Review
Cell Biology
Yuki Fujita, Toshihide Yamashita
Summary: Microglia are resident immune cells in the CNS that exhibit diversity in morphology, density, gene expression profiles, and functions. Recent studies have shown that microglia can alter their gene expression profiles in response to different contexts, such as developmental stages and disease progression. Epigenetic changes, including histone modifications and DNA methylation, play a key role in regulating gene expression and cellular state in microglia, potentially leading to advances in therapeutic approaches for diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Trisha A. Macrae, Miguel Ramalho-Santos
Summary: The study reveals a regulatory axis between the deubiquitinase Usp9x and PRC2 that is critical for self-renewal of mouse embryonic stem cells. Different levels of Usp9x lead to distinct chromatin and transcriptional patterns in ES cells, reminiscent of different developmental stages. Deletion of Usp9x in post-implantation embryos results in derepression of genes and morphological abnormalities, suggesting a crucial role of Usp9x-PRC2 axis in development.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Zhiqi Sun, Filippo M. Cernilogar, Helena Horvatic, Assa Yeroslaviz, Zeinab Abdullah, Gunnar Schotta, Veit Hornung
Summary: Fibrosis is associated with chronic inflammation due to sustained activation of myofibroblasts and excessive extracellular matrix deposition. This study reveals that b1 integrin links fibrotic signaling to RIPK3-driven inflammation through a novel mode of action involving the chromatin-remodeling factor CHD4.
Article
Multidisciplinary Sciences
Hua Yu, Zhen Sun, Tianyu Tan, Hongru Pan, Jing Zhao, Ling Zhang, Jiayu Chen, Anhua Lei, Yuqing Zhu, Lang Chen, Yuyan Xu, Yaxin Liu, Ming Chen, Jinghao Sheng, Zhengping Xu, Pengxu Qian, Cheng Li, Shaorong Gao, George Q. Daley, Jin Zhang
Summary: The nucleolus plays a crucial role in regulating the fate transition of mouse embryonic stem cells to 2 cell-stage embryo-like cells through maintaining nucleolar integrity and reshaping the 3D chromatin structure. Additionally, rRNA biogenesis is essential for the transition from 2-cell to 4-cell stage during murine pre-implantation embryo development.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Rodrigo O. de Castro, Agustin Carbajal, Luciana Previato de Almeida, Victor Goitea, Courtney T. Griffin, Roberto J. Pezza
Summary: Testis development and germ cell production rely on spermatogonia stem cells. The Chd4 chromatin remodeling complex is important for gene expression and maintenance of spermatogonia stem cells during gamete development.
EPIGENETICS & CHROMATIN
(2022)
Article
Medicine, Research & Experimental
Emmanouil Stylianakis, Jackson Ping Kei Chan, Pui Pik Law, Yi Jiang, Sanjay Khadayate, Mohammad Mahdi Karimi, Richard Festenstein, Jean-Baptiste Vannier
Summary: We found that mouse HP1 & gamme; plays a crucial role in telomere function by regulating the transcription of telomere factors and TERRAs, which has profound effects on telomere stability.
Article
Biochemistry & Molecular Biology
Yu Wei Zhang, Lingxi Chen, Shuai Cheng Li
Summary: Topologically associated domains (TADs) are crucial structural units in chromatin. RNA-associated interactions (RAIs) have been found to be associated with TAD-like domains (TLDs). A domain detection algorithm called SuperTLD was proposed to decode hierarchical TLDs from RAIs. Comparison between TLDs and TADs identified from Hi-C datasets showed moderate similarity in hierarchies and higher similarity in finer structures. Enrichment analysis revealed the novelty of TLDs in terms of boundaries and epigenetic characteristics, suggesting a close relationship between TLDs and gene regulation.
NUCLEIC ACIDS RESEARCH
(2022)
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)
Article
Neurosciences
Paul W. Frazel, David Labib, Theodore Fisher, Ran Brosh, Nicolette Pirianian, Anne Marchildon, Jef D. Boeke, Valentina Fossati, Shane A. Liddelow
Summary: Researchers used single-cell/single-nucleus RNA sequencing to analyze the differentiation of macroglia in the brain and spinal cord. They identified candidate genes involved in glial cell fate specification and observed heterogeneous expression of astrocyte surface markers during differentiation. The researchers also optimized a mouse astrocyte differentiation protocol and explored potential genomic regulatory sites mediating glial differentiation using multi-omic analysis.
NATURE NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Aditi Singh, Xyrus X. Maurer-Alcala, Therese Solberg, Lilia Haeussermann, Silvan Gisler, Michael Ignarski, Estienne C. Swart, Mariusz Nowacki
Summary: Recruiting the chromatin remodeler ISWI1 facilitates IES recognition and precise excision in Paramecium, ensuring efficient DNA elimination.
Article
Multidisciplinary Sciences
Shuyan Ji, Fengling Chen, Paula Stein, Jiacheng Wang, Ziming Zhou, Lijuan Wang, Qing Zhao, Zili Lin, Bofeng Liu, Kai Xu, Fangnong Lai, Zhuqing Xiong, Xiaoyu Hu, Tianxiang Kong, Feng Kong, Bo Huang, Qiujun Wang, Qianhua Xu, Qiang Fan, Ling Liu, Carmen J. Williams, Richard M. Schultz, Wei Xie
Summary: OBOX, a PRD-like homeobox domain transcription factor family, is a key regulator of mouse zygotic genome activation and early embryogenesis. OBOX facilitates RNA polymerase II preconfiguration, leading to the transition of gene expression during early embryonic development.
Article
Cell Biology
Ming Kong, Yuwen Zhu, Jing Shao, Zhiwen Fan, Yong Xu
Summary: BRG1 deficiency in mice results in reduced processing and nuclear accumulation of SREBP in the liver, affecting lipid metabolism. BRG1 plays a crucial role in regulating SREBP by activating SCAP transcription, ultimately influencing SREBP target gene expression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Fadoua El Abdellaoui-Soussi, Paula S. Yunes-Leites, Dolores Lopez-Maderuelo, Fernando Garcia-Marques, Jesus Vazquez, Juan Miguel Redondo, Pablo Gomez-del Arco
Summary: The sarcomere is essential for muscle contraction, and its transcriptional expression is regulated by Chd4/NuRD complex. Loss of Chd4 leads to aberrant expression of skeletal muscle genes in the heart, causing cardiac defects and arrhythmias. Identifying the transcription factors that recruit Chd4/NuRD will provide important insights into cardiac pathologies and potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Helen Hoffmeister, Simon Holzinger, Marie-Sofie Duerr, Astrid Bruckmann, Susanne Schindler, Regina Groebner-Ferreira, Reinhard Depping, Gernot Laengst
Summary: Chromatin remodeling enzymes are essential for genome regulation, and the nuclear import of the human CHD4 protein is characterized in this study. It is shown that CHD4 enters the nucleus through importin-alpha proteins (1, 5, 6 and 7) independently of importin beta 1. Importin alpha 1 directly interacts with a specific motif in CHD4, but mutating this motif only leads to a partial reduction in nuclear localization, suggesting the existence of additional import mechanisms. Furthermore, CHD4 is associated with NuRD core subunits in the cytoplasm, indicating assembly of the NuRD complex before nuclear import. We propose that CHD4 is dragged into the nucleus through a 'piggyback' mechanism using the import signals of the associated NuRD subunits.
JOURNAL OF CELL SCIENCE
(2023)
Article
Cell Biology
Zachary L. Robbe, Wei Shi, Lauren K. Wasson, Angel P. Scialdone, Caralynn M. Wilczewski, Xinlei Sheng, Austin J. Hepperla, Brynn N. Akerberg, William T. Pu, Ileana M. Cristea, Ian J. Davis, Frank L. Conlon
Summary: This study investigated how CHD4/NuRD is localized to specific cardiac target genes by coupling a bioinformatics-based approach with mass spectrometry analyses. They demonstrated that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development, providing new insights into how mutations in the CHD4 protein lead to cardiac-specific disease states.
GENES & DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Tomoko Yamada, Yue Yang, Pamela Valnegri, Ivan Juric, Armen Abnousi, Kelly H. Markwalter, Arden N. Guthrie, Abigail Godec, Anna Oldenborg, Ming Hu, Timothy E. Holy, Azad Bonni
Article
Biochemistry & Molecular Biology
Adam W. Clemens, Dennis Y. Wu, J. Russell Moore, Diana L. Christian, Guoyan Zhao, Harrison W. Gabel
Article
Biochemical Research Methods
Xiaoying Chen, Bo Zhang, Ting Wang, Azad Bonni, Guoyan Zhao
BMC BIOINFORMATICS
(2020)
Article
Multidisciplinary Sciences
Yiran Hou, Hyung Joo Lee, Yujie Chen, Jiaxin Ge, Fujr Osman Ibrahim Osman, Anthony R. McAdow, Mayssa H. Mokalled, Stephen L. Johnson, Guoyan Zhao, Ting Wang
Article
Multidisciplinary Sciences
Sarah E. Smith, Xiaoying Chen, Lindsey M. Brier, Jonathan R. Bumstead, Nicholas R. Rensing, Alison E. Ringel, Haewon Shin, Anna Oldenborg, Jan R. Crowley, Annie R. Bice, Krikor Dikranian, Joseph E. Ippolito, Marcia C. Haigis, Thomas Papouin, Guoyan Zhao, Michael Wong, Joseph P. Culver, Azad Bonni
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Eric E. Ewan, Oshri Avraham, Dan Carlin, Tassia Mangetti Goncalves, Guoyan Zhao, Valeria Cavalli
Summary: Regeneration failure after SCI is partly due to the lack of a pro-regenerative response in injured sensory neurons, with the response being less sustained compared to nerve injury. Decreased expression of lipid metabolism-related genes after SCI, including fatty acid synthase, may restrict axon regenerative capacity.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Wolfgang Pita-Thomas, Tassia Mangetti Goncalves, Ajeet Kumar, Guoyan Zhao, Valeria Cavalli
Summary: The study identified transcription factors like CREB with key roles in promoting axon regeneration in embryonic RGCs, and highlighted the importance of CREB/ATF binding motifs in regulating axon regeneration. These findings emphasize that transcription factors associated with developmental axon growth can stimulate axon regeneration in mature RGCs.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Naveen C. Reddy, Shahriyar P. Majidi, Lingchun Kong, Mati Nemera, Cole J. Ferguson, Michael Moore, Tassia M. Goncalves, Hai-Kun Liu, James A. J. Fitzpatrick, Guoyan Zhao, Tomoko Yamada, Azad Bonni, Harrison W. Gabel
Summary: This study reveals that CHD7 promotes chromatin accessibility and enhancer activity in granule cell precursors, regulating morphogenesis of the cerebellar cortex, where its depletion triggers cerebellar polymicrogyria.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Oshri Avraham, Rui Feng, Eric Edward Ewan, Justin Rustenhoven, Guoyan Zhao, Valeria Cavalli
Summary: Peripheral nerve injuries lead to the appearance of a distinct subset of satellite glial cells in DRG and activation of the PPAR alpha signaling pathway, promoting axon regeneration. Central axon injuries do not trigger the same response, highlighting the potential for manipulating non-neuronal cells to promote functional recovery after CNS injuries or disease.
Article
Multidisciplinary Sciences
Xiaoying Chen, Yanhua Du, Gerard Joey Broussard, Mikhail Kislin, Carla M. Yuede, Shuwei Zhang, Sabine Dietmann, Harrison Gabel, Guoyan Zhao, Samuel S. -H. Wang, Xiaoqing Zhang, Azad Bonni
Summary: Cellular diversification of Purkinje neurons and their transcriptomic features play a crucial role in motor learning. Plcb4(+) Purkinje neurons exhibit robust plasticity of gene expression and are essential for associative learning. Knockout of Fgfr2 in Plcb4(+) Purkinje neurons disrupts motor learning. This study provides insights into the diversity and function of Purkinje neurons in motor learning.
Article
Multidisciplinary Sciences
Sun-Ji Park, Yeawon Kim, Chuang Li, Junwoo Suh, Jothilingam Sivapackiam, Tassia M. Goncalves, George Jarad, Guoyan Zhao, Fumihiko Urano, Vijay Sharma, Ying Maggie Chen
Summary: Albuminuria is not only a symptom but also a cause of glomerular disease, leading to glomerulosclerosis and interstitial fibrosis. The study identifies CHOP and TXNIP as critical molecular linkers in albuminuria-induced kidney injury.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Jinbin Xu, Huifangjie L. Farsad, Yiran Hou, Kia Barclay, Ben Anthony Lopez, Shinnosuke Yamada, Ibrahim Olabayode Saliu, Yiming Shi, William C. Knight, Randall J. Bateman, Tammie L. S. Benzinger, Jason J. Yi, Qingyun Li, Ting Wang, Joel S. Perlmutter, John C. Morris, Guoyan Zhao
Summary: Zhao et al. discovered evolutionarily conserved astrocyte and microglia subpopulations shared across multiple brain regions, revealing similarities and differences in AD and PD glia and regional variance linked to AD pathology and neurodegeneration. Their analysis identified commonalities between AD and PD astrocytes and unique transcriptomic changes in microglia for each disorder. They also delineated undescribed subpopulations of medium spiny neurons (MSNs) and provided neuronal transcriptomic profiles suggesting disease-specific changes and selective vulnerability.