1
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Demeshkina NA, Ferré-D'Amaré AR. Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes. Cell Rep 2025; 44:115738. [PMID: 40413746 DOI: 10.1016/j.celrep.2025.115738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 03/14/2025] [Accepted: 05/02/2025] [Indexed: 05/27/2025] Open
Abstract
Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ∼200 nm cores embedded in a diffuse shell. We have developed large-scale purifications of budding yeast and mammalian (HEK293T cell) stress granule cores that do not rely on immunoprecipitation of candidate protein constituents. These unbiased preparations reveal that stress granule cores are discrete particles with variable size (average, 135 and 225 nm for yeast and human, respectively) and shape. Proteomics and transcriptomics demonstrate complex composition. The results of hybridization chain reaction fluorescence in situ hybridization (FISH) analyses in HEK293T cells are consistent with stress granule cores having heterogeneous composition, i.e., each stress granule core particle contains only a limited number of mRNA species. Biochemical purification now opens the way to mechanistic analysis of the heterogeneity and complexity of stress granules.
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Affiliation(s)
- Natalia A Demeshkina
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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2
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Harris SE, Hu Y, Bridges K, Cavazos FF, Martyr JG, Guzmán BB, Murn J, Aleman MM, Dominguez D. Dissecting RNA selectivity mediated by tandem RNA-binding domains. J Biol Chem 2025; 301:108435. [PMID: 40120682 PMCID: PMC12136788 DOI: 10.1016/j.jbc.2025.108435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 03/10/2025] [Accepted: 03/17/2025] [Indexed: 03/25/2025] Open
Abstract
RNA-protein interactions are pivotal to proper gene regulation. Many RNA-binding proteins possess multiple RNA-binding domains; however, how these domains interplay to select and regulate RNA targets remains poorly understood. Here, we investigate three multidomain proteins, Musashi-1, Musashi-2, and unkempt, which share a high degree of RNA specificity, a common feature across RNA-binding proteins. We used massively parallel in vitro assays with unprecedented depth with random or naturally derived RNA sequences and find that individual domains within a protein can have differing affinities, specificities, and motif spacing preferences. We conducted large scale competition assays between these proteins and determined how individual protein specificities and affinities influence competitive binding. Integration of binding and regulation in cells with in vitro specificities showed that target selection involves a combination of the protein intrinsic specificities described here, but cellular context is critical to drive these proteins to motifs in specific transcript regions. Finally, evolutionarily conserved RNA regions displayed evidence of binding multiple RBPs in cultured cells, and these RNA regions represent the highest affinity targets. This work emphasizes the importance of in vitro and in cultured cells studies to fully profile RNA-binding proteins and highlights the complex modes of RNA-protein interactions and the contributing factors in target selection.
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Affiliation(s)
- Sarah E Harris
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yue Hu
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kaitlin Bridges
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Francisco F Cavazos
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Justin G Martyr
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Bryan B Guzmán
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, California, USA; Division of Biomedical Sciences, Center for RNA Biology and Medicine, Riverside, California, USA
| | - Maria M Aleman
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel Dominguez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, North Carolina, USA.
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3
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Cheng LY, Parker R. ZNFX1: a multifunctional modulator of the innate immune response. Front Immunol 2025; 16:1564628. [PMID: 40170857 PMCID: PMC11959080 DOI: 10.3389/fimmu.2025.1564628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 02/28/2025] [Indexed: 04/03/2025] Open
Abstract
Recent research has identified ZNFX1 as a critical modulator of the innate immune response. Individuals with loss of function mutations in ZNFX1 have chronic inflammation and increased susceptibility to various pathogens. Several potential functions of ZNFX1 have been proposed, including binding double-stranded RNA to activate antiviral innate immunity, inhibiting the NLRP3 inflammasome, and regulating the stability of host mRNAs. Notably, homologs of ZNFX1 are implicated in innate immunity across a wide range of species, including contributing to transgenerational epigenetic inheritance of small RNA-based defense in C. elegans. In this review, we discuss the significance of ZNFX1 and explore the potential underlying mechanisms that govern its diverse functions.
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Affiliation(s)
- Li Yi Cheng
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, United States
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, United States
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4
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Lim J, Lee N, Ju S, Kim J, Mun S, Jeon M, Lee YK, Lee SH, Ku J, Kim S, Bae S, Kim JS, Kim Y. Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing. Commun Biol 2025; 8:389. [PMID: 40055516 PMCID: PMC11889100 DOI: 10.1038/s42003-025-07807-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 02/25/2025] [Indexed: 05/13/2025] Open
Abstract
RNA-binding proteins (RBPs) provide a critical post-transcriptional regulatory layer in determining RNA fate. Currently, UV crosslinking followed by oligo-dT pull-down is the gold standard in identifying the RBP repertoire of poly-adenylated RNAs, but such method is ineffective in capturing RBPs that recognize double-stranded RNAs (dsRNAs). Here, we utilize anti-dsRNA K1 antibody immunoprecipitation followed by quantitative mass spectrometry to comprehensively identify RBPs bound to cellular dsRNAs without external stimulus. Notably, our dsRNA interactome contains proteins involved in sensing N6-methyladenosine RNAs and stress granule components. We further perform targeted CRISPR-Cas9 knockout functional screening and discover proteins that can regulate the interferon (IFN) response during exogenous RNA sensing. Interestingly, most dsRBPs promote IFN-β secretion in response to dsRNA stimulation and act as antiviral factors during HCoV-OC43 infection. Our dsRNA interactome capture provides an unbiased and comprehensive characterization of putative dsRBPs and will facilitate our understanding of dsRNA sensing in physiological and pathological contexts.
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Affiliation(s)
- JinA Lim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Namseok Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seonmin Ju
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Subin Mun
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Moonhyeon Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yong-Ki Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seok-Hoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sujin Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sangsu Bae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), KAIST, Daejeon, 34141, Republic of Korea.
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5
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Silagi ES, Nduka E, Pazyra-Murphy MF, Paiz JZ, Bhuiyan SA, Segal RA. Profiling local translatomes and RNA binding proteins of somatosensory neurons reveals specializations of individual axons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.28.640799. [PMID: 40364912 PMCID: PMC12073832 DOI: 10.1101/2025.02.28.640799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
Individual neurons have one or more axons that often extend long distances and traverse multiple microenvironments. However, it is not known how the composition of individual axons is established or locally modulated to enable neuronal function and plasticity. Here, we use spatial translatomics to identify local axonal translatomes in anatomically and functionally specialized neurons in the dorsal root ganglia (DRG). DRG neurons extend long central and peripheral axons in opposite directions and distinct microenvironments to enable somatosensation. Using Translating Ribosome Affinity Purification and RNA sequencing, we generated a comprehensive resource of mRNAs preferentially translated within each axon. Locally translated proteins include pain receptors, ion channels, and translational machinery, which establish distinct electrophysiologic properties and regenerative capacities for each axon. We identify RNA-binding proteins associated with sorting and transporting functionally related mRNAs. These findings provide resources for addressing how axonal translation shapes the spatial organization of neurons and enables subcellular neuroplasticity. HIGHLIGHTS Distinct mRNAs are localized to and translated in individual axons.Axonal translatomes govern regenerative capacity, translational machinery, and electrophysiology.The RBP, SFPQ, coordinates mRNA sorting towards peripheral somatosensory axons.Axonal translatome data can be explored at painseq.shinyapps.io/CompartmentTRAP/.
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6
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Bangbo Z, Cheng Q, Zeru L, Tianyu L, Yutong Z, Weibin W, Yupei Z. RNA binding protein Pumilio2 promotes chemoresistance of pancreatic cancer via focal adhesion pathway and interacting with transcription factor EGR1. Cell Mol Life Sci 2025; 82:78. [PMID: 39961821 PMCID: PMC11832970 DOI: 10.1007/s00018-025-05599-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 01/15/2025] [Accepted: 01/16/2025] [Indexed: 02/20/2025]
Abstract
Pancreatic cancer (PCa) has insidious onset, high malignancy and poor prognosis. Gemcitabine (GEM) is one of the first-line chemotherapy drugs for PCa. However, GEM resistance has always been a bottleneck problem leading to recurrence and death of PCa patients. RNA-binding proteins (RBPs) are important proteins that regulate transportation, splicing, stability and translation of RNA. Abnormal expression of RBPs often lead to a series of abnormal accumulation or degradation of downstream RNA resulting in various diseases. In our study, we utilized RIP seq, RIP-qPCR, in vitro and in vivo experiments and found that pumilio2 (PUM2) was high expression in PCa, and promoted GEM resistance of PCa by regulating mRNA stability of integrin Alpha 3 (ITGA3) and other genes in focal adhesion pathway, and there was positive feedback regulation between PUM2 and transcription factor early growth response gene 1 (EGR1), that is PUM2 binding to 3'UTR region of EGR1 mRNA, and EGR1 binding to promoter region of PUM2 gene. The discovery of EGR1/PUM2/ITGA3 axis provided a solid experimental basis for the selection of chemotherapy regiments for PCa patients and exploration of combined regimens to reverse GEM resistance in the future.
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Affiliation(s)
- Zhao Bangbo
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qin Cheng
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Li Zeru
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Li Tianyu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhao Yutong
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Wang Weibin
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Zhao Yupei
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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7
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Vukić D, Cherian A, Keskitalo S, Bong YT, Marônek M, Yadav L, Keegan LP, Varjosalo M, O'Connell MA. Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to interferon induction. Nucleic Acids Res 2024; 52:14184-14204. [PMID: 39673305 DOI: 10.1093/nar/gkae1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 09/29/2024] [Accepted: 11/04/2024] [Indexed: 12/16/2024] Open
Abstract
The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon (IFN) inducible, is predominately cytoplasmic. Using three different methods - co-immunoprecipitation (co-IP) of endogenous ADAR1, Strep-tag co-IP and BioID with individual ADAR1 isoforms - a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors as well as editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a double-stranded RNA (dsRNA)-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with high molecular weight poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.
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Affiliation(s)
- Dragana Vukić
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
- NationalCentre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Anna Cherian
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
- NationalCentre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Salla Keskitalo
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Yih Tyng Bong
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Martin Marônek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Leena Yadav
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Liam P Keegan
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
| | - Markku Varjosalo
- Institute of Biotechnology, HelsinkiInstitute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Mary A O'Connell
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czechia
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8
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Steinbrecht D, Minia I, Milek M, Meisig J, Blüthgen N, Landthaler M. Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting. Mol Syst Biol 2024; 20:1346-1371. [PMID: 39548324 PMCID: PMC11611909 DOI: 10.1038/s44320-024-00073-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 10/17/2024] [Accepted: 10/22/2024] [Indexed: 11/17/2024] Open
Abstract
Eukaryotic mRNAs are transcribed, processed, translated, and degraded in different subcellular compartments. Here, we measured mRNA flow rates between subcellular compartments in mouse embryonic stem cells. By combining metabolic RNA labeling, biochemical fractionation, mRNA sequencing, and mathematical modeling, we determined the half-lives of nuclear pre-, nuclear mature, cytosolic, and membrane-associated mRNAs from over 9000 genes. In addition, we estimated transcript elongation rates. Many matured mRNAs have long nuclear half-lives, indicating nuclear retention as the rate-limiting step in the flow of mRNAs. In contrast, mRNA transcripts coding for transcription factors show fast kinetic rates, and in particular short nuclear half-lives. Differentially localized mRNAs have distinct rate constant combinations, implying modular regulation. Membrane stability is high for membrane-localized mRNA and cytosolic stability is high for cytosol-localized mRNA. mRNAs encoding target signals for membranes have low cytosolic and high membrane half-lives with minor differences between signals. Transcripts of nuclear-encoded mitochondrial proteins have long nuclear retention and cytoplasmic kinetics that do not reflect co-translational targeting. Our data and analyses provide a useful resource to study spatiotemporal gene expression regulation.
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Affiliation(s)
- David Steinbrecht
- Charite-Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Igor Minia
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Miha Milek
- Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany
| | - Johannes Meisig
- Charite-Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Nils Blüthgen
- Charite-Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany.
- Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany.
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany.
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9
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Schmeing S, Hart P'. Challenges in Therapeutically Targeting the RNA-Recognition Motif. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1877. [PMID: 39668490 PMCID: PMC11638515 DOI: 10.1002/wrna.1877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 10/16/2024] [Accepted: 11/07/2024] [Indexed: 12/14/2024]
Abstract
The RNA recognition motif (RRM) is the most common RNA binding domain found in the human proteome. RRM domains provide RNA-binding proteins with sequence specific RNA recognition allowing them to participate in RNA-centric processes such as mRNA maturation, translation initiation, splicing, and RNA degradation. They are drivers of various diseases through overexpression or mutation, making them attractive therapeutic targets and addressing these proteins through their RRM domains with chemical compounds is gaining ever more attention. However, it is still very challenging to find selective and potent RNA-competitors due to the small size of the domain and high structural conservation of its RNA binding interface. Despite these challenges, a selection of compounds has been reported for several RRM containing proteins, but often with limited biophysical evidence and low selectivity. A solution to selectively targeting RRM domains might be through avoiding the RNA-binding surface altogether, but rather look for composite pockets formed with other proteins or for protein-protein interaction sites that regulate the target's activity but are less conserved. Alternative modalities, such as oligonucleotides, peptides, and molecular glues, are exciting new approaches to address these challenging targets and achieve the goal of therapeutic intervention at the RNA regulatory level.
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Affiliation(s)
- Stefan Schmeing
- Chemical Genomics Centre of the Max Planck SocietyMax Planck Institute of Molecular PhysiologyDortmundGermany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck SocietyMax Planck Institute of Molecular PhysiologyDortmundGermany
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10
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Seidler JF, Sträßer K. Understanding nuclear mRNA export: Survival under stress. Mol Cell 2024; 84:3681-3691. [PMID: 39366354 DOI: 10.1016/j.molcel.2024.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/13/2024] [Accepted: 08/23/2024] [Indexed: 10/06/2024]
Abstract
Nuclear messenger RNA (mRNA) export is vital for cell survival under both physiological and stress conditions. To cope with stress, cells block bulk mRNA export while selectively exporting stress-specific mRNAs. Under physiological conditions, nuclear adaptor proteins recruit the mRNA exporter to the mRNA for export. By contrast, during stress conditions, the mRNA exporter is likely directly recruited to stress-specific mRNAs at their transcription sites to facilitate selective mRNA export. In this review, we summarize our current understanding of nuclear mRNA export. Importantly, we explore insights into the mechanisms that block bulk mRNA export and facilitate transcript-specific mRNA export under stress, highlighting the gaps that still need to be filled.
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Affiliation(s)
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany; Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany.
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11
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Dargan R, Mikheenko A, Johnson NL, Packer B, Li Z, Craig EJ, Sarbanes SL, Bereda C, Mehta PR, Keuss M, Nalls MA, Qi YA, Weller CA, Fratta P, Ryan VH. Altered mRNA transport and local translation in iNeurons with RNA binding protein knockdown. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615153. [PMID: 39386562 PMCID: PMC11463369 DOI: 10.1101/2024.09.26.615153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Neurons rely on mRNA transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by RNA binding proteins (RBPs), including those known to be associated with neurodegenerative diseases. Here, we use proteomics, transcriptomics, and microscopy to investigate the impact of RBP knockdown on mRNA transport and local translation in iPSC-derived neurons. We find thousands of transcripts enriched in neurites and that many of these transcripts are locally translated, possibly due to the shorter length of transcripts in neurites. Loss of frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS)-associated RBPs TDP-43 and hnRNPA1 lead to distinct alterations in the neuritic proteome and transcriptome. TDP-43 knockdown (KD) leads to increased neuritic mRNA and translation. In contrast, hnRNPA1 leads to increased neuritic mRNA, but not translation, and more moderate effects on local mRNA profiles, possibly due to compensation by hnRNPA3. These results highlight the crucial role of FTD/ALS-associated RBPs in mRNA transport and local translation in neurons and the importance of these processes in neuron health and disease.
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Affiliation(s)
- Rachael Dargan
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicholas L Johnson
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Benjamin Packer
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Emma J Craig
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie L Sarbanes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Cory A Weller
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Veronica H Ryan
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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12
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Chen S, Jiang Q, Fan J, Cheng H. Nuclear mRNA export. Acta Biochim Biophys Sin (Shanghai) 2024; 57:84-100. [PMID: 39243141 PMCID: PMC11802349 DOI: 10.3724/abbs.2024145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/17/2024] [Indexed: 09/09/2024] Open
Abstract
In eukaryotic cells, gene expression begins with transcription in the nucleus, followed by the maturation of messenger RNAs (mRNAs). These mRNA molecules are then exported to the cytoplasm through the nuclear pore complex (NPC), a process that serves as a critical regulatory phase of gene expression. The export of mRNA is intricately linked to precursor mRNA (pre-mRNA) processing, ensuring that only properly processed mRNA reaches the cytoplasm. This coordination is essential, as recent studies have revealed that mRNA export factors not only assist in transport but also influence upstream processing steps, adding a layer of complexity to gene regulation. Furthermore, the export process competes with RNA processing and degradation pathways, maintaining a delicate balance vital for accurate gene expression. While these mechanisms are generally conserved across eukaryotes, significant differences exist between yeast and higher eukaryotic cells, particularly due to the more genome complexity of the latter. This review delves into the current research on mRNA export in higher eukaryotic cells, focusing on its role in the broader context of gene expression regulation and highlighting how it interacts with other gene expression processes to ensure precise and efficient gene functionality in complex organisms.
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Affiliation(s)
- Suli Chen
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
| | - Qingyi Jiang
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
| | - Jing Fan
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
- The Key Laboratory of Developmental Genes and Human DiseaseSchool of Life Science and TechnologySoutheast UniversityNanjing210096China
| | - Hong Cheng
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
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Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell 2024; 84:2765-2784.e16. [PMID: 38964322 PMCID: PMC11315470 DOI: 10.1016/j.molcel.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/15/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024]
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ziad Mohamoud Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal K Guegler
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Luke Gilbert
- Arc Institute, Palo Alto, CA 94305, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94518, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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