao, Marit van der Does, Chirantani Mukherjee, Joao G. S. C. Souto Goncalves, Martin E. van Royen, Pim J. French, Jeroen Demmers, Ihor Smal, Hannes Lans, David Wheeler, Jos Jonkers, Arnab Ray Chaudhuri, Jurgen A. Marteijn, Nitika Taneja
Summary: The BRCA1/2-mediated fork protection pathway is crucial for replication fork stability, but additional mechanisms, like SMARCAD1, are also necessary to prevent toxic accumulation of 53BP1 at the forks. Without SMARCAD1, there is frequent fork stalling and single-stranded DNA accumulation.
Article
Multidisciplinary Sciences
Jun-Yeong Lee, Ian Davis, Elliot H. H. Youth, Jonghwan Kim, Gary Churchill, James Godwin, Ron Korstanje, Samuel Beck
Summary: Cellular aging is characterized by disruption of the nuclear lamina and its associated heterochromatin, with the activation of CGI(-) genes being a common feature of normal and pathological aging in mice and humans. This up-regulation of CGI(-) genes is directly responsible for age-related physiological deterioration, including increased secretion of inflammatory mediators.
Article
Multidisciplinary Sciences
Tyler K. Fenstermaker, Svetlana Petruk, Sina K. Kovermann, Hugh W. Brock, Alexander Mazo
Summary: During DNA replication, the transcriptional machinery is believed to dissociate from DNA. However, our study shows that immediately after replication, Pol II, together with other general transcription proteins and immature RNA, re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that epigenetic marks may not be required for the recruitment of Pol II to newly synthesized DNA during the transition from replication to transcription.
Review
Cell Biology
Aidan J. Levinsky, Gregor McEdwards, Nasha Sethna, Mark A. Currie
Summary: H3K9 methyltransferases play crucial roles in genome stability, cell type-specific gene expression, and non-histone methylation. They are involved in histone modification and regulate the methylation of various non-histone targets, contributing to genome regulation and cellular functions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Kyle Brown, Pin Yu Chew, Steven Ingersoll, Jorge R. Espinosa, Anne Aguirre, Axel Espinoza, Joey Wen, Kalkidan Astatike, Tatiana G. Kutateladze, Rosana Collepardo-Guevara, Xiaojun Ren
Summary: This study reveals the assembly and regulation mechanism of Polycomb repressive complex 1 (PRC1). The findings demonstrate that the formation and dynamic properties of PRC1 condensates are sensitively regulated by their composition and stoichiometry.
Article
Genetics & Heredity
John M. Schoelz, Justina X. Feng, Nicole C. Riddle
Summary: The study reveals that Drosophila HP1 proteins have complex transcriptional regulatory roles in chromatin, closely associated with active histone modifications, and can also affect the levels of RNA polymerase pausing and gene expression.
Article
Cell Biology
Koh Nakayama, Sigal Shachar, Elizabeth H. Finn, Hiroyuki Sato, Akihiro Hirakawa, Tom Misteli
Summary: Chromosome structure and nuclear organization play important roles in gene expression regulation. The relationship between the 3D position of a gene in the nucleus and its activity is still not clear. A study on nearly 100 hypoxia-responsive genes found that most of them are located in the intermediate region of the nucleus, and some of them change their position under hypoxic conditions. However, gene position changes are not directly related to gene activity.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Oncology
Carla Guenther, Imrul Faisal, Manlio Fusciello, Maria Sokolova, Heidi Harjunpaa, Mette Ilander, Robert Tallberg, Maria Kristina Vartiainen, Ronen Alon, Jose-Maria Gonzalez-Granado, Vincenzo Cerullo, Susanna Carola Fagerholm
Summary: The study found that bone marrow-derived DCs expressing dysfunctional beta 2-integrin adhesion receptors displayed enhanced tumor rejection capabilities in melanoma models, showing spontaneous maturation. This maturation was associated with alterations in the cellular epigenetic/transcriptional profile and a potential role of integrins in regulating cell function.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Multidisciplinary Sciences
Leticia Laura Niborski, Paul Gueguen, Mengliang Ye, Allan Thiolat, Rodrigo Nalio Ramos, Pamela Caudana, Jordan Denizeau, Ludovic Colombeau, Raphael Rodriguez, Christel Goudot, Jean-Michel Luccarini, Anne Soude, Bruno Bournique, Pierre Broqua, Luigia Pace, Sylvain Baulande, Christine Sedlik, Jean-Pierre Quivy, Genevieve Almouzni, Jose L. Cohen, Elina Zueva, Joshua J. Waterfall, Sebastian Amigorena, Eliane Piaggio
Summary: This study reveals that the inhibition of histone lysine methyltransferase Suv39h1 can delay tumor growth and enhance the anti-tumor effect of anti-PD-1 therapy. In the absence of Suv39h1, alternative activation pathways induced by anti-PD-1 allow the survival and differentiation of effector cells, resulting in a biomarker of clinical response. The findings suggest that Suv39h1 acts as an epigenetic checkpoint for tumor immunity.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Yukiko Kuroda, Aiko Iwata-Otsubo, Kerith-Rae Dias, Suzanna E. L. Temple, Koji Nagao, Lachlan De Hayr, Ying Zhu, Shin-Ya Isobe, Gohei Nishibuchi, Sarah K. Fiordaliso, Yuki Fujita, Alyssa L. Rippert, Samuel W. Baker, Marco L. Leung, Daniel C. Koboldt, Adele Harman, Beth A. Keena, Izumi Kazama, Gopinath Musuwadi Subramanian, Kandamurugu Manickam, Betsy Schmalz, Maeson Latsko, Elaine H. Zackai, Matt Edwards, Carey-Anne Evans, Matthew C. Dulik, Michael F. Buckley, Toshihide Yamashita, W. Timothy O'Brien, Robert J. Harvey, Chikashi Obuse, Tony Roscioli, Kosuke Izumi
Summary: This study identified heterozygous de novo variants in the CBX1 gene, encoding HP1β, as a cause of a novel syndromic neurodevelopmental disorder. In vitro cellular assays, neurobehavioral and cytological analyses of neuronal cells, and mouse models confirmed the pathogenicity of the identified variants. The disruption of HP1β chromatin binding during neurocognitive development contributes to developmental disabilities.
GENETICS IN MEDICINE
(2023)
Review
Plant Sciences
Florent Velay, Louis-Valentin Meteignier, Christophe Laloi
Summary: This article summarizes the recent findings on the interplay between euchromatin and heterochromatin in the plant genome and proposes avenues for improving our understanding of chromatin architecture and transitions in plants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Anastasia K. Pickford, Lucas Michel-Todo, Florian Dupuy, Alfredo Mayor, Pedro L. Alonso, Catherine Lavazec, Alfred Cortes
Summary: Clonally variant genes (CVGs) are crucial for Plasmodium falciparum to adapt to the human host's changing blood environment, with major differences in their expression patterns compared to in vitro-cultured parasites. During the transmission stages, previous expression patterns for many CVG families are lost and new patterns are established.
Article
Cell Biology
Elettra Musolino, Christina Pagiatakis, Federica Pierin, Daniele Sabatino, Giovanna Finzi, Rosalba Gornati, Giovanni Bernardini, Roberto Papait
Summary: Three-dimensional chromatin organization plays a crucial role in defining cell transcription program during development. A new electron-microscopy staining technique called ChromEM has been developed to selectively mark nuclear DNA without altering its structure, allowing better visualization of 3D chromatin conformation. In this study, the protocol for applying ChromEM on myocardial tissue from mice is provided, along with the use of transmission electron microscopy (TEM) to measure morphological parameters of peripheral heterochromatin in cardiomyocytes. This protocol can also be used with electron tomography to study 3D chromatin organization in different aspects of heart pathobiology and establish ChromEM in other tissues.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Gabrielle J. Grundy, Luis M. Polo, Zhihong Zeng, Stuart L. Rulten, Nicolas C. Hoch, Pathompong Paomephan, Yingqi Xu, Steve M. Sweet, Alan W. Thorne, Antony W. Oliver, Steve J. Matthews, Laurence H. Pearl, Keith W. Caldecott
NATURE COMMUNICATIONS
(2016)
Article
Genetics & Heredity
Liliya Nazlamova, Anna Noble, Frank R. Schubert, John McGeehan, Fiona Myers, Matt Guille, Garry Scarlett
Article
Biotechnology & Applied Microbiology
Nelly Sapojnikova, Nino Asatiani, Tamar Kartvelishvili, Lali Asanishvili, Vitaly Zinkevich, Irina Bogdarina, Julian Mitchell, Abdulmohsen Al-Humam
JOURNAL OF BIOTECHNOLOGY
(2017)
Article
Multidisciplinary Sciences
Harry P. Austin, Mark D. Allen, Bryon S. Donohoe, Nicholas A. Rorrer, Fiona L. Kearns, Rodrigo L. Silveira, Benjamin C. Pollard, Graham Dominick, Ramona Duman, Kamel El Omari, Vitaliy Mykhaylyk, Armin Wagner, William E. Michener, Antonella Amore, Munir S. Skaf, Michael F. Crowley, Alan W. Thorne, Christopher W. Johnson, H. Lee Woodcock, John E. McGeehan, Gregg T. Beckham
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biochemistry & Molecular Biology
Nelly Sapojnikova, Tamar Kartvelishvili, Nino Asatiani, Vitaly Zinkevich, Iagor Kalandadze, Darejan Gugutsidze, Roman Shakarishvili, Alexander Tsiskaridze
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2014)
Article
Medicine, Legal
Katherine Brown, Alan Thorne, Michelle Harvey
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2015)
Article
Multidisciplinary Sciences
Vitaly Zinkevich, Nelly Sapojnikova, Julian Mitchell, Tamar Kartvelishvili, Nino Asatiani, Samia Alkhalil, Irina Bogdarina, Abdulmohsen A. Al-Humam
Article
Multidisciplinary Sciences
Ioannis M. Roussis, Matthew Guille, Fiona A. Myers, Garry P. Scarlett
Article
Environmental Sciences
Nino Asatiani, Tamar Kartvelishvili, Nelly Sapojnikova, Marina Abuladze, Lali Asanishvili, Mariam Osepashvili
WATER AIR AND SOIL POLLUTION
(2018)
Article
Environmental Sciences
Evgeni Bunin, Gia Khatisashvili, Tamar Varazi, Tamar Kartvelishvili, Nino Asatiani, Nelly Sapojnikova
WATER AIR AND SOIL POLLUTION
(2020)
Article
Nutrition & Dietetics
Rianne Costello, Mark E. T. Willems, Stephen D. Myers, Fiona Myers, Nathan A. Lewis, Ben J. Lee, Sam D. Blacker
INTERNATIONAL JOURNAL OF SPORT NUTRITION AND EXERCISE METABOLISM
(2020)
Article
Environmental Sciences
Nino Asatiani, Marina Abuladze, Tamar Kartvelishvili, Mariam Osepashvili, Alexander Shengelaya, Dimitri Daraselia, David Japaridze, Gia Khatisashvili, Tamar Varazi, Hoi-Ying Holman, Nelly Sapojnikova
Summary: This article explores the effects of copper on soil bacteria, finding that certain Bacillus species are tolerant to copper while Arthrobacter species are not. The oxidative stress response is crucial for adaptation to copper, which can influence soil restoration processes.
WATER AIR AND SOIL POLLUTION
(2021)
Article
Nutrition & Dietetics
Rianne Costello, Karen M. Keane, Ben J. Lee, Mark E. T. Willems, Stephen D. Myers, Fiona Myers, Nathan A. Lewis, Sam D. Blacker
Summary: The study demonstrates that supplementing with NZBC extract can increase the plasma uptake of phenolic acids GA and PCA, even when following a habitual diet in the days leading up to the trial. However, there is apparent variability between individuals in the response to the supplementation.
JOURNAL OF DIETARY SUPPLEMENTS
(2022)
Article
Sport Sciences
Samuel J. E. Lucas, William L. Malein, Owen D. Thomas, Kimberly M. Ashdown, Carla A. Rue, Kelsey E. Joyce, Charles Newman, Patrick Cadigan, Brian Johnson, Stephen D. Myers, Fiona A. Myers, Alexander D. Wright, John Delamere, Chris H. E. Imray, Arthur R. Bradwell, Mark Edsell
Summary: This study suggests that taking losartan at high altitude does not have a significant effect on blood pressure, cardiopulmonary function, and exercise performance.
BMJ OPEN SPORT & EXERCISE MEDICINE
(2021)
Article
Sport Sciences
Kelsley E. Joyce, John Delamere, Susie Bradwell, Stephen David Myers, Kimberly Ashdown, Carla Rue, Samuel J. E. Lucas, Owen D. Thomas, Amy Fountain, Mark Edsell, Fiona Myers, Will Malein, Chris Imray, Alex Clarke, Chrisopher T. Lewis, Charles Newman, Brian Johnson, Patrick Cadigan, Alexander Wright, Arthur Bradwell
BMJ OPEN SPORT & EXERCISE MEDICINE
(2020)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)
