Article
Cell Biology
Mingxuan Li, Yutao Shen, Yujia Xiong, Shuai Wang, Chuzhong Li, Jiwei Bai, Yazhuo Zhang
Summary: The study revealed that SMARCB1 functions as a tumor suppressor in chordoma by inhibiting the malignant phenotype of chordoma cells. SMARCB1 inhibits autophagy through direct binding to the ATG5 promoter, leading to decreased ATG5 expression and impaired autophagy. High ATG5 expression is associated with adverse outcomes in recurrent chordoma patients.
CELL PROLIFERATION
(2021)
Review
Oncology
Jaren Mullen, Shumei Kato, Jason K. Sicklick, Razelle Kurzrock
Summary: Mutations in ARID1A, a subunit gene of the SWI/SNF chromatin remodeling complex, are common in various cancers and play a crucial role in regulating gene expression related to oncogenesis and tumor suppression. Targeting ARID1A-altered cancers may involve a combination of immune checkpoint blockade and inhibitors of various pathways.ARID1A alterations may also mediate resistance to specific chemotherapies and hormone therapies.
CANCER TREATMENT REVIEWS
(2021)
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
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
Biochemistry & Molecular Biology
Yaoguang Yu, Wei Fu, Jianqu Xu, Yawen Lei, Xin Song, Zhenwei Liang, Tao Zhu, Yuhui Liang, Yuanhao Hao, Liangbing Yuan, Chenlong Li
Summary: The Arabidopsis thaliana bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and play critical roles in genomic targeting. These BRDs interact directly with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit, to control gene expression and developmental processes. The bromodomains of BRDs are essential for genomic targeting of SWI/SNF complexes.
Article
Oncology
Seong Hwi Hong, Keun Hong Son, Sang Yun Ha, Tae In Wee, Sung Kyung Choi, Ji Eun Won, Hee Dong Han, Youngtae Ro, Yeong-Min Park, Jung Woo Eun, Suk Woo Nam, Jeung-Whan Han, Keunsoo Kang, Jueng Soo You
Summary: This study uncovers a novel protumorigenic role for SMARCB1 in liver cancer and reveals significant links between nucleoporins and chromatin remodelers in cancer through identifying NUP210 as a critical coregulator of SMARCB1 chromatin remodeling activity.
Article
Biochemistry & Molecular Biology
Carlos Jimenez, Roberta Antonelli, Mariona Nadal-Ribelles, Laura Devis-Jauregui, Pablo Latorre, Carme Sole, Marc Masanas, Adria Molero-Valenzuela, Aroa Soriano, Josep Sanchez de Toledo, David Llobet-Navas, Josep Roma, Francesc Posas, Eulalia de Nadal, Soledad Gallego, Lucas Moreno, Miguel F. Segura
Summary: Loss of function of mSWI/SNF complexes in neuroblastoma impairs cell proliferation and inhibits tumor invasion and metastasis. Disruption of the BAF complex results in epigenetic repression of invasion-related genes, significantly inhibiting neuroblastoma metastasis. These findings provide important insights for the development of new therapeutic strategies targeting mSWI/SNF complexes in neuroblastoma.
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
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
Rodrigo O. de Castro, Luciana Previato de Almeida, Agustin Carbajal, Irma Gryniuk, Roberto J. Pezza
Summary: Gametogenesis in mammals involves regulated developmental transitions and changes in gene transcription. SWI/SNF chromatin remodelers are involved in gene transcription and DNA repair, but their role in meiosis is not well understood. Conditional knockout mice for ARID2, a regulatory subunit of PBAF, were generated and compared with BRG1 knockout mice. ARID2 activity is required at the end of prophase I, while BRG1 acts at an early stage of meiosis. Defects in spindle assembly and chromosome-spindle attachment in ARID2 knockout mice are attributed to an increase in aurora B kinase at centromeres. Different PBAF complexes regulate different stages of meiosis and gametogenesis.
Article
Biochemistry & Molecular Biology
Javeed Ahmad Bhat, Angela J. Balliano, Jeffrey J. Hayes
Summary: Chromatin remodeling enzymes use energy to alter the structure of nucleosomes, facilitating DNA access. This study reveals that the RSC complex requires access to the trailing protein surface of the nucleosome for mobilization, indicating a mechanism for regulating DNA sequences.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Bongwoo Kim, Yi Luo, Xiaoming Zhan, Zilai Zhang, Xuanming Shi, Jiaqing Yi, Zhenyu Xuan, Jiang Wu
Summary: The core subunit BRG1 of the SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes regulates neuronal activity-induced enhancers by affecting enhancer activities and inducibility. BRG1 phosphorylation induced by neuronal stimulations modulates its interaction with transcription co-factors, potentially influencing transcription outcomes. Non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, while phosphomimic BRG1 increases enhancer activity and inducibility.
Article
Plant Sciences
Tian Ma, Shuge Wang, Cunyi Sun, Jiawang Tian, Hong Guo, Sujuan Cui, Hongtao Zhao
Summary: In this study, the mutation of LFR in Arabidopsis resulted in hypersensitivity to freezing stress and reduced expression levels of CBFs and COR genes. LFR was found to interact directly with ICE1 and activate ICE1 and CBF3 gene expression in response to cold stress.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Cell Biology
Luca Pagliaroli, Marco Trizzino
Summary: Organismal development is a complex process involving fine-tuned control of cell fate and identity through transcription factors and protein complexes. Mutations in the SWI/SNF chromatin remodeler complex subunits ARID1A and ARID1B are associated with a wide array of developmental disorders, highlighting their important role in cell fate determination.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Teresita Padilla-Benavides, Monserrat Olea-Flores, Tapan Sharma, Sabriya A. Syed, Hanna Witwicka, Miriam D. Zuniga-Eulogio, Kexin Zhang, Napoleon Navarro-Tito, Anthony N. Imbalzano
Summary: Mammalian SWI/SNF (mSWI/SNF) complexes are vital ATP-dependent chromatin remodeling enzymes for normal cellular functions. They consist of three sub-families, namely BAF, ncBAF, and PBAF, based on the presence of specific subunit proteins. This study investigated the role of these sub-families in myoblast differentiation by knocking down the genes encoding their unique subunit proteins. The results revealed that the BAF complex and Baf250A were necessary for lineage-specific gene expression, while Brd9 and the ncBAF complex indirectly contributed to differentiation. Baf180 was found to be dispensable for myoblast differentiation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Jae-Ho Lee, Sun Hee Lee, Eun-Ho Lee, Jeong-Yong Cho, Dae-Kyu Song, Young Jae Lee, Taeg Kyu Kwon, Byung-Chul Oh, Kae Won Cho, Timothy F. Osborne, Tae-Il Jeon, Seung-Soon Im
Summary: The study found that fat accumulation and inflammation of proinflammatory M1 macrophages were higher in HFHS-fed SCAP mKO mice compared to control mice. This effect was attributed to a defect in the lipopolysaccharide-mediated increase in SREBP-1a. Mechanistically, SREBP-1a increased the expression of cholesterol 25-hydroxylase transcription, leading to an increase in the production of 25-hydroxycholesterol (25-HC) and subsequent activation of liver X receptor alpha (LXRa), which promoted cholesterol efflux and limited cholesterol accumulation and M1 polarization. The activation of the SCAP-SREBP-1a pathway in macrophages could be a potential therapeutic strategy for controlling cholesterol homeostasis and ameliorating obesity.
JOURNAL OF ADVANCED RESEARCH
(2023)
Review
Pathology
Christopher Auger, Shingo Kajimura
Summary: Adipose tissue is not just an observer, but a complex endocrine organ and active participant in disease initiation and progression. Disruptions in biological processes within adipose can lead to metabolic disorders such as obesity and type 2 diabetes. Despite progress in understanding adipose tissue function and dysfunction, few diseases are treated by targeting maladaptation in adipose, which is often overlooked.
ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE
(2023)
Article
Biochemistry & Molecular Biology
Ksenia Kuznetsova, Noemie M. Chabot, Martino Ugolini, Edlyn Wu, Manan Lalit, Haruka Oda, Yuko Sato, Hiroshi Kimura, Florian Jug, Nadine L. Vastenhouw
Summary: The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. Proteins of the transcriptional machinery come together to form these bodies, but the process is not well understood. In this study, two large, isolated, and long-lived transcription bodies in zebrafish embryos were studied to characterize the dynamics of transcription body formation. The clustering of transcription factors, particularly Nanog and Sox19b, play a crucial role in initiating transcription and organizing these bodies.
Article
Immunology
Wei Luo, Julia Z. Z. Adamska, Chunfeng Li, Rohit Verma, Qing Liu, Thomas Hagan, Florian Wimmers, Shakti Gupta, Yupeng Feng, Wenxia Jiang, Jiehao Zhou, Erika Valore, Yanli Wang, Meera Trisal, Shankar Subramaniam, Timothy F. Osborne, Bali Pulendran
Summary: Our previous study showed that the sterol regulatory binding protein (SREBP) pathway is associated with humoral immune response. We generated mice with specific deletion of SCAP, an essential regulator of SREBP signaling, in B cells or CD11c(+) antigen-presenting cells (APCs). Deletion of SCAP in CD11c(+) APCs had no impact on immune responses, whereas SREBP signaling in B cells was crucial for antibody responses and the development of immune cells. These studies reveal the regulatory role of sterol metabolism in humoral immunity.
Article
Cell & Tissue Engineering
Hiroki Ozawa, Azusa Kambe, Kodai Hibi, Satoshi Murakami, Akira Oikawa, Tetsuya Handa, Katsunori Fujiki, Ryuichiro Nakato, Katsuhiko Shirahige, Hiroshi Kimura, Nobuaki Shiraki, Shoen Kume
Summary: Human induced pluripotent stem cells (iPSCs) require high levels of methionine (Met) for maintaining pluripotency. Met deprivation leads to decreased levels of intracellular S-adenosyl-methionine (SAM), triggering differentiation and apoptosis of undifferentiated cells. Short-term Met deprivation affects the pluripotency network through epigenetic modifications, specifically on histone H3 trimethylation at lysine 4 (H3K4me3). The transcription start site (TSS) region of genes involved in transforming growth factor beta pathway, cholesterol biosynthetic process, as well as key pluripotent genes NANOG and POU5F1, are specifically affected by Met deprivation. Upon differentiation, loss of H3K27me3 occurs in many endodermal genes, leading to their activation and switching from a bivalent to a monovalent state (H3K4me3).
Article
Chemistry, Analytical
Junya Adachi, Haruka Oda, Toshiaki Fukushima, Beni Lestari, Hiroshi Kimura, Hiroka Sugai, Kentaro Shiraki, Rei Hamaguchi, Kohei Sato, Kazushi Kinbara
Summary: Cell-imaging methods with functional fluorescent probes are widely used for evaluating physical parameters in cellular microenvironments. In this study, we developed viscosity-responsive fluorescent probes that are not dependent on the twisted intramolecular charge transfer (TICT) process. These probes showed enhanced fluorescence as the viscosity increased, allowing specific visualization of dense organelles in living cells under washout-free conditions. This research provides a new direction for developing functional fluorescent probes targeting dense organelles.
ANALYTICAL CHEMISTRY
(2023)
Article
Endocrinology & Metabolism
Melia Granath-Panelo, Anna Krook, Jared Rutter, Shingo Kajimura
Summary: The field of bioenergetics is expanding rapidly with new discoveries and potential therapeutic targets. The 2023 Keystone symposium on 'Bioenergetics in Health and Disease', jointly held with the symposium 'Adipose Tissue: Energizing Good Fat', featured a lineup of influential researchers who shared their insights.
NATURE REVIEWS ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tomohiro Suzuki, Tetsuro Komatsu, Hiroshi Shibata, Akiko Tanioka, Diana Vargas, Reika Kawabata-Iwakawa, Fumihito Miura, Shinnosuke Masuda, Mayuko Hayashi, Kyoko Tanimura-Inagaki, Sumiyo Morita, Junki Kohmaru, Koji Adachi, Masayuki Tobo, Hideru Obinata, Tasuku Hirayama, Hiroshi Kimura, Juro Sakai, Hideko Nagasawa, Hideyuki Itabashi, Izuho Hatada, Takashi Ito, Takeshi Inagaki
Summary: Iron is essential for rewriting of epigenetic marks during adipocyte differentiation. Iron supply, mediated by lysosome-mediated ferritinophagy, plays a crucial role in the early stage of adipocyte differentiation. Iron deficiency during this period suppresses subsequent terminal differentiation and is associated with demethylation of repressive histone marks and DNA in the genomic regions of adipocyte differentiation-associated genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jin-Seon Yook, Zachary H. Taxin, Bo Yuan, Satoshi Oikawa, Christopher Auger, Beste Mutlu, Pere Puigserver, Sheng Hui, Shingo Kajimura
Summary: This study identified a crucial regulatory node in liver mitochondria that can affect fasting-induced gluconeogenesis and energy homeostasis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Haruka Oda, Yuko Sato, Shigehiro A. Kawashima, Yusuke Fujiwara, Mate Palfy, Edlyn Wu, Nadine L. Vastenhouw, Motomu Kanai, Hiroshi Kimura
Summary: Filamentous actin (F-actin) in the cytoplasm plays a crucial role in cell regulation, and recent studies have discovered its association with various functions in the nucleus. By live imaging of zebrafish embryos, it was shown that F-actin accumulates in nuclei during the interphase and reaches a peak during the prophase. Even after the breakdown of the nuclear envelope, patches of F-actin remain near the condensing chromosomes. This accumulation of F-actin in the nucleus may contribute to proper mitotic progression in zebrafish embryos.
Article
Radiology, Nuclear Medicine & Medical Imaging
Sonam Vadera, Timothy Osborne, Vikas Shah, James A. Stephenson
Summary: This study evaluated the use of vertebral CT attenuation measures to predict osteoporosis in a British population. The findings suggest that routine abdominal CT can be used as an opportunistic screening method for osteoporosis without additional cost or radiation exposure. The thresholds identified in this study are comparable to previous studies in other populations and can guide further investigation.
INSIGHTS INTO IMAGING
(2023)
Review
Endocrinology & Metabolism
Yoshihiro Matsumura, Fan-Yan Wei, Juro Sakai
Summary: Epitranscriptomic modifications, recently discovered post-transcriptional RNA modifications, have a profound impact on gene expression by regulating RNA stability, localization, and decoding efficiency. Genetic variations or environmental perturbations of epitranscriptome modifiers are associated with obesity and metabolic diseases. The epitranscriptome is closely linked to the epigenome, and can also affect organismal phenotypes in the next generation.
Article
Biochemistry & Molecular Biology
Hiroshi Ochiai, Hiroaki Ohishi, Yuko Sato, Hiroshi Kimura
Summary: Higher-order genomic structures and the formation of condensates around genes have been found to play important roles in regulating gene expression. Recent advancements in technology allow for the visualization of the dynamic spatiotemporal relationship between these structures and transcriptional activity in living cells.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Letter
Multidisciplinary Sciences
Jin-Seon Yook, Zachary H. Taxin, Satoshi Oikawa, Masanori Fujimoto, Shingo Kajimura
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Correction
Biochemical Research Methods
Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Shoko Sato, Masaru Nakao, Naoki Goto, Hitoshi Kurumizaka, Yasuyuki Ohkawa, Hiroshi Kimura