Article
Cell Biology
Joanna Moronczyk, Agnieszka Braszewska, Barbara Wojcikowska, Karolina Chwialkowska, Katarzyna Nowak, Anna M. Wojcik, Miroslaw Kwasniewski, Malgorzata D. Gaj
Summary: Somatic embryogenesis (SE) is a complex process involving the reprogramming of plant somatic cells, and histone acetylation plays a crucial role in regulating the expression of key transcription factor genes during SE. This study investigated the global and gene-specific changes in histone acetylation in Arabidopsis explants undergoing SE and identified H3 and H4 acetylation as potential regulators of critical TF genes. The findings also revealed that HDA19 negatively affects SE by regulating LEC1, LEC2, and BBM, and provided evidence of HDA19's involvement in histone acetylation-mediated regulation of LEC2 during SE.
Article
Multidisciplinary Sciences
Tasniem Fetian, Brendan M. McShane, Nicole L. Horan, Donya N. Shodja, Jason D. True, Amber L. Mosley, Karen M. Arndt
Summary: Histone modifications coupled to transcription elongation play important roles in regulating gene expression. The Paf1 transcription elongation complex (Paf1C) interacts with the ubiquitin conjugase Rad6 through its histone modification domain (HMD), leading to H2BK123 ubiquitylation. The specific interface between a transcription elongation factor and a ubiquitin conjugase guides substrate selection during active gene expression.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Prajakta Tathe, K. V. S. Rammohan Chowdary, Krushna Chandra Murmu, Punit Prasad, Subbareddy Maddika
Summary: In this study, the researchers discovered that the tyrosine phosphatase SHP-1 can dephosphorylate histone H2B and plays a critical role in transcription. SHP-1 dephosphorylates H2B at tyrosine 121, promoting H2B ubiquitination and maintaining basal autophagic flux. This study reveals the importance of SHP-1-regulated modification of H2B in eukaryotic transcription.
Article
Multidisciplinary Sciences
Yoshihiro Matsumura, Ryo Ito, Ayumu Yajima, Rei Yamaguchi, Toshiya Tanaka, Takeshi Kawamura, Kenta Magoori, Yohei Abe, Aoi Uchida, Takeshi Yoneshiro, Hiroyuki Hirakawa, Ji Zhang, Makoto Arai, Chaoran Yang, Ge Yang, Hiroki Takahashi, Hitomi Fujihashi, Ryo Nakaki, Shogo Yamamoto, Satoshi Ota, Shuichi Tsutsumi, Shin-ichi Inoue, Hiroshi Kimura, Youichiro Wada, Tatsuhiko Kodama, Takeshi Inagaki, Timothy F. Osborne, Hiroyuki Aburatani, Koichi Node, Juro Sakai
Summary: The authors demonstrate that SETD5 forms a complex with NCoR-HDAC3 co-repressor to prevent histone acetylation of master adipogenic gene enhancers, while degradation of SETD5 leads to enhancer hyperacetylation and transition to an active state. Activation of the CDC20 co-activator of the ubiquitin ligase results in APC/C mediated degradation of SETD5, acting as a molecular switch that facilitates adipogenesis.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Fan Kou, Lei Wu, Yu Zheng, Yeran Yi, Zhenyu Ji, Ziqi Huang, Shiwei Guo, Lili Yang
Summary: This study reveals the critical role of HMGB1 in glycolysis and metastasis in LUAD, by attenuating H3K9ace and H3K27ace through physical interaction with SET and HAT1.
Article
Biochemistry & Molecular Biology
Fan Kou, Lei Wu, Yu Zheng, Yeran Yi, Zhenyu Ji, Ziqi Huang, Shiwei Guo, Lili Yang
Summary: This study found that in lung adenocarcinoma, the overexpression of HMGB1 is associated with tumor grade and poor survival. HMGB1 interacts physically with SET and HAT1 to suppress H3K9ace and H3K27ace acetylation, promoting glycolysis and metastasis.
Review
Biochemistry & Molecular Biology
Pin Zhao, Samiullah Malik
Summary: This review describes how phosphorylation affects the transcription activity and other functions of DNA/histone modifying enzymes. Although the phosphorylated sites of these enzymes have been classified and partially explained, further research is still needed to determine their relationship with disease-associated transcriptional regulation.
CELL AND BIOSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Anagh Ray, Preeti Khan, Ronita Nag Chaudhuri
Summary: The study highlights the importance of lysine acetylation in maintaining chromatin structure and function, specifically focusing on the role of H4K16 acetylation in regulating the expression of constitutive genes. Deacetylation of H4K16 is associated with hypoacetylation of H4K12 and H3K9, along with hyperacetylation of H3K56, creating a chromatin landscape conducive for transcription of constitutive genes.
Article
Oncology
Xiaohui Pan, Wenxin Zhang, Longsheng Wang, Hongjie Guo, Mingming Zheng, Honghai Wu, Qinjie Weng, Qiaojun He, Ling Ding, Bo Yang
Summary: Recent studies have shown that Krupple-like factor 12 (KLF12) plays a crucial role in cancer-associated processes in non-small cell lung cancer (NSCLC), including proliferation, apoptosis, and metastasis. KLF12 is positively correlated with programmed death-ligand 1 (PD-L1) expression and can bind to the CACCC motif of the PD-L1 promoter to promote transcription. Knockout of KLF12 inhibits tumor growth and enhances infiltration of CD8(+) T cells in immunocompetent mice.
MOLECULAR ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Daniel Schator, Sonia Mondino, Jeremy Berthelet, Cristina Di Silvestre, Mathilde Ben Assaya, Christophe Rusniok, Fernando Rodrigues-Lima, Annemarie Wehenkel, Carmen Buchrieser, Monica Rolando
Summary: Legionella pneumophilia secretes more than 300 effectors, including RomA and LphD, via a type IV secretion system. RomA methylates histone H3 at K14 to counteract host immune responses, while LphD deacetylates H3K14 to work synergistically with RomA. The two effectors target host chromatin and bind the HBO1 histone acetyltransferase complex to regulate histone modifications.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Fengyue Zhao, Mande Xue, Huairen Zhang, Hui Li, Ting Zhao, Danhua Jiang
Summary: Plants can adjust their development and morphology in response to temperature changes through a process called thermomorphogenesis. The regulation of gene expression reprogramming in this process involves the eviction of a histone variant H2A.Z by INO80 and the deposition of another histone variant H3.3. These processes are coordinated and play a crucial role in gene activation induced by high temperature.
Article
Biology
Alicia Tapias, David Lazaro, Bo-Kun Yin, Seyed Mohammad Mahdi Rasa, Anna Krepelova, Erika Kelmer Sacramento, Paulius Grigaravicius, Philipp Koch, Joanna Kirkpatrick, Alessandro Ori, Francesco Neri, Zhao-Qi Wang
Summary: The study reveals the importance of TRRAP for neuroprotection and the network connecting TRRAP, HAT, and SP1 in regulating microtubule dynamics.
Article
Plant Sciences
Peng Feng, Xiaohuan Sun, Xiaodong Liu, Yuqiu Li, Qi Sun, Haoran Lu, Minglong Li, Xiaodong Ding, Yingshan Dong
Summary: The study found that the interaction between GsMYST1 and GsSnRK1 can regulate the expression of the COR15B gene through acetylation. Additionally, it was demonstrated that salt stress can activate GsSnRK1, which subsequently phosphorylates GsMYST1 to enhance its acetyltransferase activity, potentially promoting target gene expression through epigenetics.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Seung Hee Choi, Woo Seok Ahn, Myoung Hui Lee, Da Mon Jin, Areum Lee, Eun Yee Jie, Su Ji Ju, Sung Ju Ahn, Suk Weon Kim
Summary: Whole-plant regeneration through plant tissue culture is a complex process regulated by genetic and environmental factors. Epigenetic regulation has been found to play a crucial role in plant cell differentiation and pluripotency. In this study, the effects of epigenetic regulators on lettuce and tobacco protoplasts were tested, and it was found that these chemicals promoted cell division and callus formation. These findings suggest that these chemicals can be used to enhance plant regeneration and crop improvement.
Article
Cell Biology
Fabien Moretto, N. Ezgi Wood, Minghao Chia, Cai Li, Nicholas M. Luscombe, Folkert J. van Werven
Summary: In this study, it is found that the transcription levels of the noncoding region IRT2 in S. cerevisiae can regulate opposing chromatin and transcription states, thus affecting the expression of the IME1 promoter and meiotic entry. The findings illustrate how intergenic transcription is crucial in controlling local chromatin state, gene expression, and cell fate outcomes.
Article
Developmental Biology
Anna B. Osipovich, Karrie D. Dudek, Emily Greenfest-Allen, Jean-Philippe Cartailler, Elisabetta Manduchi, Leah Potter Case, Eunyoung Choi, Austin G. Chapman, Hannah W. Clayton, Guoqiang Gu, Christian J. Stoeckert, Mark A. Magnuson
Summary: This study used gene co-expression network analysis from 11 murine cell populations to identify specific gene expression patterns during pancreatic development, particularly focusing on zinc finger protein genes preferentially expressed during endocrine specification and beta-cell maturation. Further experimental analysis validated the key roles of several ZFP genes in pancreatic development.
Article
Agriculture, Dairy & Animal Science
L. A. Lyons, R. M. Buckley, R. J. Harvey, Danielle Aberdein, Asa Ohlsson Andersson, Tomas F. Bergstrom, Adam R. Boyko, Margret L. Casal, Brian W. Davis, Ottmar Distl, N. Matthew Ellinwood, Oliver P. Forman, Edward Ginns, Daisuke Hasegawa, Vidhya Jagannathan, Isabel Hernandez, Maria Kaukonen, Emilie Leclerc, Tosso Leeb, Hannes Lohi, Mark A. Magnuson, Shrinivasrao P. Mane, John S. Munday, Alexandra N. Myers, Simon M. Peterson-Jones, Clare Rusbridge, Beth Shapiro, William F. Swanson, Rory J. Todhunter, Elizabeth A. Wilcox, Yoshihiko Yu
Summary: Tabby patterns in cats are influenced by at least three loci, including Tabby and Ticked loci. The Ticked locus on cat chromosome B1 is suggested to control the presence or absence of ticked patterns. Variant analysis identified candidate genes and variants associated with the Ticked locus, including Dickkopf Wnt Signaling Pathway Inhibitor 4 (DKK4) variants.
Article
Multidisciplinary Sciences
Francesca Genova, Simona Nonnis, Elisa Maffioli, Gabriella Tedeschi, Maria Giuseppina Strillacci, Michela Carisetti, Giuseppe Sironi, Francesca Anna Cupaioli, Noemi Di Nanni, Alessandra Mezzelani, Ettore Mosca, Christopher R. Helps, Peter A. J. Leegwater, Laetitia Dorso, Maria Longeri, Reuben M. Buckley, Danielle Aberdein, Paulo C. Alves, Asa Ohlsson Andersson, Gregory S. Barsh, Rebecca R. Bellone, Tomas F. Bergstrom, Adam R. Boyko, Jeffrey A. Brockman, Margret L. Casal, Marta G. Castelhano, Ottmar Distl, Nicholas H. Dodman, N. Matthew Ellinwood, Jonathan E. Fogle, Oliver P. Forman, Dorian J. Garrick, Edward Ginns, Bianca Haase, Jens Haggstrom, Robert J. Harvey, Daisuke Hasegawa, Isabel Hernandez, Marjo K. Hytonen, Maria Kaukonen, Christopher B. Kaelin, Tomoki Kosho, Emilie Leclerc, Teri L. Lear, Tosso Leeb, Ronald H. L. Li, Hannes Lohi, Mark A. Magnuson, Richard Malik, Shrinivasrao P. Mane, John S. Munday, William J. Murphy, Niels C. Pedersen, Simon M. Peterson-Jones, Max F. Rothschild, Clare Rusbridge, Beth Shapiro, Joshua A. Stern, William F. Swanson, Karen A. Terio, Rory J. Todhunter, Wesley C. Warren, Elizabeth A. Wilcox, Julia H. Wildschutte, Yoshihiko Yu, Leslie A. Lyons
Summary: The study utilized multi-omics analyses to explore unknown pathogenetic processes in Abyssinian cats with amyloidosis, revealing genomic variants, protein expression differences, and differential miRNA expression. The familial amyloid renal form is not a simple monogenic trait and amyloid deposition is triggered by a mix of proteins coded by wild-type genes. This form of amyloidosis in Abyssinian cats can be biochemically classified as AA amyloidosis.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Tiziana Sanavia, Chen Huang, Elisabetta Manduchi, Yanwen Xu, Prasanna K. Dadi, Leah A. Potter, David A. Jacobson, Barbara Di Camillo, Mark A. Magnuson, Christian J. Stoeckert, Guoqiang Gu
Summary: The study analyzed the global gene expression dynamics across six beta-cell developmental stages in mice, revealing the timing of important biological processes such as beta-cell developmental pathway deregulation, activation of molecular machineries for vesicle biosynthesis and transport, and glucose-induced Ca2+ influx. Temporal gene expression patterns were correlated with experimental GSIS, calcium influx, and insulin granule formation data, providing insights into the molecular components and biological mechanisms driving beta-cell maturation at different temporal stages. The findings suggest that genes associated with calcium-mediated processes show increased expression across beta-cell stages, indicating the temporal acquisition of proper GSIS.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Karrie D. Dudek, Anna B. Osipovich, Jean-Philippe Cartailler, Guoquing Gu, Mark A. Magnuson
Summary: Insm1, Neurod1, and Pax6 are crucial for the formation and function of pancreatic endocrine cells. Knocking out these genes in mice showed varying impairments in the proliferation, survival, and differentiation of endocrine cells. Transcriptomic and functional enrichment analyses revealed unique contributions of each gene to the transcriptome and highlighted the involvement of genes related to mRNA metabolism, chromatin organization, and cell cycle regulation.
G3-GENES GENOMES GENETICS
(2021)
Article
Biology
Kathryn P. Trogden, Justin Lee, Kai M. Bracey, Kung-Hsien Ho, Hudson McKinney, Xiaodong Zhu, Goker Arpag, Thomas G. Folland, Anna B. Osipovich, Mark A. Magnuson, Marija Zanic, Guoqiang Gu, William R. Holmes, Irina Kaverina
Summary: The study reveals the important role of microtubules in regulating insulin secretion hot spots, where unstable microtubules activate dormant cells for secretion and promote functional heterogeneity of beta cells.
Article
Multidisciplinary Sciences
Linh T. Trinh, Anna B. Osipovich, Leesa Sampson, Jonathan Wong, Chris V. E. Wright, Mark A. Magnuson
Summary: The expression of Sox17 gene is crucial for the differentiation of both endothelial and endodermal cells. The study reveals that two evolutionarily conserved promoter regions (CRs) have different roles in regulating the Sox17 gene. Deletion of CR1 only has a modest effect on lympho-vasculogenesis, while deletion of CR2 impairs both vascular and endodermal development.
Editorial Material
Endocrinology & Metabolism
Mitchell A. Lazar, Mark A. Magnuson, Klaus H. Kaestner
Article
Multidisciplinary Sciences
Hui-Young Lee, Hye Rim Jang, Hui Li, Varman T. Samuel, Karrie D. Dudek, Anna B. Osipovich, Mark A. Magnuson, Jeffrey Sklar, Gerald I. Shulmane
Summary: This study found that knockout of the JAZF1 gene leads to early growth retardation and late onset insulin resistance. The experiment showed that Jazf1 KO mice had reduced plasma IGF-1 concentration, shorter stature in young mice, increased fat mass and reduced lean body mass in adult mice. Additionally, adult mice also exhibited muscle insulin resistance and increased plasma GH concentration. Gene set enrichment analysis identified a decrease in hepatocyte hepatic nuclear factor 4 alpha (HNF4α) in Jazf1 KO liver.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Kung-Hsien Ho, Anissa Jayathilake, Yagan Mahircan, Aisha Nour, Anna B. Osipovich, Mark A. Magnuson, Guoqiang Gu, Irina Kaverina
Summary: Glucose stimulation remodels microtubules to enhance insulin secretion in pancreatic beta-cells. CAMSAP2 binds to microtubule minus ends to stabilize them in cultured clonal cells. Knockdown of CAMSAP2 in primary beta-cells reduces insulin content and impairs glucose-stimulated insulin secretion, without affecting insulin vesicle releasability. Surprisingly, CAMSAP2 knockdown does not alter microtubule stability and exhibits a different localization pattern in primary beta-cells compared to insulinoma cells. CAMSAP2 primarily localizes to the Golgi apparatus in primary beta-cells and promotes efficient Golgi-ER trafficking to support insulin production and secretion.
Article
Cell & Tissue Engineering
Linh T. Trinh, Anna B. Osipovich, Bryan Liu, Shristi Shrestha, Jean-Philippe Cartailler, Christopher V. E. Wright, Mark A. Magnuson
Summary: During early embryogenesis, the transcription factor SOX17 plays a role in the formation of the hepato-pancreato-biliary system and vascular-hematopoietic emergence. Using a dual-color temporal lineage-tracing strategy combined with single-cell RNA sequencing, researchers analyzed cells from Sox17-expressing lineages and identified distinct cellular clusters from all 3 germ layers. Differential gene expression analysis revealed specialized subtypes of endothelial cells and subsets of hepatic, pancreatic, and biliary progenitors within the posterior foregut endoderm.