Article
Microbiology
Qizhao Ma, Yangyang Pan, Yang Chen, Shuxing Yu, Jun Huang, Yaqi Liu, Tao Gong, Jing Zou, Yuqing Li
Summary: The study elucidated the important role of lysine acetylation in bacteria by identifying and characterizing ActG, a GNAT family member that catalyzes the acetylation of GtfB and GtfC in S. mutans, subsequently affecting EPS synthesis and biofilm formation, while also reducing cariogenicity in a rat caries model. This provides insight into the impact of lysine acetylation on bacterial virulence and pathogenicity by regulating protein functions and physiological processes.
Article
Medicine, Research & Experimental
Jianjun Hou, Shaobing Yang, Ying Guo, Ning Yan, Shaobin Jia
Summary: The RNA-binding capacity of FUS in atherosclerosis and its impact on gene expression and alternative splicing were investigated. Knockdown of FUS significantly affected gene expression in human umbilical vein endothelial cells (HUVECs) and extensively regulated alternative splicing events. Functional analysis revealed its involvement in cell cycle and cell population proliferation pathways.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2023)
Article
Microbiology
Qizhao Ma, Yangyang Pan, Yang Chen, Shuxing Yu, Jun Huang, Yaqi Liu, Tao Gong, Qiong Zhang, Qun Sun, Jing Zou, Yuqing Li
Summary: The article investigates the impact of lysine acetylation on bacterial virulence factors, particularly in Streptococcus mutans, and focuses on the acetylation of lactate dehydrogenase (LDH). The acetyltransferase ActA was found to inhibit LDH enzymatic activity through acetylation, affecting the cariogenicity of S. mutans.
Article
Biochemistry & Molecular Biology
Anna Ostendorp, Steffen Ostendorp, Yuan Zhou, Zoe Chaudron, Lukas Wolffram, Khadija Rombi, Linn von Pein, Sven Falke, Cy M. Jeffries, Dmitri I. Svergun, Christian Betzel, Richard J. Morris, Friedrich Kragler, Julia Kehr
Summary: Long-distance RNA transport via the phloem is crucial for communication between different plant tissues. In this study, the phloem-associated RNA chaperone-like (PARCL) protein was characterized and its role in RNA binding and condensate formation was investigated. The results suggest that the function and structure of PARCL can be regulated by modifications.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Plant Sciences
Daniel Neusius, Laura Kleinknecht, Jing Tsong Teh, Matthias Ostermeier, Simon Kelterborn, Jurgen Eirich, Peter Hegemann, Iris Finkemeier, Alexandra-Viola Bohne, Joerg Nickelsen
Summary: The dihydrolipoamide acetyltransferase subunit DLA2 of the chloroplast pyruvate dehydrogenase complex (cpPDC) in the green alga Chlamydomonas reinhardtii plays important roles in carbon metabolism and D1 synthesis. By forming a ribonucleoprotein particle with psbA mRNA, DLA2 is involved in the synthesis of D1 protein in the photosystem II reaction center. Acetylation of DLA2 induces its release from cpPDC and promotes its functional shift towards RNA binding.
Article
Microbiology
Min Jia, Xuanyi Chen, Xuetao Shi, Yiling Fang, Yangnan Gu
Summary: Plant karyopherins have a noncanonical chaperoning activity that modulates the nuclear condensation of a conserved splicing regulatory complex to coordinate plant immune activation.
CELL HOST & MICROBE
(2023)
Review
Biochemical Research Methods
Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther
Summary: RNA localization is important for spatial translation regulation, and this review discusses its molecular mechanisms, experimental techniques, and machine learning-based prediction tools. The three main molecular mechanisms controlling RNA localization to distinct cellular compartments, including directed transport, mRNA degradation protection, and diffusion/local entrapment, are reviewed. Advances in experimental methods provide ample data resources for the design of powerful machine learning models in RNA localization prediction. The review also covers publicly available predictive tools, serving as a guide for users and encouraging the development of more effective prediction models. Lastly, an overview of multimodal learning is presented as a potential new avenue for RNA localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Bo-Kun Yin, David Lazaro, Zhao-Qi Wang
Summary: Adult hippocampal neurogenesis is essential for central nervous system function, including memory, cognition, and emotions. The deficiency of adult neural stem cells (aNSCs) negatively affects the integrity and function of neurons in the adult brain. Histone acetyltransferase (HAT) and histone deacetylase (HDAC) play important roles in neurogenesis and gene regulation. Trrap, an adapter for HAT complexes, is required for Sp1 transcriptional control and microtubule dynamics in neurons. Trrap deletion impairs aNSC self-renewal and differentiation, and the acetylation pattern at K639 determines Sp1's role in adult neurogenesis regulation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Mahmood Hassan Dalhat, Hani Choudhry, Mohammad Imran Khan
Summary: Recently, we found that NAT10 plays a role in regulating fatty acid metabolism and also noticed its potential involvement in ferroptosis, a negatively enriched pathway in NAT10-depleted cancer cells. Through experiments, we showed that NAT10 depletion resulted in downregulation of ferroptosis-related genes, decreased cystine uptake and reduced GSH levels, as well as elevated ROS and lipid peroxidation levels in cancer cells. Mechanistically, NAT10 stabilizes SLC7A11 mRNA transcripts to avoid oxidative stress and initiate ferroptosis. These findings suggest that NAT10 acts as an epitranscriptomic regulator of the ferroptosis pathway.
Article
Cell Biology
Xueju Wei, Yue Huo, Jingnan Pi, Yufeng Gao, Shuan Rao, Manman He, Qinglv Wei, Peng Song, Yiying Chen, Dongxu Lu, Wei Song, Junbo Liang, Lingjie Xu, Haixia Wang, Guolin Hong, Yuehong Guo, Yanmin Si, Jiayue Xu, Xiaoshuang Wang, Yanni Ma, Shuyang Yu, Dongling Zou, Jing Jin, Fang Wang, Jia Yu
Summary: Wei et al. find that cytoplasmic METTL3 promotes tumour progression by facilitating the translation of epigenetic factor mRNAs without m(6)A modification. This study suggests an m(6)A-independent mechanism for METTL3 in cancer development, highlighting its significance in oncogenesis.
NATURE CELL BIOLOGY
(2022)
Article
Oncology
Shuang Tao, Shu-Juan Xie, Li-Ting Diao, Guo Lv, Ya-Rui Hou, Yan-Xia Hu, Wan-Yi Xu, Bin Du, Zhen-Dong Xiao
Summary: The study reveals that CCDC137 is upregulated in HCC and correlates with poor clinical outcomes. CCDC137 binds with FOXM1, JTV1, LASP1, and FLOT2 mRNAs, promoting their cytoplasmic localization and protein expression, subsequently activating the AKT signaling pathway and promoting HCC progression.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Article
Multidisciplinary Sciences
Saumyak Mukherjee, Lars V. Schaefer
Summary: This study investigates the thermodynamic contributions of water and protein molecules to the formation of FUS protein condensates through atomistic molecular dynamics simulations. The results reveal that solvation entropy and protein-protein interactions are the main driving forces for the formation of FUS condensates.
NATURE COMMUNICATIONS
(2023)
Review
Neurosciences
Clara Tejido, Donya Pakravan, Ludo Van Den Bosch
Summary: Mutations in the FUS gene lead to amyotrophic lateral sclerosis (ALS-FUS) with unclear pathogenic mechanisms regarding the mislocalization and aggregation of RNA binding protein FUS. Therapies targeting post-translational modifications, particularly acetylation, are being explored as potential treatments for ALS by influencing the dynamics of RBPs. Inhibition of histone deacetylases (HDACs) may play a role in promoting FUS maintenance in the nucleus and affecting its incorporation into pathological inclusions.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Ru-Xuan Tsai, Kuo-Chen Fang, Po-Cheng Yang, Yu-Hung Hsieh, I-Tien Chiang, Yunfei Chen, Hun-Goo Lee, Jeannie T. Lee, Hsueh-Ping Catherine Chu
Summary: TERRA is an RNA molecule that interacts with the chromatin remodeler ATRX and plays a role in regulating genome stability and transcription. It maintains the stability of DNA G-quadruplex structures and prevents ATRX from binding to subtelomeric regions, thereby repressing H3K9me3 formation. Depletion of TERRA leads to a decrease in G-quadruplex abundance at transcription start sites (TSS), which is associated with increased ATRX occupancy and differential gene expression. Loss of ATRX alleviates the gene repression caused by TERRA depletion, while knockdown of TERRA diminishes DNA G-quadruplex signals and silencing of ATRX increases G-quadruplex formation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cardiac & Cardiovascular Systems
Vagner Oliveira Carvalho Rigaud, Robert C. Hoy, Justin Kurian, Clare Zarka, Michael Behanan, Isabella Brosious, Jennifer Pennise, Tej Patel, Tao Wang, Jaslyn Johnson, Lindsay M. Kraus, Sadia Mohsin, Steven R. Houser, Mohsin Khan
Summary: This study identifies a novel role for RNA-binding protein LIN28a in cardiac repair after injury. LIN28a reprograms cardiomyocyte metabolism, enhances the persistence of regenerative mononuclear diploid cardiomyocytes, and promotes proreparative processes in the injured heart.
Article
Clinical Neurology
Jozsef Gal, Lisha Kuang, Kelly R. Barnett, Brian Z. Zhu, Susannah C. Shissler, Konstantin V. Korotkov, Lawrence J. Hayward, Edward J. Kasarskis, Haining Zhu
ACTA NEUROPATHOLOGICA
(2016)
Article
Multidisciplinary Sciences
Kristy R. Stengel, Kelly R. Barnett, Jing Wang, Qi Liu, Emily Hodges, Scott W. Hiebert, Srividya Bhaskara
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Biochemistry & Molecular Biology
Jozsef Gal, Jing Chen, Kelly R. Barnett, Liuqing Yang, Erin Brumley, Haining Zhu
JOURNAL OF BIOLOGICAL CHEMISTRY
(2013)
Article
Biochemistry & Molecular Biology
Jozsef Gal, Jing Chen, Duck-Young Na, Laura Tichacek, Kelly R. Barnett, Haining Zhu
MOLECULAR AND CELLULAR BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Kelly R. Barnett, Benjamin E. Decato, Timothy J. Scott, Tyler J. Hansen, Bob Chen, Jonathan Attalla, Andrew D. Smith, Emily Hodges
Article
Biochemical Research Methods
Lindsey N. Guerin, Kelly R. Barnett, Emily Hodges
Summary: The epigenome is multidimensional, involving molecular components working on different levels to control transcriptional output. ATAC-Me is an integrated method for probing DNA methylation and chromatin accessibility from a single DNA fragment library, suitable for time course studies to capture chromatin and DNA methylation dynamics.
Article
Hematology
Daniel C. Ferguson, J. Robert McCorkle, Kelly R. Barnett, Erik J. Bonten, Brennan P. Bergeron, Kashi Raj Bhattarai, Wenjian Yang, Colton Smith, Baranda S. Hansen, Richa Bajpai, Qian Dong, Robert J. Autry, Yoshihiro Gocho, Jonathan D. Diedrich, Kristine R. Crews, Shondra M. Pruett-Miller, Kathryn G. Roberts, Wendy Stock, Charles G. Mullighan, Hiroto Inaba, Sima Jeha, Ching-Hon Pui, Jun J. Yang, Mary Relling, William E. Evans, Daniel Savic
Summary: The study identified LASP response genes in ALL cell lines and patient samples, revealed the role of the ATF4 transcription factor in ALL cell lines, and highlighted the significance of SLC7A11 in LASP resistance and sensitivity.
Article
Oncology
Brennan P. Bergeron, Jonathan D. Diedrich, Yang Zhang, Kelly R. Barnett, Qian Dong, Daniel C. Ferguson, Robert J. Autry, Wenjian Yang, Baranda S. Hansen, Colton Smith, Kristine R. Crews, Yiping Fan, Ching-Hon Pui, Shondra M. Pruett-Miller, Mary Relling, Jun J. Yang, Chunliang Li, William E. Evans, Daniel Savic
Summary: Glucocorticoids (GCs), as a common drug in the treatment of childhood acute lymphoblastic leukemia (ALL), face challenges of drug resistance. This study investigated the gene regulatory response to GCs in ALL cell lines and discovered disruptions in cis-regulatory elements that are associated with GC resistance. Integrating these findings with genetic and epigenetic datasets from primary ALL cells, the study also identified cis-regulatory disruptions that impact GC resistance in childhood ALL.
Article
Multidisciplinary Sciences
Xujie Zhao, Ping Wang, Jonathan D. Diedrich, Brandon Smart, Noemi Reyes, Satoshi Yoshimura, Jingliao Zhang, Wentao Yang, Kelly Barnett, Beisi Xu, Zhenhua Li, Xin Huang, Jiyang Yu, Kristine Crews, Allen Eng Juh Yeoh, Marina Konopleva, Chia-Lin Wei, Ching-Hon Pui, Daniel Savic, Jun J. Yang
Summary: FLT3 is overexpressed in ZNF384-rearranged ALL, with exclusive activation of an intergenic enhancer element at the FLT3 locus and global enrichment of active enhancers within ZNF384 binding sites. Downregulation of ZNF384 decreases FLT3 activation and sensitizes ALL cells to FLT3 inhibitor gilteritinib. Moreover, gilteritinib shows significant anti-leukemia efficacy as a monotherapy in patient-derived xenograft models of ZNF384-rearranged ALL.
NATURE COMMUNICATIONS
(2022)