Article
Biochemistry & Molecular Biology
Eunhye Lee, Chanshin Kang, Pasi Purhonen, Hans Hebert, Karim Bouazoune, Sungchul Hohng, Ji-Joon Song
Summary: CHD7 is a crucial chromatin remodeler, and its N-CRD region is essential for its ATPase stimulation and nucleosome remodeling activity. Mutations in this region can lead to defects in CHD7 function, affecting remodeling activity.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Corinna Lieleg, Ana Novacic, Sanja Musladin, Andrea Schmid, Goezde Gueclueler Akpinar, Slobodan Barbaric, Philipp Korber
Summary: Chromatin remodeling by ATP-dependent enzymes is crucial for genomic processes. The recruitment of remodelers, such as the SWI/SNF complex, in the removal of nucleosomes in yeast PHO gene induction is specific and may affect the outcome of remodeling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Jiyoon Beon, Sungwook Han, Hyeokjun Yang, Seung Eun Park, Kwangbeom Hyun, Song-Yi Lee, Hyun-Woo Rhee, Jeong Kon Seo, Jaehoon Kim, Seyun Kim, Daeyoup Lee
Summary: Inositol polyphosphate multikinase (IPMK) interacts with the chromatin remodeling complex SWI/SNF and regulates its function in mouse embryonic stem cells, contributing to transcription and differentiation.
Article
Developmental Biology
Yu-Chun Tseng, Jennifer S. Crodian, Ryan Cabot
Summary: This study aims to determine the developmental requirements of two SWI/SNF subunits, SMARCB1 and BRD7, in porcine embryos. The findings indicate that knockdown of SMARCB1 dramatically reduces embryo developmental potential, while knockdown of BRD7 has a less severe impact. Furthermore, knockdown of SMARCB1 alters the expression of NANOG and POU5F1.
REPRODUCTION FERTILITY AND DEVELOPMENT
(2022)
Article
Oncology
Corey M. Gill, Joshua Loewenstern, John W. Rutland, Hanane Arib, Margaret Pain, Melissa Umphlett, Yayoi Kinoshita, Russell B. McBride, Joshua Bederson, Michael Donovan, Robert Sebra, Mary Fowkes, Raj K. Shrivastava
Summary: ARID1A mutations occur with similar frequency between low and high-grade meningiomas, but ARID1A mutations are independently prognostic of worse prognosis beyond clinical and histopathologic features.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Cell Biology
Mizuki Sakamoto, Shusaku Abe, Yuka Miki, Yusuke Miyanari, Hiroyuki Sasaki, Takashi Ishiuchi
Summary: In this study, the authors investigate the characteristics and dynamic nucleosome positioning at promoters during early embryonic development. They also uncover the role of the zygotic transcription factor YY1 in the formation of well-positioned nucleosome arrays at regulatory elements. Nucleosome organization is crucial for cell identity and function, and the authors demonstrate the remodeling of nucleosome organization and its underlying mechanism during early mouse development. This study provides valuable insights into the epigenetic control during this critical developmental phase.
GENES & DEVELOPMENT
(2023)
Review
Biochemistry & Molecular Biology
Ji-Yun Shang, Xin-Jian He
Summary: Adenosine triphosphate-dependent chromatin remodeling complexes play a crucial role in transcription, DNA replication, and genome stability regulation in eukaryotes. However, the study of chromatin remodeling complexes in plants lags behind yeast and animals. Recent research has identified and characterized the composition and function of chromatin remodeling enzymes in Arabidopsis, providing a foundation for further investigation into the molecular mechanisms.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Plant Sciences
Tomasz Bieluszewski, Sandhan Prakash, Thomas Roule, Doris Wagner
Summary: SWI/SNF class chromatin remodeling complexes play crucial roles in facilitating access of proteins to the genomic DNA and altering chromatin compaction and accessibility. Recent studies have identified different subtypes of SWI/SNF complexes with unique properties and functions. Understanding the complex regulation of SWI/SNF activity and its impact on proper development and response to extrinsic cues is of great importance.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Ieva Vaicekauskaite, Rasa Sabaliauskaite, Juozas Rimantas Lazutka, Sonata Jarmalaite
Summary: Ovarian cancer is the fifth leading cause of women's death from cancers, with high mortality rate due to late presence and lack of modern diagnostic tools. It is a highly heterogeneous disease, leading to early treatment failure. Exploring molecular mechanisms of ovarian cancer can enhance our understanding and provide new treatment options.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Elzbieta Sarnowska, Szymon Kubala, Pawel Cwiek, Sebastian Sacharowski, Paulina Oksinska, Jaroslaw Steciuk, Magdalena Zaborowska, Jakub M. Szurmak, Roman Dubianski, Anna Maassen, Malgorzata Stachowiak, Bruno Huettel, Monika Ciesla, Klaudia Nowicka, Anna T. Rolicka, Saleh Alseekh, Ernest Bucior, Rainer Franzen, Anna Skoneczna, Malgorzata A. Domagalska, Samija Amar, Mohammad-Reza Hajirezaei, Janusz A. Siedlecki, Alisdair R. Fernie, Seth J. Davis, Tomasz J. Sarnowski
Summary: The Arabidopsis ERECTA family of leucine-rich repeat receptor-like kinases (LRR-RLKs) controls various developmental processes and interacts with the SWI/SNF chromatin remodeling complex. The er/erl1/erl2 mutant shows impaired gibberellin signaling, decreased SWI3B protein level, and altered chromatin structure. ERf-SWI/SNF CRC interaction plays an important role in transcriptional control of gibberellin receptors.
Article
Biology
Elizabeth T. Wiles, Colleen C. Mumford, Kevin J. McNaught, Hideki Tanizawa, Eric U. Selker
Summary: Establishing and maintaining appropriate gene repression is crucial for multicellular organisms. H3K27 methylation is a common modification associated with gene repression, and recent research has identified the involvement of ISWI and ACF1 genes in the repression of H3K27-methylated genes in the filamentous fungus Neurospora crassa. These genes form an ACF chromatin-remodeling complex and interact with chromatin throughout the genome. Proper nucleosome positioning is critical for the repression of H3K27-methylated genes.
Article
Oncology
Colin Kenny, Elaine O'Meara, Mevlut Ulas, Karsten Hokamp, Maureen J. O'Sullivan
Summary: Malignant rhabdoid tumors (MRT) are lethal and treatment-resistant cancers, primarily affecting young children with only a single DNA spelling change leading to this deadly outcome. Research shows that this single mutation alters the arrangement of the entire DNA, keeping cells in a cancerous state.
Article
Cell Biology
Mahsa S. Ahadi, Talia L. Fuchs, Adele Clarkson, Amy Sheen, Loretta Sioson, Angela Chou, Anthony J. Gill
Summary: Loss of expression of mammalian SWI/SNF complex subunits is rare but enriched in MMRd cases of CRC. This deficiency is associated with higher grade, right-sided location, mismatch repair deficiency, and BRAF V600E mutation, and shows statistically worse overall survival and prognosis.
Article
Biochemistry & Molecular Biology
Roberto Amigo, Fernanda Raiqueo, Estefania Tarifeno, Carlos Farkas, Jose L. Gutierrez
Summary: The establishment and maintenance of nucleosome-free regions (NFRs) are essential processes in chromatin dynamics. This study investigates the role of transcription factors, chromatin remodeling complexes, and DNA sequences, particularly poly(dA:dT) tracts, in nucleosome remodeling. The results show that poly(dA:dT) tracts have differential effects on the activity of chromatin remodeling complexes and affect the directionality of nucleosome sliding. These findings shed light on the mechanisms underlying asymmetrical chromatin opening around poly(dA:dT) tracts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Ying Ye, Xi Chen, Wensheng Zhang
Summary: Embryonic stem cells have a unique ability to maintain and regulate the balance between self-renewal and multi-lineage cellular differentiation, largely dependent on gene expression regulations. Chromatin remodeling complexes play a crucial role in promoting chromatin structural changes that ultimately affect ESC fate choices.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
John D. Bagert, Michelle M. Mitchener, Agata L. Patriotis, Barbara E. Dul, Felix Wojcik, Benjamin A. Nacev, Lijuan Feng, C. David Allis, Tom W. Muir
Summary: The research has identified numerous histone mutations in cancer, particularly in the context of chromatin remodeling and gene regulation pathways. These mutations may play a critical role in disease development by perturbing nucleosome remodeling processes.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Shuai Zhao, Kelly N. Chuh, Baichao Zhang, Barbara E. Dul, Robert E. Thompson, Lorna A. Farrelly, Xiaohui Liu, Ning Xu, Yi Xue, Robert G. Roeder, Ian Maze, Tom W. Muir, Haitao Li
Summary: The study found that the readers of H3K4me3 retain binding to H3K4me3Q5ser, while the erasers are significantly inhibited. The results suggest that H3Q5ser may potentially fine-tune critical gene expression programs by stabilizing H3K4me3 from dynamic turnover or enhancing its physical readout by downstream effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Haigang Song, Antony J. Burton, Sally L. Shirran, Jurate Fahrig-Kamarauskaite, Hannelore Kaspar, Tom W. Muir, Markus Kunzler, James H. Naismith
Summary: The introduction of alpha-N-methylated non-proteinogenic amino acids into peptides can enhance their biological activities. An engineered enzyme called OphMA has been shown to methylate amide bonds in non-natural amides, offering potential applications in biotechnological production of therapeutic peptides.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Multidisciplinary
Michelle M. Mitchener, Tom W. Muir
Summary: The nucleosome, the fundamental repeating unit of chromatin, is composed of DNA wrapped around four canonical histone proteins, possessing 2-fold pseudo-symmetry that can be disrupted in cellular contexts. Post-translational modification of histones, histone removal/swapping for variants, or histone mutation may render nucleosomes asymmetric. Various techniques have been developed to investigate nucleosome asymmetry, including affinity tag-based purification, transient cross-linking strategies, synthetic biology techniques, and split intein technology. These chemical biology tools provide a means to biochemically interrogate a variety of asymmetric nucleosome species, contributing to the understanding of chromatin structure and function.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
John D. Bagert, Tom W. Muir
Summary: The field of epigenetics has rapidly expanded in the past two decades, revealing the complexity of genetic information storage and access in eukaryotes, with chemistry playing an increasingly important role. Molecular precision afforded by chemical tools is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Chemistry, Multidisciplinary
Nir Hananya, Sara K. Daley, John D. Bagert, Tom W. Muir
Summary: The study developed a efficient semi-synthesis method to create full-length ADP-ribosylated histones H3 and H2B, which were used to investigate the roles of histone ADP-ribosylation in DNA damage response. The results showed that ADP-ribosylation of serine-6 of histone H2B inhibits chromatin folding and higher-order organization, providing new insights into the impact of histone modifications on chromatin structure.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Aiwei Wu, Junhong Zhi, Tian Tian, Ali Cihan, Murat A. Cevher, Ziling Liu, Yael David, Tom W. Muir, Robert G. Roeder, Ming Yu
Summary: The study showed that DOT1L depletion in erythroleukemic cells does not affect the elongation rate of RNA polymerase II, but plays a significant role in transcription initiation by regulating the recruitment of transcription factor IID along with ENL. This is achieved by enhancing H2Bub1 levels and limiting the recruitment of the SAGA complex. These findings provide new insights into the role of the DOT1L complex in transcriptional regulation and its implications for MLLr leukemias.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell & Tissue Engineering
Fikri Birey, Min-Yin Li, Aaron Gordon, Mayuri Thete, Alfredo M. Valencia, Omer Revah, Anca M. Pasca, Daniel H. Geschwind, Sergiu P. Pasca
Summary: In this study, it was found that the role of L-type calcium channel in neurodevelopmental diseases is complex, as it can regulate the saltation length and frequency of interneuron migration. Inhibition of GABA-A receptors can restore the defect in migration frequency, while modulation of actomyosin and myosin light chain phosphorylation can improve the defect in saltation length.
Article
Chemistry, Multidisciplinary
Hai T. Dao, Hengyuan Liu, Nazar Mashtalir, Cigall Kadoch, Tom W. Muir
Summary: This study reports a strategy for controlling the orientation of asymmetric nucleosomes and hexasomes, providing an efficient method for studying gene regulation. By using truncated DNA templates and DNA ligation, the researchers successfully prepared desymmetrized mononucleosomes and oligonucleosomes with varied DNA sequences and histone compositions. Using this technology, they investigated the impact of asymmetry on chromatin remodeling and found that cancer-associated histone mutations can cause aberrant chromatin structure.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Editorial Material
Cell Biology
Alfredo M. Valencia, Sergiu P. Pasca
Summary: This article describes how recent advances in transcriptional and chromatin profiling, combined with cellular models, are informing our understanding of neurodevelopment and chromatinopathies.
TRENDS IN CELL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Bradley J. Lukasak, Robert E. Thompson, Michelle M. Mitchener, Vanessa J. Feng, John D. Bagert, Tom W. Muir
Summary: In this study, the SpyCatcher/SpyTag system was used to assemble desymmetrized nucleoprotein complexes. This method allows for the generation of nucleosomes with asymmetric modifications and facilitates the investigation of the effects of nucleosome asymmetry on chromatin remodeling processes and histone enzyme activity.
ACS CENTRAL SCIENCE
(2022)
Article
Oncology
Julia A. Belk, Winnie Yao, Nghi Ly, Katherine A. Freitas, Yan-Ting Chen, Quanming Shi, Alfredo M. Valencia, Eric Shifrut, Nupura Kale, Kathryn E. Yost, Connor V. Duffy, Bence Daniel, Madeline A. Hwee, Zhuang Miao, Alan Ashworth, Crystal L. Mackall, Alexander Marson, Julia Carnevale, Santosh A. Vardhana, Ansuman T. Satpathy
Summary: This study demonstrates that modulation of chromatin remodeling complexes improves the persistence of T cells in tumors and enhances antitumor immunity, providing important insights into the genetic regulators of T cell exhaustion.
Article
Multidisciplinary Sciences
Aishan Zhao, Steven P. Bodine, Qian Xie, Boyuan Wang, Geeta Ram, Richard P. Novick, Tom W. Muir
Summary: This study reveals the involvement of membrane protease regulator of agr QS (MroQ) in the production of autoinducing peptide (AIP) in Staphylococcus aureus. It also uncovers the different roles of MroQ in different agr specificity groups, enhancing our understanding of the agr response and Staphylococcus aureus virulence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Giridhar Sekar, Adam J. Stevens, Anahita Z. Mostafavi, Pulikallu Sashi, Tom W. Muir, David Cowburn
Summary: Split intein-mediated protein trans-splicing (PTS) is a widely used method in chemical biology and biotechnology for traceless and specific protein ligation. The efficiency of PTS can be limited by external residues flanking the intein. In this study, a recently developed atypically split intein (Cat) was further modified to enhance its PTS activity in the presence of unfavorable N-extein residues. The mechanism behind the enhanced activity was explored using nuclear magnetic resonance spectroscopy and molecular dynamics simulations, highlighting the contribution of a conserved histidine residue. This enhanced extein tolerance of Cat* expands the applicability of atypically split inteins and reveals common principles of extein dependence.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biochemistry & Molecular Biology
Michelle M. Mitchener, Tom W. Muir
Summary: Research over the past decade has revealed a new layer of epigenetic dysregulation, uncovering the association between somatic missense mutations in histones and human pathologies, especially cancer. While some of these mutations are believed to be key drivers of cancer, the effects of the majority of them on disease onset and progression are still unclear. Studies have shown that even at low dosage, histone mutants can corrupt chromatin states, providing insights into the intricate mechanisms of epigenetic control.