Review
Biochemistry & Molecular Biology
Larisa Melnikova, Anton Golovnin
Summary: This review discusses the roles of dADD1, dXNP, and ATRX proteins in regulating cellular processes such as chromatin status and gene expression in the Drosophila model. Disruption of ATRX expression in humans is associated with alpha-thalassemia and cancer development. However, the mechanisms by which ATRX regulates cellular processes are still poorly understood. Studying the functioning of dADD1/dXNP in the Drosophila model can provide insights into the multifunctional action of ATRX and its connection with cellular processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Lorenzo Rinaldi, Gregory Fettweis, Sohyoung Kim, David A. Garcia, Saori Fujiwara, Thomas A. Johnson, Theophilus T. Tettey, Laurent Ozbun, Gianluca Pegoraro, Michele Puglia, Blagoy Blagoev, Arpita Upadhyaya, Diana A. Stavreva, Gordon L. Hager
Summary: This study reveals that the interaction between a transcription factor and the cohesin loader NIPBL regulates gene activity, and this mechanism is achieved by promoting loop extrusion and long-range gene regulation at the chromatin level. Additionally, it is discovered that patients with cohesin mutations exhibit a reduced response to glucocorticoids.
Article
Multidisciplinary Sciences
Naihua N. Gong, Leela Chakravarti Dilley, Charlette E. Williams, Emilia H. Moscato, Milan Szuperak, Qin Wang, Matthew Jensen, Santhosh Girirajan, Tiong Yang Tan, Matthew A. Deardorff, Dong Li, Yuanquan Song, Matthew S. Kayser
Summary: The chromatin remodeler ISWI is essential for adult fly sleep and its loss leads to disrupted circadian rhythms, memory, and social behavior. Expressing human ISWI homologs in flies can rescue adult phenotypes to different extents, highlighting the importance of chromatin remodeling machinery for sleep circuit formation in neurodevelopmental disorders.
Article
Oncology
Micol Di Segni, Ilaria Virdia, Alessandra Verdina, Carla Azzurra Amoreo, Silvia Baldari, Gabriele Toietta, Maria Grazia Diodoro, Marcella Mottolese, Isabella Sperduti, Fabiola Moretti, Simonetta Buglioni, Silvia Soddu, Giuliana Di Rocco
Summary: This study investigated the expression of HIPK2 in colorectal cancer and its association with disease progression and mutational patterns. The results showed that the percentage of HIPK2-positive cells increased with tumor progression and was significantly correlated with tumor-stage and poorer prognosis. Additionally, high HIPK2 expression was found to be significantly associated with KRAS mutations but not with other cancer-related genes. Functional analysis revealed that activation of the RAS pathway, either through KRAS mutation or upstream receptor stimulation, increased HIPK2 expression. Depletion of HIPK2 impaired ERK phosphorylation and tumor growth in colorectal cancer cells with KRAS mutations.
MOLECULAR CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yahan Li, Frimpong Boadu, Max R. Highsmith, Darren E. Hagen, Jianlin Cheng, Rocio Melissa Rivera
Summary: Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome show similarities in gene misregulation and chromosome architecture, with LOS associated with altered chromosome structure due to methylome epimutations, leading to gene misregulation.
Article
Oncology
Juho J. Miettinen, Romika Kumari, Gunnhildur Asta Traustadottir, Maiju-Emilia Huppunen, Philipp Sergeev, Muntasir M. Majumder, Alexander Schepsky, Thorarinn Gudjonsson, Juha Lievonen, Despina Bazou, Paul Dowling, Peter O'Gorman, Ana Slipicevic, Pekka Anttila, Raija Silvennoinen, Nina N. Nupponen, Fredrik Lehmann, Caroline A. Heckman
Summary: The study identified differential expression of aminopeptidases associated with survival in multiple myeloma patients, highlighted the effectiveness of melflufen in relapsed/refractory cases, and demonstrated the role of specific aminopeptidases in activating the drug.
Article
Biochemistry & Molecular Biology
Lia M. Pinto, Alexandros Pailas, Max Bondarchenko, Abhishek Bharadwaj Sharma, Katrin Neumann, Anthony J. Rizzo, Celine Jeanty, Nathalie Nicot, Carine Racca, Mindy K. Graham, Catherine Naughton, Yaqun Liu, Chun-Long Chen, Paul J. Meakin, Nick Gilbert, Sebastien Britton, Alan K. Meeker, Christopher M. Heaphy, Florence Larminat, Eric Van Dyck
Summary: Maintaining chromatin integrity at centromeres is crucial for preventing DNA breaks and genomic instability. The histone chaperone complex ATRX/DAXX is involved in establishing and maintaining centromeric chromatin structure. We discovered a novel ATRX-independent function for DAXX in promoting genome stability by preventing R-loop accumulation and DNA double-strand break formation at centromeres.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Clinical Neurology
Stella G. Cavalcante, Benedito J. A. Pereira, Antonio M. Lerario, Paula R. Sola, Sueli M. Oba-Shinjo, Suely K. N. Marie
Summary: The ATRX-DAXX-H3.3 chromatin remodeler complex is associated with telomere dysfunction and tumor progression in different types of cancer, with ATRX upregulation observed in grade II/III meningiomas. Telomere length in meningiomas shows low variability across different ages and malignant grades, in contrast to the shortening observed in normal controls with aging.
CLINICAL NEUROLOGY AND NEUROSURGERY
(2021)
Article
Medicine, Research & Experimental
Chin Wen Png, Wei Jie Jonathan Lee, Shijia Joy Chua, Feng Zhu, Khay Guan Yeoh, Yongliang Zhang
Summary: This study identified early microbial changes associated with gastric cancer development, highlighting the potential role of prospective microbiome surveillance in gastric cancer.
Article
Biology
Luka Bacic, Guillaume Gaullier, Anton Sabantsev, Laura C. Lehmann, Klaus Brackmann, Despoina Dimakou, Mario Halic, Graeme Hewitt, Simon J. Boulton, Sebastian Deindl
Summary: Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro, enabling cryo-EM structure determination to visualize several intermediate states of ALC1. Functional biochemical assays with PARylated nucleosomes highlighted the importance of nucleosomal epitopes for productive remodeling, and suggested that ALC1 prefers sliding nucleosomes away from DNA breaks.
Article
Biochemistry & Molecular Biology
Yulii V. Shidlovskii, Oleg V. Bylino, Alexander V. Shaposhnikov, Zaur M. Kachaev, Lyubov A. Lebedeva, Valeria V. Kolesnik, Diego Amendola, Giovanna De Simone, Nadia Formicola, Paul Schedl, Filomena Anna Digilio, Ennio Giordano
Summary: The chromatin remodeler SWI/SNF plays a key role in gene activation by opening chromatin structure on promoters and enhancers. A study on Drosophila showed that SWI/SNF factors, specifically the BAP170 and SAYP subunits of the PBAP subfamily, mediate enhancer-dependent transcription of a reporter gene. This suggests that SWI/SNF and its subunits are critical for establishing enhancer-mediated transcription.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Parysatis Sachs, Philipp Bergmaier, Katrin Treutwein, Jacqueline E. Mermoud
Summary: SMARCAD1 participates in transcriptional regulation, chromatin organization, and interacts with other chromatin-related proteins in vertebrates.
Review
Biochemistry & Molecular Biology
Namita Chutani, Sandhya Ragula, Khajamohiddin Syed, Suresh B. Pakala
Summary: MORC2, a recently discovered chromatin remodeler, plays a crucial role in cancer development by promoting cancer cell growth and migration, regulating gene transcription, and participating in DNA repair.
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.
Article
Multidisciplinary Sciences
Sebastian Cremer, Lisa Pilgram, Alexander Berkowitsch, Melanie Stecher, Siegbert Rieg, Mariana Shumliakivska, Denisa Bojkova, Julian Uwe Gabriel Wagner, Galip Servet Aslan, Christoph Spinner, Guillermo Luxan, Frank Hanses, Sebastian Dolff, Christiane Piepel, Clemens Ruppert, Andreas Guenther, Maria Madeleine Ruethrich, Joerg Janne Vehreschild, Kai Wille, Martina Haselberger, Hanno Heuzeroth, Arne Hansen, Thomas Eschenhagen, Jindrich Cinatl, Sandra Ciesek, Stefanie Dimmeler, Stefan Borgmann, Andreas Zeiher
Summary: Patients with cardiovascular comorbidities who take angiotensin II receptor blockers have lower mortality rates in COVID-19 compared to those who do not take these medications. This effect is particularly significant in patients who present early in the course of the disease. Additionally, these patients on ARBs also show lower levels of inflammatory markers and reduced frequency of reaching mortality-predicting thresholds.
Article
Biochemistry & Molecular Biology
Chiara Vardabasso, Alexandre Gaspar-Maia, Dan Hasson, Sebastian Puenzeler, David Valle-Garcia, Tobias Straub, Eva C. Keilhauer, Thomas Strub, Joanna Dong, Taniya Panda, Chi-Yeh Chung, Jonathan L. Yao, Rajendra Singh, Miguel F. Segura, Barbara Fontanals-Cirera, Amit Verma, Matthias Mann, Eva Hernando, Sandra B. Hake, Emily Bernstein
Article
Biochemistry & Molecular Biology
David Valle-Garcia, Zulekha A. Qadeer, Domhnall S. McHugh, Flavia G. Ghiraldini, Asif H. Chowdhury, Dan Hasson, Michael A. Dyer, Felix Recillas-Targa, Emily Bernstein
Article
Cell Biology
Chi-Yeh Chung, Zhen Sun, Gavriel Mullokandov, Almudena Bosch, Zulekha A. Qadeer, Esma Cihan, Zachary Rapp, Ramon Parsons, Julio A. Aguirre-Ghiso, Eduardo F. Farias, Brian D. Brown, Alexandre Gaspar-Maia, Emily Bernstein
Article
Biochemistry & Molecular Biology
Barbara Fontanals-Cirera, Dan Hasson, Chiara Vardabasso, Raffaella Di Micco, Praveen Agrawal, Asif Chowdhury, Madeleine Gantz, Ana de Pablos-Aragoneses, Ari Morgenstern, Pamela Wu, Dan Filipescu, David Valle-Garcia, Farbod Darvishian, Jae-Seok Roe, Michael A. Davies, Christopher R. Vakoc, Eva Hernando, Emily Bernstein
Article
Medicine, Research & Experimental
Michael A. Dyer, Zulekha A. Qadeer, David Valle-Garcia, Emily Bernstein
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE
(2017)
Article
Cell Biology
Andrea K. Byrum, Denisse Carvajal-Maldonado, Miranda C. Mudge, David Valle-Garcia, Mona C. Majid, Romil Patel, Mathew E. Sowa, Steven P. Gygi, J. Wade Harper, Yang Shi, Alessandro Vindigni, Nima Mosammaparast
JOURNAL OF CELL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Erdem Sendinc, David Valle-Garcia, Abhinav Dhall, Hao Chen, Telmo Henriques, Jose Navarrete-Perea, Wanqiang Sheng, Steven P. Gygi, Karen Adelman, Yang Shi
Article
Oncology
Zulekha A. Qadeer, David Valle-Garcia, Dan Hasson, Zhen Sun, April Cook, Christie Nguyen, Aroa Soriano, Anqi Ma, Lyra M. Griffiths, Maged Zeineldin, Dan Filipescu, Luz Jubierre, Asif Chowdhury, Orla Deevy, Xiang Chen, David B. Finkelstein, Armita Bahrami, Elizabeth Stewart, Sara Federico, Soledad Gallego, Fumiko Dekio, Mary Fowkes, David Meni, John M. Maris, William A. Weiss, Stephen S. Roberts, Nai-Kong V. Cheung, Jian Jin, Miguel F. Segura, Michael A. Dyer, Emily Bernstein
Letter
Cell Biology
Erdem Sendinc, David Valle-Garcia, Alan Jiao, Yang Shi
Article
Multidisciplinary Sciences
Ying Zhang, Xuemei Xie, Pourya Naderi Yeganeh, Dian-Jang Lee, David Valle-Garcia, Karla F. Meza-Sosa, Caroline Junqueira, Jiayu Su, Hongbo R. Luo, Winston Hide, Judy Lieberman
Summary: New cancer immunotherapy strategies using EpCAM aptamer-linked small-interfering RNA chimeras (AsiCs) were effective in selectively knocking down genes in EpCAM(+) tumors to enhance immune recognition. Four of the six AsiC (Upf2, Parp1, Cd47, and Mcl1) were able to inhibit tumor growth and improve tumor-infiltrating immune cell functions. AsiC mixtures showed better efficacy than individual AsiC and could synergize with anti-PD-1 checkpoint inhibition.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Editorial Material
Immunology
Zulekha A. Qadeer, William A. Weiss
Summary: The study reveals that bone morphogenetic proteins and Sox9 promote the transdifferentiation of tumor cells into tumor-derived astrocytes, which can be targeted by BMP inhibitors.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Cell Biology
Sol Diaz de Leon-Guerrero, Jonathan Salazar-Leon, Karla F. Meza-Sosa, David Valle-Garcia, Diana Aguilar-Leon, Gustavo Pedraza-Alva, Leonor Perez-Martinez
Summary: Obesity can cause chronic inflammation and disruptions in glucose and lipid metabolism, leading to degenerative diseases. Research shows that an enriched environment (EE), which enhances central nervous system activity, can improve metabolic abnormalities by reducing hepatic steatosis and inflammation, and promoting lipolysis and browning.
DISEASE MODELS & MECHANISMS
(2022)
Article
Multidisciplinary Sciences
Changying Guo, Karla F. Meza-Sosa, David Valle-Garcia, Guomeng Zhao, Kun Gao, Liting Yu, Hongying Zhang, Yeqing Chen, Liang Sun, Shira Rockowitz, Shouyu Wang, Sheng Jiang, Judy Lieberman
Summary: SET is a multifunctional histone-binding oncoprotein that enhances estrogen-dependent transcription. It binds to estrogen receptor alpha (ER alpha) and is recruited to ER alpha-bound enhancers and promoters at estrogen response elements (EREs). SET acts as a histone H2 chaperone, promotes H2A.Z incorporation, and modulates histone methylation at EREs. It also affects enhancer-promoter looping and recruitment of condensin complexes, crucial for E2-induced gene expression and transcriptional activation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
