1
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Wassmer E, Koppány G, Hermes M, Diederichs S, Caudron-Herger M. Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins. Nucleic Acids Res 2024; 52:7504-7522. [PMID: 38917322 PMCID: PMC11260472 DOI: 10.1093/nar/gkae536] [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: 08/17/2023] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
From transcription to decay, RNA-binding proteins (RBPs) influence RNA metabolism. Using the RBP2GO database that combines proteome-wide RBP screens from 13 species, we investigated the RNA-binding features of 176 896 proteins. By compiling published lists of RNA-binding domains (RBDs) and RNA-related protein family (Rfam) IDs with lists from the InterPro database, we analyzed the distribution of the RBDs and Rfam IDs in RBPs and non-RBPs to select RBDs and Rfam IDs that were enriched in RBPs. We also explored proteins for their content in intrinsically disordered regions (IDRs) and low complexity regions (LCRs). We found a strong positive correlation between IDRs and RBDs and a co-occurrence of specific LCRs. Our bioinformatic analysis indicated that RBDs/Rfam IDs were strong indicators of the RNA-binding potential of proteins and helped predicting new RBP candidates, especially in less investigated species. By further analyzing RBPs without RBD, we predicted new RBDs that were validated by RNA-bound peptides. Finally, we created the RBP2GO composite score by combining the RBP2GO score with new quality factors linked to RBDs and Rfam IDs. Based on the RBP2GO composite score, we compiled a list of 2018 high-confidence human RBPs. The knowledge collected here was integrated into the RBP2GO database at https://RBP2GO-2-Beta.dkfz.de.
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Affiliation(s)
- Elsa Wassmer
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gergely Koppány
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Malte Hermes
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, and German Cancer Consortium (DKTK), partner site Freiburg, a partnership between DKFZ and University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Maïwen Caudron-Herger
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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2
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Lorenzo-Orts L, Pauli A. The molecular mechanisms underpinning maternal mRNA dormancy. Biochem Soc Trans 2024; 52:861-871. [PMID: 38477334 PMCID: PMC11088918 DOI: 10.1042/bst20231122] [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: 12/14/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
A large number of mRNAs of maternal origin are produced during oogenesis and deposited in the oocyte. Since transcription stops at the onset of meiosis during oogenesis and does not resume until later in embryogenesis, maternal mRNAs are the only templates for protein synthesis during this period. To ensure that a protein is made in the right place at the right time, the translation of maternal mRNAs must be activated at a specific stage of development. Here we summarize our current understanding of the sophisticated mechanisms that contribute to the temporal repression of maternal mRNAs, termed maternal mRNA dormancy. We discuss mechanisms at the level of the RNA itself, such as the regulation of polyadenine tail length and RNA modifications, as well as at the level of RNA-binding proteins, which often block the assembly of translation initiation complexes at the 5' end of an mRNA or recruit mRNAs to specific subcellular compartments. We also review microRNAs and other mechanisms that contribute to repressing translation, such as ribosome dormancy. Importantly, the mechanisms responsible for mRNA dormancy during the oocyte-to-embryo transition are also relevant to cellular quiescence in other biological contexts.
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Affiliation(s)
- Laura Lorenzo-Orts
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
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3
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Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024; 25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [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: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. RESULTS By employing SLAM-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional activation events and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA-430 function, a key post transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression. CONCLUSION These insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. The findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.
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Affiliation(s)
- Danielson Baia Amaral
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Rhonda Egidy
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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4
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Heins-Marroquin U, Singh RR, Perathoner S, Gavotto F, Merino Ruiz C, Patraskaki M, Gomez-Giro G, Kleine Borgmann F, Meyer M, Carpentier A, Warmoes MO, Jäger C, Mittelbronn M, Schwamborn JC, Cordero-Maldonado ML, Crawford AD, Schymanski EL, Linster CL. CLN3 deficiency leads to neurological and metabolic perturbations during early development. Life Sci Alliance 2024; 7:e202302057. [PMID: 38195117 PMCID: PMC10776888 DOI: 10.26508/lsa.202302057] [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: 03/24/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Juvenile neuronal ceroid lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 yr and is most commonly caused by mutations in the highly conserved CLN3 gene. Here, we generated cln3 morphants and stable mutant lines in zebrafish. Although neither morphant nor mutant cln3 larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and cholesteryl esters, and a global decrease in bis(monoacylglycero)phosphate species, two of which (GPDs and bis(monoacylglycero)phosphates) were previously proposed as potential biomarkers for CLN3 disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant for CLN3 Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomatic CLN3 disease.
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Affiliation(s)
- Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- https://ror.org/00hj8s172 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Simon Perathoner
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Floriane Gavotto
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carla Merino Ruiz
- Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
- Biosfer Teslab SL, Reus, Spain
| | - Myrto Patraskaki
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Felix Kleine Borgmann
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Melanie Meyer
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Anaïs Carpentier
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Marc O Warmoes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Institute for Orphan Drug Discovery, Bremerhaven, Germany
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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5
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Huang W, Xiong T, Zhao Y, Heng J, Han G, Wang P, Zhao Z, Shi M, Li J, Wang J, Wu Y, Liu F, Xi JJ, Wang Y, Zhang QC. Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human. Nat Genet 2024; 56:124-135. [PMID: 38195860 PMCID: PMC10786727 DOI: 10.1038/s41588-023-01620-7] [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: 08/19/2022] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects, which were subsequently rescued by predicted zebrafish homologs. Knocking down coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Furthermore, we verified that human, mouse and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved functions relying on specific RBP-binding sites. Overall, our study demonstrates a comprehensive approach for studying the functional conservation of lncRNAs and implicates numerous lncRNAs in regulating vertebrate physiology.
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Affiliation(s)
- Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Tuanlin Xiong
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuting Zhao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jian Heng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ge Han
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Pengfei Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhihua Zhao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Ming Shi
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Jiazhen Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yixia Wu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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6
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Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568470. [PMID: 38045294 PMCID: PMC10690280 DOI: 10.1101/2023.11.23.568470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The 5' UTRs of mRNAs are critical for translation regulation, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR is sufficient to confer temporal dynamics to translation initiation, and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, DaniO5P, revealed a combined role for 5' UTR length, translation initiation site context, upstream AUGs and sequence motifs on in vivo ribosome recruitment. DaniO5P predicts the activities of 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in early vertebrate development and lays the foundation for identifying the underlying molecular effectors. Highlights In vivo MPRA systematically interrogates the regulatory potential of endogenous 5' UTRs The 5' UTR alone is sufficient to regulate the dynamics of ribosome recruitment during early embryogenesis The MPRA identifies 5' UTR cis -regulatory motifs for translation initiation control 5' UTR length, upstream AUGs and motif grammar contribute to the differential regulatory capability of 5' UTR switching isoforms.
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7
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Liu L, Trendel J, Jiang G, Liu Y, Bruckmann A, Küster B, Sprunck S, Dresselhaus T, Bleckmann A. RBPome identification in egg-cell like callus of Arabidopsis. Biol Chem 2023; 404:1137-1149. [PMID: 37768858 DOI: 10.1515/hsz-2023-0195] [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: 04/29/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
RNA binding proteins (RBPs) have multiple and essential roles in transcriptional and posttranscriptional regulation of gene expression in all living organisms. Their biochemical identification in the proteome of a given cell or tissue requires significant protein amounts, which limits studies in rare and highly specialized cells. As a consequence, we know almost nothing about the role(s) of RBPs in reproductive processes such as egg cell development, fertilization and early embryogenesis in flowering plants. To systematically identify the RBPome of egg cells in the model plant Arabidopsis, we performed RNA interactome capture (RIC) experiments using the egg cell-like RKD2-callus and were able to identify 728 proteins associated with poly(A+)-RNA. Transcripts for 97 % of identified proteins could be verified in the egg cell transcriptome. 46 % of identified proteins can be associated with the RNA life cycle. Proteins involved in mRNA binding, RNA processing and metabolism are highly enriched. Compared with the few available RBPome datasets of vegetative plant tissues, we identified 475 egg cell-enriched RBPs, which will now serve as a resource to study RBP function(s) during egg cell development, fertilization and early embryogenesis. First candidates were already identified showing an egg cell-specific expression pattern in ovules.
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Affiliation(s)
- Liping Liu
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Guojing Jiang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Yanhui Liu
- College of Life Science, Longyan University, Longyan 364012, China
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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8
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Wu S, Xie H, Su Y, Jia X, Mi Y, Jia Y, Ying H. The landscape of implantation and placentation: deciphering the function of dynamic RNA methylation at the maternal-fetal interface. Front Endocrinol (Lausanne) 2023; 14:1205408. [PMID: 37720526 PMCID: PMC10499623 DOI: 10.3389/fendo.2023.1205408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
The maternal-fetal interface is defined as the interface between maternal tissue and sections of the fetus in close contact. RNA methylation modifications are the most frequent kind of RNA alterations. It is effective throughout both normal and pathological implantation and placentation during pregnancy. By influencing early embryo development, embryo implantation, endometrium receptivity, immune microenvironment, as well as some implantation and placentation-related disorders like miscarriage and preeclampsia, it is essential for the establishment of the maternal-fetal interface. Our review focuses on the role of dynamic RNA methylation at the maternal-fetal interface, which has received little attention thus far. It has given the mechanistic underpinnings for both normal and abnormal implantation and placentation and could eventually provide an entirely novel approach to treating related complications.
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Affiliation(s)
- Shengyu Wu
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Han Xie
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yao Su
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinrui Jia
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yabing Mi
- Department of Clinical Medicine, Tongji University School of Medicine, Shanghai, China
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuanhui Jia
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hao Ying
- Department of Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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9
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Zhang Y, Xu Y, Skaggs TH, Ferreira JFS, Chen X, Sandhu D. Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants. THE PLANT CELL 2023; 35:2750-2772. [PMID: 37144845 PMCID: PMC10396368 DOI: 10.1093/plcell/koad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs in plants have been predominantly limited to proteins interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded a highly comprehensive RNA-binding proteome (RBPome), uncovering 2,517 RBPs from Arabidopsis (Arabidopsis thaliana) leaf and root samples with a highly diverse array of RNA-binding domains. We identified traditional RBPs that participate in various aspects of RNA metabolism and a plethora of nonclassical proteins moonlighting as RBPs. We uncovered constitutive and tissue-specific RBPs essential for normal development and, more importantly, revealed RBPs crucial for salinity stress responses from a RBP-RNA dynamics perspective. Remarkably, 40% of the RBPs are non-poly(A) RBPs that were not previously annotated as RBPs, signifying the advantage of PPE in unbiasedly retrieving RBPs. We propose that intrinsically disordered regions contribute to their nonclassical binding and provide evidence that enzymatic domains from metabolic enzymes have additional roles in RNA binding. Taken together, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues and pave the way for investigating RBP functions under different physiological and stress conditions at the posttranscriptional level.
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Affiliation(s)
- Yong Zhang
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Todd H Skaggs
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
| | | | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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10
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Perez-Perri JI, Ferring-Appel D, Huppertz I, Schwarzl T, Sahadevan S, Stein F, Rettel M, Galy B, Hentze MW. The RNA-binding protein landscapes differ between mammalian organs and cultured cells. Nat Commun 2023; 14:2074. [PMID: 37045843 PMCID: PMC10097726 DOI: 10.1038/s41467-023-37494-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
System-wide approaches have unveiled an unexpected breadth of the RNA-bound proteomes of cultured cells. Corresponding information regarding RNA-binding proteins (RBPs) of mammalian organs is still missing, largely due to technical challenges. Here, we describe ex vivo enhanced RNA interactome capture (eRIC) to characterize the RNA-bound proteomes of three different mouse organs. The resulting organ atlases encompass more than 1300 RBPs active in brain, kidney or liver. Nearly a quarter (291) of these had formerly not been identified in cultured cells, with more than 100 being metabolic enzymes. Remarkably, RBP activity differs between organs independent of RBP abundance, suggesting organ-specific levels of control. Similarly, we identify systematic differences in RNA binding between animal organs and cultured cells. The pervasive RNA binding of enzymes of intermediary metabolism in organs points to tightly knit connections between gene expression and metabolism, and displays a particular enrichment for enzymes that use nucleotide cofactors. We describe a generically applicable refinement of the eRIC technology and provide an instructive resource of RBPs active in intact mammalian organs, including the brain.
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Affiliation(s)
- Joel I Perez-Perri
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dunja Ferring-Appel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ina Huppertz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sudeep Sahadevan
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-associated Carcinogenesis, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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11
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Lorenz DA, Her HL, Shen KA, Rothamel K, Hutt KR, Nojadera AC, Bruns SC, Manakov SA, Yee BA, Chapman KB, Yeo GW. Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. Nat Methods 2023; 20:65-69. [PMID: 36550273 PMCID: PMC9834051 DOI: 10.1038/s41592-022-01708-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022]
Abstract
Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process several RBPs in parallel. We present a new method termed antibody-barcode eCLIP that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate several RBPs simultaneously. We observe performance comparable with that of eCLIP with the advantage of dramatically increased scaling while maintaining the same material requirement of a single eCLIP experiment.
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Affiliation(s)
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | | | - Katie Rothamel
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | | | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
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12
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Liu H, Zheng J, Liao A. The regulation and potential roles of m6A modifications in early embryonic development and immune tolerance at the maternal-fetal interface. Front Immunol 2022; 13:988130. [PMID: 36225914 PMCID: PMC9549360 DOI: 10.3389/fimmu.2022.988130] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/09/2022] [Indexed: 12/16/2022] Open
Abstract
The immune microenvironment at the maternal-fetal interface was determined by the crosstalk between the trophoblast and maternal-derived cells, which dynamically changed during the whole gestation. Trophoblasts act as innate immune cells and dialogue with maternal-derived cells to ensure early embryonic development, depending on the local immune microenvironment. Therefore, dysfunctions in trophoblasts and maternal decidual cells contribute to pregnancy complications, especially recurrent pregnancy loss in early pregnancy. Since many unknown regulatory factors still affect the complex immune status, exploring new potential aspects that could influence early pregnancy is essential. RNA methylation plays an important role in contributing to the transcriptional regulation of various cells. Sufficient studies have shown the crucial roles of N6-methyladenosine (m6A)- and m6A-associated- regulators in embryogenesis during implantation. They are also essential in regulating innate and adaptive immune cells and the immune response and shaping the local and systemic immune microenvironment. However, the function of m6A modifications at the maternal-fetal interface still lacks wide research. This review highlights the critical functions of m6A in early embryonic development, summarizes the reported research on m6A in regulating immune cells and tumor immune microenvironment, and identifies the potential value of m6A modifications in shaping trophoblasts, decidual immune cells, and the microenvironment at the maternal-fetal interface. The m6A modifications are more likely to contribute to embryogenesis, placentation and shape the immune microenvironment at the maternal-fetal interface. Uncovering these crucial regulatory mechanisms could provide novel therapeutic targets for RNA methylation in early pregnancy.
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Affiliation(s)
- Hong Liu
- Department of Reproduction, Maternal and Child Health Hospital of Hubei Province, Affiliated in Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Zheng
- Department of Reproduction, Maternal and Child Health Hospital of Hubei Province, Affiliated in Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jie Zheng, ; Aihua Liao,
| | - Aihua Liao
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jie Zheng, ; Aihua Liao,
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13
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Mestre-Farràs N, Guerrero S, Bley N, Rivero E, Coll O, Borràs E, Sabidó E, Indacochea A, Casillas-Serra C, Järvelin AI, Oliva B, Castello A, Hüttelmaier S, Gebauer F. Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis. Nucleic Acids Res 2022; 50:8207-8225. [PMID: 35848924 PMCID: PMC9371929 DOI: 10.1093/nar/gkac605] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of a non-tumoral versus a metastatic cell line revealed prevalent changes in RNA-binding capacities that were not associated with changes in RBP levels. Extensive functional validation of a selected group of 24 RBPs using five different in vitro assays unveiled unanticipated roles of RBPs in melanoma malignancy. As proof-of-principle we focused on PDIA6, an ER-lumen chaperone that displayed a novel RNA-binding activity. We show that PDIA6 is involved in metastatic progression, map its RNA-binding domain, and find that RNA binding is required for PDIA6 tumorigenic properties. These results exemplify how RIC technologies can be harnessed to uncover novel vulnerabilities of cancer cells.
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Affiliation(s)
- Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Santiago Guerrero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Ezequiel Rivero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Olga Coll
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alberto Indacochea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Carlos Casillas-Serra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Baldomero Oliva
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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14
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Ma P, Liu X, Xu Z, Liu H, Ding X, Huang Z, Shi C, Liang L, Xu L, Li X, Li G, He Y, Ding Z, Chai C, Wang H, Qiu J, Zhu J, Wang X, Ding P, Zhou S, Yuan Y, Wu W, Wan C, Yan Y, Zhou Y, Zhou QJ, Wang GD, Zhang Q, Xu X, Li G, Zhang S, Mao B, Chen D. Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution. Cell Rep 2022; 39:110979. [PMID: 35732129 DOI: 10.1016/j.celrep.2022.110979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/21/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022] Open
Abstract
Vertebrate evolution was accompanied by two rounds of whole-genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single-cell sequencing has been widely used to construct the developmental cell atlas of several representative species of vertebrates (human, mouse, zebrafish, and frog) and tunicates (sea squirts). Here, we perform single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated, we constructed a developmental tree for amphioxus cell fate commitment and lineage specification and characterize the underlying key regulators and genetic regulatory networks. The data are publicly available on the online platform AmphioxusAtlas.
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Affiliation(s)
- Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xingyan Liu
- Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing 100190, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaoxu Xu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huimin Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China
| | - Xiangning Ding
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Huang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China; Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China
| | - Langchao Liang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaolu Li
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Guimei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuqi He
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Zhaoli Ding
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Chaochao Chai
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoyu Wang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaying Qiu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Peiwen Ding
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wendi Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Cen Wan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Yanan Yan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Yitao Zhou
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Qi-Jun Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qiujin Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China.
| | - Shihua Zhang
- Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing 100190, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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15
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Maternally loaded RNAs: no time to die. Cell Res 2022; 32:707-708. [PMID: 35637270 PMCID: PMC9343350 DOI: 10.1038/s41422-022-00670-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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16
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Kalesh K, Wei W, Mantilla BS, Roumeliotis TI, Choudhary J, Denny PW. Transcriptome-Wide Identification of Coding and Noncoding RNA-Binding Proteins Defines the Comprehensive RNA Interactome of Leishmania mexicana. Microbiol Spectr 2022; 10:e0242221. [PMID: 35138191 PMCID: PMC8826732 DOI: 10.1128/spectrum.02422-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
Proteomic profiling of RNA-binding proteins in Leishmania is currently limited to polyadenylated mRNA-binding proteins, leaving proteins that interact with nonadenylated RNAs, including noncoding RNAs and pre-mRNAs, unidentified. Using a combination of unbiased orthogonal organic phase separation methodology and tandem mass tag-labeling-based high resolution quantitative proteomic mass spectrometry, we robustly identified 2,417 RNA-binding proteins, including 1289 putative novel non-poly(A)-RNA-binding proteins across the two main Leishmania life cycle stages. Eight out of 20 Leishmania deubiquitinases, including the recently characterized L. mexicana DUB2 with an elaborate RNA-binding protein interactome were exclusively identified in the non-poly(A)-RNA-interactome. Additionally, an increased representation of WD40 repeat domains were observed in the Leishmania non-poly(A)-RNA-interactome, thus uncovering potential involvement of this protein domain in RNA-protein interactions in Leishmania. We also characterize the protein-bound RNAs using RNA-sequencing and show that in addition to protein coding transcripts ncRNAs are also enriched in the protein-RNA interactome. Differential gene expression analysis revealed enrichment of 142 out of 195 total L. mexicana protein kinase genes in the protein-RNA-interactome, suggesting important role of protein-RNA interactions in the regulation of the Leishmania protein kinome. Additionally, we characterize the quantitative changes in RNA-protein interactions in hundreds of Leishmania proteins following inhibition of heat shock protein 90 (Hsp90). Our results show that the Hsp90 inhibition in Leishmania causes widespread disruption of RNA-protein interactions in ribosomal proteins, proteasomal proteins and translation factors in both life cycle stages, suggesting downstream effect of the inhibition on protein synthesis and degradation pathways in Leishmania. This study defines the comprehensive RNA interactome of Leishmania and provides in-depth insight into the widespread involvement of RNA-protein interactions in Leishmania biology. IMPORTANCE Advances in proteomics and mass spectrometry have revealed the mRNA-binding proteins in many eukaryotic organisms, including the protozoan parasites Leishmania spp., the causative agents of leishmaniasis, a major infectious disease in over 90 tropical and subtropical countries. However, in addition to mRNAs, which constitute only 2 to 5% of the total transcripts, many types of non-coding RNAs participate in crucial biological processes. In Leishmania, RNA-binding proteins serve as primary gene regulators. Therefore, transcriptome-wide identification of RNA-binding proteins is necessary for deciphering the distinctive posttranscriptional mechanisms of gene regulation in Leishmania. Using a combination of highly efficient orthogonal organic phase separation method and tandem mass tag-labeling-based quantitative proteomic mass spectrometry, we provide unprecedented comprehensive molecular definition of the total RNA interactome across the two main Leishmania life cycle stages. In addition, we characterize for the first time the quantitative changes in RNA-protein interactions in Leishmania following inhibition of heat shock protein 90, shedding light into hitherto unknown large-scale downstream molecular effect of the protein inhibition in the parasite. This work provides insight into the importance of total RNA-protein interactions in Leishmania, thus significantly expanding our knowledge of the emergence of RNA-protein interactions in Leishmania biology.
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Affiliation(s)
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Brian S. Mantilla
- Department of Biosciences, Durham University, Durham, United Kingdom
| | | | - Jyoti Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
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17
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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18
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Zhao LW, Zhu YZ, Wu YW, Pi SB, Shen L, Fan HY. Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development. Nucleic Acids Res 2021; 50:458-472. [PMID: 34904664 PMCID: PMC8855302 DOI: 10.1093/nar/gkab1213] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the maternally encoded mRNA decay pathway (M-decay) and the zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. In this study, we identified the zygotically encoded nuclear poly(A) binding protein 1 (PABPN1) as a factor required for maternal mRNA turnover, with a previously undescribed cytoplasmic function. Cytoplasmic PABPN1 docks on 3'-uridylated transcripts, downstream of terminal uridylyl transferases TUT4 and TUT7, and recruits 3'-5' exoribonuclease DIS3L2 to its targets, facilitating maternal mRNA decay. Pabpn1-knockout in mice resulted in preimplantation stage mortality due to early developmental arrest at the morula stage. Maternal mRNAs to be eliminated via the Z-decay pathway failed to be removed from Pabpn1-depleted embryos. Furthermore, PABPN1-mediated Z-decay is essential for major ZGA and regulates the expression of cell fate-determining factors in mouse preimplantation embryos. This study revealed an unforeseen cytoplasmic function of PABPN1 coupled with early embryonic development, characterized the presence of a zygotic destabilizer of maternal mRNA, and elucidated the Z-decay process mechanisms, which potentially contribute to human fertility.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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19
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Abstract
Hypoxia inhibits the tricarboxylic acid (TCA) cycle and leaves glycolysis as the primary metabolic pathway responsible for converting glucose into usable energy. However, the mechanisms that compensate for this loss in energy production due to TCA cycle inactivation remain poorly understood. Glycolysis enzymes are typically diffuse and soluble in the cytoplasm under normoxic conditions. In contrast, recent studies have revealed dynamic compartmentalization of glycolysis enzymes in response to hypoxic stress in yeast, C. elegans and mammalian cells. These messenger ribonucleoprotein (mRNP) structures, termed glycolytic (G) bodies in yeast, lack membrane enclosure and display properties of phase-separated biomolecular condensates. Disruption of condensate formation correlates with defects such as impaired synaptic function in C. elegans neurons and decreased glucose flux in yeast. Concentrating glycolysis enzymes into condensates may lead to their functioning as 'metabolons' that enhance rates of glucose utilization for increased energy production. Besides condensates, glycolysis enzymes functionally associate in other organisms and specific tissues through protein-protein interactions and membrane association. However, as discussed in this Review, the functional consequences of coalescing glycolytic machinery are only just beginning to be revealed. Through ongoing studies, we anticipate the physiological importance of metabolic regulation mediated by the compartmentalization of glycolysis enzymes will continue to emerge.
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Affiliation(s)
- Gregory G Fuller
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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20
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Abstract
Similar to epigenetic DNA and histone modifications, epitranscriptomic modifications (RNA modifications) have emerged as crucial regulators in temporal and spatial gene expression during eukaryotic development. To date, over 170 diverse types of chemical modifications have been identified upon RNA nucleobases. Some of these post-synthesized modifications can be reversibly installed, removed, and decoded by their specific cellular components and play critical roles in different biological processes. Accordingly, dysregulation of RNA modification effectors is tightly orchestrated with developmental processes. Here, we particularly focus on three well-studied RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), and N1-methyladenosine (m1A), and summarize recent knowledge of underlying mechanisms and critical roles of these RNA modifications in stem cell fate determination, embryonic development, and cancer progression, providing a better understanding of the whole association between epitranscriptomic regulation and mammalian development.
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21
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The expanding world of metabolic enzymes moonlighting as RNA binding proteins. Biochem Soc Trans 2021; 49:1099-1108. [PMID: 34110361 DOI: 10.1042/bst20200664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022]
Abstract
RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. The effects on RNA function are likely to be wider than regulation of translation, and some enzyme-RNA interactions have been found to regulate the enzyme's catalytic activity. Several enzyme-RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme-RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme-RNA interactions in connecting intermediary metabolism and gene expression.
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22
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Vieira-Vieira CH, Selbach M. Opportunities and Challenges in Global Quantification of RNA-Protein Interaction via UV Cross-Linking. Front Mol Biosci 2021; 8:669939. [PMID: 34055886 PMCID: PMC8155585 DOI: 10.3389/fmolb.2021.669939] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
RNA-binding proteins (RBPs) are key mediators of posttranscriptional gene expression control. However, the links between cell signaling on the one hand and RBP function on the other are understudied. While thousands of posttranslational modification (PTM) sites on RBPs have been identified, their functional roles are only poorly characterized. RNA-interactome capture (RIC) and cross-linking and immunoprecipitation (CLIP) are attractive methods that provide information about RBP-RNA interactions on a genome-wide scale. Both approaches rely on the in situ UV cross-linking of RBPs and RNAs, biochemical enrichment and analysis by RNA-sequencing (CLIP) or mass spectrometry (RIC). In principle, RIC- and CLIP-like methods could be used to globally quantify RBP-RNA interactions in response to perturbations. However, several biases have to be taken into account to avoid misinterpretation of the results obtained. Here, we focus on RIC-like methods and discuss four key aspects relevant for quantitative interpretation: (1) the RNA isolation efficiency, (2) the inefficient and highly variable UV cross-linking, (3) the baseline RNA occupancy of RBPs, and (4) indirect factors affecting RBP-RNA interaction. We highlight these points by presenting selected examples of PTMs that might induce differential quantification in RIC-like experiments without necessarily affecting RNA-binding. We conclude that quantifying RBP-RNA interactions via RIC or CLIP-like methods should not be regarded as an end in itself but rather as starting points for deeper analysis.
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Affiliation(s)
- Carlos H Vieira-Vieira
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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23
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Porter DF, Miao W, Yang X, Goda GA, Ji AL, Donohue LKH, Aleman MM, Dominguez D, Khavari PA. easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. Nat Commun 2021; 12:1569. [PMID: 33692367 PMCID: PMC7946914 DOI: 10.1038/s41467-021-21623-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP. easyCLIP provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize RNA libraries during sequencing library preparation. Measurement of >200 independent cross-link experiments across >35 proteins identifies an RNA cross-link rate threshold that distinguishes RBPs from non-RBPs and defines target RNAs as those with a complex frequency unlikely for a random protein. We apply easyCLIP to the 33 most recurrent cancer mutations across 28 RBPs, finding increased RNA binding per RBP molecule for KHDRBS2 R168C, A1CF E34K and PCBP1 L100P/Q cancer mutations. Quantitating RBP-RNA interactions can thus nominate proteins as RBPs and define the impact of specific disease-associated RBP mutations on RNA association.
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Affiliation(s)
- Douglas F. Porter
- grid.168010.e0000000419368956Program in Epithelial Biology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Program in Cancer Biology, Stanford University, Stanford, CA USA
| | - Weili Miao
- grid.168010.e0000000419368956Program in Epithelial Biology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Program in Cancer Biology, Stanford University, Stanford, CA USA
| | - Xue Yang
- grid.168010.e0000000419368956Program in Epithelial Biology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Program in Cancer Biology, Stanford University, Stanford, CA USA
| | - Grant A. Goda
- grid.10698.360000000122483208Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ,grid.10698.360000000122483208Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Andrew L. Ji
- grid.168010.e0000000419368956Program in Epithelial Biology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Program in Cancer Biology, Stanford University, Stanford, CA USA
| | - Laura K. H. Donohue
- grid.168010.e0000000419368956Program in Epithelial Biology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University, Stanford, CA USA
| | - Maria M. Aleman
- grid.10698.360000000122483208Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Daniel Dominguez
- grid.10698.360000000122483208Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ,grid.10698.360000000122483208Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Paul A. Khavari
- grid.168010.e0000000419368956Program in Epithelial Biology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Program in Cancer Biology, Stanford University, Stanford, CA USA ,Veterans Affairs, Palo Alto Healthcare System, Palo Alto, CA USA
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24
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Abstract
In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. While transcription and RNA have been implicated in euchromatin organization, it remains unclear how their interplay forms and maintains transcription pockets. Here we combine theory and experiment to analyze the dynamics of euchromatin organization as pluripotent zebrafish cells exit mitosis and begin transcription. We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. Instead, smaller scale microphases emerge that do not grow further and form the typical pattern of euchromatin organization.
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25
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Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Ythdf m 6A Readers Function Redundantly during Zebrafish Development. Cell Rep 2020; 33:108598. [PMID: 33378672 PMCID: PMC11407899 DOI: 10.1016/j.celrep.2020.108598] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/09/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022] Open
Abstract
During the maternal-to-zygotic transition (MZT), multiple mechanisms precisely control massive decay of maternal mRNAs. N6-methyladenosine (m6A) is known to regulate mRNA decay, yet how this modification promotes maternal transcript degradation remains unclear. Here, we find that m6A promotes maternal mRNA deadenylation. Yet, genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance, zygotic genome activation, or the onset of gastrulation, challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development, as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally, we show that the microRNA miR-430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.
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Affiliation(s)
- Cassandra Kontur
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Minsun Jeong
- Chey Institute for Advanced Studies, Seoul 06141, Republic of Korea
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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26
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Perez-Perri JI, Noerenberg M, Kamel W, Lenz CE, Mohammed S, Hentze MW, Castello A. Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture. Nat Protoc 2020; 16:27-60. [PMID: 33208978 DOI: 10.1038/s41596-020-00404-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Interactions between RNA-binding proteins (RBPs) and RNAs are critical to cell biology. However, methods to comprehensively and quantitatively assess these interactions within cells were lacking. RNA interactome capture (RIC) uses in vivo UV crosslinking, oligo(dT) capture, and proteomics to identify RNA-binding proteomes. Recent advances have empowered RIC to quantify RBP responses to biological cues such as metabolic imbalance or virus infection. Enhanced RIC exploits the stronger binding of locked nucleic acid (LNA)-containing oligo(dT) probes to poly(A) tails to maximize RNA capture selectivity and efficiency, profoundly improving signal-to-noise ratios. The subsequent analytical use of SILAC and TMT proteomic approaches, together with high-sensitivity sample preparation and tailored statistical data analysis, substantially improves RIC's quantitative accuracy and reproducibility. This optimized approach is an extension of the original RIC protocol. It takes 3 d plus 2 weeks for proteomics and data analysis and will enable the study of RBP dynamics under different physiological and pathological conditions.
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Affiliation(s)
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, Oxford, UK.,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, Scotland, UK
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Caroline E Lenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK.,The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, Oxford, UK. .,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, Scotland, UK.
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27
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Single and Combined Methods to Specifically or Bulk-Purify RNA-Protein Complexes. Biomolecules 2020; 10:biom10081160. [PMID: 32784769 PMCID: PMC7464009 DOI: 10.3390/biom10081160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
The ribonome interconnects the proteome and the transcriptome. Specific biology is situated at this interface, which can be studied in bulk using omics approaches or specifically by targeting an individual protein or RNA species. In this review, we focus on both RNA- and ribonucleoprotein-(RNP) centric methods. These methods can be used to study the dynamics of the ribonome in response to a stimulus or to identify the proteins that interact with a specific RNA species. The purpose of this review is to provide and discuss an overview of strategies to cross-link RNA to proteins and the currently available RNA- and RNP-centric approaches to study RNPs. We elaborate on some major challenges common to most methods, involving RNP yield, purity and experimental cost. We identify the origin of these difficulties and propose to combine existing approaches to overcome these challenges. The solutions provided build on the recently developed organic phase separation protocols, such as Cross-Linked RNA eXtraction (XRNAX), orthogonal organic phase separation (OOPS) and Phenol-Toluol extraction (PTex).
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28
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Zhao LW, Zhu YZ, Chen H, Wu YW, Pi SB, Chen L, Shen L, Fan HY. PABPN1L mediates cytoplasmic mRNA decay as a placeholder during the maternal-to-zygotic transition. EMBO Rep 2020; 21:e49956. [PMID: 32558204 DOI: 10.15252/embr.201949956] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Maternal mRNA degradation is a critical event of the maternal-to-zygotic transition (MZT) that determines the developmental potential of early embryos. Nuclear Poly(A)-binding proteins (PABPNs) are extensively involved in mRNA post-transcriptional regulation, but their function in the MZT has not been investigated. In this study, we find that the maternally expressed PABPN1-like (PABPN1L), rather than its ubiquitously expressed homolog PABPN1, acts as an mRNA-binding adapter of the mammalian MZT licensing factor BTG4, which mediates maternal mRNA clearance. Female Pabpn1l null mice produce morphologically normal oocytes but are infertile owing to early developmental arrest of the resultant embryos at the 1- to 2-cell stage. Deletion of Pabpn1l impairs the deadenylation and degradation of a subset of BTG4-targeted maternal mRNAs during the MZT. In addition to recruiting BTG4 to the mRNA 3'-poly(A) tails, PABPN1L is also required for BTG4 protein accumulation in maturing oocytes by protecting BTG4 from SCF-βTrCP1 E3 ubiquitin ligase-mediated polyubiquitination and degradation. This study highlights a noncanonical cytoplasmic function of nuclear poly(A)-binding protein in mRNA turnover, as well as its physiological importance during the MZT.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hao Chen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lu Chen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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29
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Shi B, Zhang J, Heng J, Gong J, Zhang T, Li P, Sun BF, Yang Y, Zhang N, Zhao YL, Wang HL, Liu F, Zhang QC, Yang YG. RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function. Genome Biol 2020; 21:120. [PMID: 32423473 PMCID: PMC7236375 DOI: 10.1186/s13059-020-02022-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined. RESULTS Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3' UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1a's binding leading to the decay of its maternal targets. CONCLUSIONS Our study finds that RNA structurally variable regions are enriched in mRNA 3' UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
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Affiliation(s)
- Boyang Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian Heng
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Gong
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ting Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bao-Fa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai-Lin Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Feng Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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30
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Bach-Pages M, Homma F, Kourelis J, Kaschani F, Mohammed S, Kaiser M, van der Hoorn RAL, Castello A, Preston GM. Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method. Biomolecules 2020; 10:E661. [PMID: 32344669 PMCID: PMC7226388 DOI: 10.3390/biom10040661] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) play a crucial role in regulating RNA function and fate. However, the full complement of RBPs has only recently begun to be uncovered through proteome-wide approaches such as RNA interactome capture (RIC). RIC has been applied to various cell lines and organisms, including plants, greatly expanding the repertoire of RBPs. However, several technical challenges have limited the efficacy of RIC when applied to plant tissues. Here, we report an improved version of RIC that overcomes the difficulties imposed by leaf tissue. Using this improved RIC method in Arabidopsis leaves, we identified 717 RBPs, generating a deep RNA-binding proteome for leaf tissues. While 75% of these RBPs can be linked to RNA biology, the remaining 25% were previously not known to interact with RNA. Interestingly, we observed that a large number of proteins related to photosynthesis associate with RNA in vivo, including proteins from the four major photosynthetic supercomplexes. As has previously been reported for mammals, a large proportion of leaf RBPs lack known RNA-binding domains, suggesting unconventional modes of RNA binding. We anticipate that this improved RIC method will provide critical insights into RNA metabolism in plants, including how cellular RBPs respond to environmental, physiological and pathological cues.
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Affiliation(s)
- Marcel Bach-Pages
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Felix Homma
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Jiorgos Kourelis
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Fakultät für Biologie, Universität Duisburg-Essen, North Rhine-Westphalia, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Markus Kaiser
- Fakultät für Biologie, Universität Duisburg-Essen, North Rhine-Westphalia, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Gail M. Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
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31
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Smith T, Villanueva E, Queiroz RML, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS. Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome. Curr Opin Chem Biol 2020; 54:70-75. [PMID: 32131038 DOI: 10.1016/j.cbpa.2020.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023]
Abstract
Protein-RNA interactions regulate all aspects of RNA metabolism and are crucial to the function of catalytic ribonucleoproteins. Until recently, the available technologies to capture RNA-bound proteins have been biased toward poly(A) RNA-binding proteins (RBPs) or involve molecular labeling, limiting their application. With the advent of organic-aqueous phase separation-based methods, we now have technologies that efficiently enrich the complete suite of RBPs and enable quantification of RBP dynamics. These flexible approaches to study RBPs and their bound RNA open up new research avenues for systems-level interrogation of protein-RNA interactions.
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Affiliation(s)
- Tom Smith
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Eneko Villanueva
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Rayner M L Queiroz
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Charlotte S Dawson
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Mohamed Elzek
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Erika C Urdaneta
- Humboldt University Berlin, IRI Life Sciences, Philippstr. 13 10115 Berlin, Germany
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Leicester, LE1 7BH, UK
| | - Benedikt M Beckmann
- Humboldt University Berlin, IRI Life Sciences, Philippstr. 13 10115 Berlin, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Kathryn S Lilley
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
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32
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Kilchert C, Sträßer K, Kunetsky V, Änkö ML. From parts lists to functional significance-RNA-protein interactions in gene regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1582. [PMID: 31883228 DOI: 10.1002/wrna.1582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
Hundreds of canonical RNA binding proteins facilitate diverse and essential RNA processing steps in cells forming a central regulatory point in gene expression. However, recent discoveries including the identification of a large number of noncanonical proteins bound to RNA have changed our view on RNA-protein interactions merely as necessary steps in RNA biogenesis. As the list of proteins interacting with RNA has expanded, so has the scope of regulation through RNA-protein interactions. In addition to facilitating RNA metabolism, RNA binding proteins help to form subcellular structures and membraneless organelles, and provide means to recruit components of macromolecular complexes to their sites of action. Moreover, RNA-protein interactions are not static in cells but the ribonucleoprotein (RNP) complexes are highly dynamic in response to cellular cues. The identification of novel proteins in complex with RNA and ways cells use these interactions to control cellular functions continues to broaden the scope of RNA regulation in cells and the current challenge is to move from cataloguing the components of RNPs into assigning them functions. This will not only facilitate our understanding of cellular homeostasis but may bring in key insights into human disease conditions where RNP components play a central role. This review brings together the classical view of regulation accomplished through RNA-protein interactions with the novel insights gained from the identification of RNA binding interactomes. We discuss the challenges in combining molecular mechanism with cellular functions on the journey towards a comprehensive understanding of the regulatory functions of RNA-protein interactions in cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications aRNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Katja Sträßer
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Vladislav Kunetsky
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Minna-Liisa Änkö
- Centre for Reproductive Health and Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
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33
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Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans. iScience 2019; 22:466-476. [PMID: 31835171 PMCID: PMC6926210 DOI: 10.1016/j.isci.2019.11.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/17/2019] [Accepted: 11/21/2019] [Indexed: 01/30/2023] Open
Abstract
The cellular response to hypoxia is crucial to organismal survival, and hypoxia-inducible factors (HIF) are the key mediators of this response. HIF-signaling is central to many human diseases and mediates longevity in the nematode. Despite the rapidly increasing knowledge on RNA-binding proteins (RBPs), little is known about their contribution to hypoxia-induced cellular adaptation. We used RNA interactome capture (RIC) in wild-type Caenorhabditis elegans and vhl-1 loss-of-function mutants to fill this gap. This approach identifies more than 1,300 nematode RBPs, 270 of which can be considered novel RBPs. Interestingly, loss of vhl-1 modulates the RBPome. This difference is not primarily explained by protein abundance suggesting differential RNA-binding. Taken together, our study provides a global view on the nematode RBPome and proteome as well as their modulation by HIF-signaling. The resulting RBP atlas is also provided as an interactive online data mining tool (http://shiny.cecad.uni-koeln.de:3838/celegans_rbpome). RNA interactome capture in wild-type C. elegans and vhl-1 loss-of-function mutants Identification of 1,354 nematode RBPs, 270 of which can be considered novel RBPs The modulation of the RBPome by vhl-1 is primary explained by differential RNA-binding The resulting RBP atlas is provided as an interactive online data mining tool
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34
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Dai XX, Jiang JC, Sha QQ, Jiang Y, Ou XH, Fan HY. A combinatorial code for mRNA 3'-UTR-mediated translational control in the mouse oocyte. Nucleic Acids Res 2019; 47:328-340. [PMID: 30335155 PMCID: PMC6326793 DOI: 10.1093/nar/gky971] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/06/2018] [Indexed: 12/16/2022] Open
Abstract
Meiotic maturation of mammalian oocytes depends on the temporally and spatially regulated cytoplasmic polyadenylation and translational activation of maternal mRNAs. Cytoplasmic polyadenylation is controlled by cis-elements in the 3′-UTRs of mRNAs including the polyadenylation signal (PAS), which is bound by the cleavage and polyadenylation specificity factor (CPSF) and the cytoplasmic polyadenylation element (CPE), which recruits CPE binding proteins. Using the 3′-UTRs of mouse Cpeb1, Btg4 and Cnot6l mRNAs, we deciphered the combinatorial code that controls developmental stage-specific translation during meiotic maturation: (i) translation of a maternal transcript at the germinal vesicle (GV) stage requires one or more PASs that locate far away from CPEs; (ii) PASs distal and proximal to the 3′-end of the transcripts are equally effective in mediating translation at the GV stage, as long as they are not close to the CPEs; (iii) Both translational repression at the GV stage and activation after germinal vesicle breakdown require at least one CPE adjacent to the PAS; (iv) The numbers and positions of CPEs in relation to PASs within the 3′-UTR of a given transcript determines its repression efficiency in GV oocytes. This study reveals a previously unrecognized non-canonical mechanism by which the proximal PASs mediate 3′-terminal polyadenylation and translation of maternal transcripts.
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Affiliation(s)
- Xing-Xing Dai
- MOEKey Laboratory for Biosystems Homeostasis & Protection and InnovationCenter for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jun-Chao Jiang
- MOEKey Laboratory for Biosystems Homeostasis & Protection and InnovationCenter for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qian-Qian Sha
- MOEKey Laboratory for Biosystems Homeostasis & Protection and InnovationCenter for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yu Jiang
- MOEKey Laboratory for Biosystems Homeostasis & Protection and InnovationCenter for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiang-Hong Ou
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Heng-Yu Fan
- MOEKey Laboratory for Biosystems Homeostasis & Protection and InnovationCenter for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
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35
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Sarangdhar MA, Chaubey D, Srikakulam N, Pillai B. Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment. Nucleic Acids Res 2019; 46:9726-9735. [PMID: 30011017 PMCID: PMC6182166 DOI: 10.1093/nar/gky628] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
Transfer of genetic material from parents to progeny via fusion of gametes is a way to ensure flow of information from one generation to the next. Apart from the genetic material, gametes provide a rich source of other factors such as RNA and proteins which can control traits of the embryo. Non-coding RNAs are not only carriers of regulatory information but can also encode memory of events of parental life. Here, we explore the possibility of parental inheritance of non-coding RNAs, especially long non-coding RNAs. Meta-analysis of RNA-seq data revealed several non-coding RNAs present in zebrafish oocyte, sperm and 2cell-stage. The embryo is transcriptionally silent at this stage, we rationalize that all the RNAs detectable at 2cell-stage are deposited either by sperm or oocyte or both and thus inherited. In the inherited pool, we noticed a conserved lncRNA, Cyrano previously known for zebrafish brain development. Knockdown of inherited Cyrano by miR-7 without changing zygotic Cyrano altered brain morphology at 24 hpf and 48 hpf. This defect could be partially rescued by injecting full length Cyrano lncRNA or a mutant resilient to knock-down by miR-7. In future, there is ample scope to check the possibility of inherited lncRNAs as carriers of memory of parental life events and building blocks that set up an initial platform for development.
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Affiliation(s)
- Mayuresh Anant Sarangdhar
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Divya Chaubey
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Nagesh Srikakulam
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi, India
| | - Beena Pillai
- CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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36
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Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Res 2019; 29:1100-1114. [PMID: 31227602 PMCID: PMC6633259 DOI: 10.1101/gr.245159.118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
Posttranscriptional regulation plays a crucial role in shaping gene expression. During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different cis-elements and trans-factors are integrated to determine mRNA stability remains poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3' UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA-protein interactions and found that poly(U)-binding proteins are preferentially associated with 3' UTR sequences and stabilizing motifs. We show that this activity is antagonized by C-rich motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Mario Abdel Messih
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- University of New Haven, West Haven, Connecticut 06516, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Genentech, Incorporated, South San Francisco, California 94080, USA
| | - Panos Oikonomou
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Romain Christiano
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Marlon Stoeckius
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- New York Genome Center, New York, New York 10013, USA
| | - Stephanie Lau
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Hiba Darwich-Codore
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02124, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Saeed Tavazoie
- Department of Biochemistry and Molecular Biophysics, and Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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37
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Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development 2019; 146:146/11/dev161471. [PMID: 31189646 DOI: 10.1242/dev.161471] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of animal embryos is initially directed by maternal gene products. Then, during the maternal-to-zygotic transition (MZT), developmental control is handed to the zygotic genome. Extensive research in both vertebrate and invertebrate model organisms has revealed that the MZT can be subdivided into two phases, during which very different modes of gene regulation are implemented: initially, regulation is exclusively post-transcriptional and post-translational, following which gradual activation of the zygotic genome leads to predominance of transcriptional regulation. These changes in the gene expression program of embryos are precisely controlled and highly interconnected. Here, we review current understanding of the mechanisms that underlie handover of developmental control during the MZT.
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Affiliation(s)
- Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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38
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Packaging development: how chromatin controls transcription in zebrafish embryogenesis. Biochem Soc Trans 2019; 47:713-724. [DOI: 10.1042/bst20180617] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
How developmental gene expression is activated, co-ordinated and maintained is one of the biggest questions in developmental biology. While transcription factors lead the way in directing developmental gene expression, their accessibility to the correct repertoire of genes can depend on other factors such as DNA methylation, the presence of particular histone variants and post-translational modifications of histones. Collectively, factors that modify DNA or affect its packaging and accessibility contribute to a chromatin landscape that helps to control the timely expression of developmental genes. Zebrafish, perhaps better known for their strength as a model of embryology and organogenesis during development, are coming to the fore as a powerful model for interpreting the role played by chromatin in gene expression. Several recent advances have shown that zebrafish exhibit both similarities and differences to other models (and humans) in the way that they employ chromatin mechanisms of gene regulation. Here, I review how chromatin influences developmental transcriptional programmes during early zebrafish development, patterning and organogenesis. Lastly, I briefly highlight the importance of zebrafish chromatin research towards the understanding of human disease and transgenerational inheritance.
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39
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Beckmann BM, Granneman S. Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges. Methods Mol Biol 2019; 2049:213-231. [PMID: 31602614 DOI: 10.1007/978-1-4939-9736-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA-binding proteins are important for core cellular processes such as mRNA transcription, splicing, transport, translation, and degradation. Recently, hundreds of novel RNA-binders have been identified in vivo in various organisms and cell types. We discuss the RNA interactome capture technique which enabled this boost in identifying new RNA-binding proteins in eukaryotes. A focus of this chapter, however, is the presentation of different challenges and problems that need to be addressed to be able to understand the conserved mRNA-bound proteomes from yeast to man.
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Affiliation(s)
- Benedikt M Beckmann
- Molecular Infection Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Sander Granneman
- Centre for Systems and Synthetic Biology (SynthSys), University of Edinburgh, Edinburgh, UK
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40
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Huang R, Han M, Meng L, Chen X. Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy. J Vis Exp 2018. [PMID: 30394395 DOI: 10.3791/58580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A comprehensive identification of RNA-binding proteins (RBPs) is key to understanding the posttranscriptional regulatory network in cells. A widely used strategy for RBP capture exploits the polyadenylation [poly(A)] of target RNAs, which mostly occurs on eukaryotic mature mRNAs, leaving most binding proteins of non-poly(A) RNAs unidentified. Here we describe the detailed procedures of a recently reported method termed click chemistry-assisted RNA-interactome capture (CARIC), which enables the transcriptome-wide capture of both poly(A) and non-poly(A) RBPs by combining the metabolic labeling of RNAs, in vivo UV cross-linking, and bioorthogonal tagging.
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Affiliation(s)
- Rongbing Huang
- College of Chemistry and Molecular Engineering, Peking University; Beijing National Laboratory for Molecular Sciences, Peking University
| | - Mengting Han
- College of Chemistry and Molecular Engineering, Peking University; Beijing National Laboratory for Molecular Sciences, Peking University
| | - Liying Meng
- College of Chemistry and Molecular Engineering, Peking University; Peking-Tsinghua Center for Life Sciences, Peking University
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University; Beijing National Laboratory for Molecular Sciences, Peking University; Peking-Tsinghua Center for Life Sciences, Peking University; Synthetic and Functional Biomolecules Center, Peking University; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University;
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41
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Iadevaia V, Matia-González AM, Gerber AP. An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes. J Vis Exp 2018. [PMID: 30176020 PMCID: PMC6128116 DOI: 10.3791/58223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins (RBPs) play key roles in the post-transcriptional control of gene expression. Therefore, biochemical characterization of mRNA-protein complexes is essential to understanding mRNA regulation inferred by interacting proteins or non-coding RNAs. Herein, we describe a tandem RNA isolation procedure (TRIP) that enables the purification of endogenously formed mRNA-protein complexes from cellular extracts. The two-step protocol involves the isolation of polyadenylated mRNAs with antisense oligo(dT) beads and subsequent capture of an mRNA of interest with 3'-biotinylated 2'-O-methylated antisense RNA oligonucleotides, which can then be isolated with streptavidin beads. TRIP was used to recover in vivo crosslinked mRNA-ribonucleoprotein (mRNP) complexes from yeast, nematodes and human cells for further RNA and protein analysis. Thus, TRIP is a versatile approach that can be adapted to all types of polyadenylated RNAs across organisms to study the dynamic re-arrangement of mRNPs imposed by intracellular or environmental cues.
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Affiliation(s)
- Valentina Iadevaia
- Dept. of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey
| | - Ana M Matia-González
- Dept. of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey
| | - André P Gerber
- Dept. of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey;
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42
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Albihlal WS, Gerber AP. Unconventional
RNA
‐binding proteins: an uncharted zone in
RNA
biology. FEBS Lett 2018; 592:2917-2931. [DOI: 10.1002/1873-3468.13161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Waleed S. Albihlal
- Department of Microbial Sciences School of Biosciences and Medicine Faculty of Health and Medical Sciences University of Surrey Guildford UK
| | - André P. Gerber
- Department of Microbial Sciences School of Biosciences and Medicine Faculty of Health and Medical Sciences University of Surrey Guildford UK
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43
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Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. Proc Natl Acad Sci U S A 2018; 115:E3879-E3887. [PMID: 29636419 DOI: 10.1073/pnas.1718406115] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transcriptome-wide identification of RNA-binding proteins (RBPs) is a prerequisite for understanding the posttranscriptional gene regulation networks. However, proteomic profiling of RBPs has been mostly limited to polyadenylated mRNA-binding proteins, leaving RBPs on nonpoly(A) RNAs, including most noncoding RNAs (ncRNAs) and pre-mRNAs, largely undiscovered. Here we present a click chemistry-assisted RNA interactome capture (CARIC) strategy, which enables unbiased identification of RBPs, independent of the polyadenylation state of RNAs. CARIC combines metabolic labeling of RNAs with an alkynyl uridine analog and in vivo RNA-protein photocross-linking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. Applying CARIC, we identified 597 RBPs in HeLa cells, including 130 previously unknown RBPs. These newly discovered RBPs can likely bind ncRNAs, thus uncovering potential involvement of ncRNAs in processes previously unknown to be ncRNA-related, such as proteasome function and intermediary metabolism. The CARIC strategy should be broadly applicable across various organisms to complete the census of RBPs.
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44
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Arias Escayola D, Neugebauer KM. Dynamics and Function of Nuclear Bodies during Embryogenesis. Biochemistry 2018; 57:2462-2469. [PMID: 29473743 DOI: 10.1021/acs.biochem.7b01262] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nuclear bodies are RNA-rich membraneless organelles in the cell nucleus that concentrate specific sets of nuclear proteins and RNA-protein complexes. Nuclear bodies such as the nucleolus, Cajal body (CB), and the histone locus body (HLB) concentrate factors required for nuclear steps of RNA processing. Formation of these nuclear bodies occurs on genomic loci and is frequently associated with active sites of transcription. Whether nuclear body formation is dependent on a particular gene element, an active process such as transcription, or the nascent RNA present at gene loci is a topic of debate. Recently, this question has been addressed through studies in model organisms and their embryos. The switch from maternally provided RNA and protein to zygotic gene products in early embryos has been well characterized in a variety of organisms. This process, termed maternal-to-zygotic transition, provides an excellent model for studying formation of nuclear bodies before, during, and after the transcriptional activation of the zygotic genome. Here, we review findings in embryos that reveal key principles in the study of the formation and function of nucleoli, CBs, and HLBs. We propose that while particular gene elements may contribute to formation of these nuclear bodies, active transcription promotes maturation of nuclear bodies and efficient RNA processing within them.
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Affiliation(s)
- Dahyana Arias Escayola
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
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45
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Abstract
RNA-binding proteins (RBPs) are typically thought of as proteins that bind RNA through one or multiple globular RNA-binding domains (RBDs) and change the fate or function of the bound RNAs. Several hundred such RBPs have been discovered and investigated over the years. Recent proteome-wide studies have more than doubled the number of proteins implicated in RNA binding and uncovered hundreds of additional RBPs lacking conventional RBDs. In this Review, we discuss these new RBPs and the emerging understanding of their unexpected modes of RNA binding, which can be mediated by intrinsically disordered regions, protein-protein interaction interfaces and enzymatic cores, among others. We also discuss the RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA.
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46
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Meier M, Grant J, Dowdle A, Thomas A, Gerton J, Collas P, O'Sullivan JM, Horsfield JA. Cohesin facilitates zygotic genome activation in zebrafish. Development 2018; 145:dev156521. [PMID: 29158440 DOI: 10.1242/dev.156521] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 11/07/2017] [Indexed: 02/01/2023]
Abstract
At zygotic genome activation (ZGA), changes in chromatin structure are associated with new transcription immediately following the maternal-to-zygotic transition (MZT). The nuclear architectural proteins cohesin and CCCTC-binding factor (CTCF) contribute to chromatin structure and gene regulation. We show here that normal cohesin function is important for ZGA in zebrafish. Depletion of the cohesin subunit Rad21 delays ZGA without affecting cell cycle progression. In contrast, CTCF depletion has little effect on ZGA, whereas complete abrogation is lethal. Genome-wide analysis of Rad21 binding reveals a change in distribution from pericentromeric satellite DNA and other locations, including the miR-430 locus (the products of which are responsible for maternal transcript degradation), to genes, as embryos progress through the MZT. After MZT, a subset of Rad21 binding overlaps the pioneer factor Pou5f3, which activates early expressed genes. Rad21 depletion disrupts the formation of nucleoli and RNA polymerase II foci, suggestive of global defects in chromosome architecture. We propose that Rad21/cohesin redistribution to active areas of the genome is key to the establishment of chromosome organization and the embryonic developmental program.
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Affiliation(s)
- Michael Meier
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Jenny Grant
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Amy Dowdle
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Amarni Thomas
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Jennifer Gerton
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo 0316, Norway
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Private Bag 92019, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Julia A Horsfield
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
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Despic V, Neugebauer KM. RNA tales – how embryos read and discard messages from mom. J Cell Sci 2018; 131:jcs.201996. [DOI: 10.1242/jcs.201996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Following fertilization, embryos develop for a substantial amount of time with a transcriptionally silent genome. Thus, early development is maternally programmed, as it solely relies on RNAs and proteins that are provided by the female gamete. However, these maternal instructions are not sufficient to support later steps of embryogenesis and are therefore gradually replaced by novel products synthesized from the zygotic genome. This switch in the origin of molecular players that drive early development is known as the maternal-to-zygotic transition (MZT). MZT is a universal phenomenon among all metazoans and comprises two interconnected processes: maternal mRNA degradation and the transcriptional awakening of the zygotic genome. The recent adaptation of high-throughput methods for use in embryos has deepened our knowledge of the molecular principles underlying MZT. These mechanisms comprise conserved strategies for RNA regulation that operate in many well-studied cellular contexts but that have adapted differently to early development. In this Review, we will discuss advances in our understanding of post-transcriptional regulatory pathways that drive maternal mRNA clearance during MZT, with an emphasis on recent data in zebrafish embryos on codon-mediated mRNA decay, the contributions of microRNAs (miRNAs) and RNA-binding proteins to this process, and the roles of RNA modifications in the stability control of maternal mRNAs.
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Affiliation(s)
- Vladimir Despic
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Abazova N, Krijgsveld J. Advances in stem cell proteomics. Curr Opin Genet Dev 2017; 46:149-155. [PMID: 28806595 DOI: 10.1016/j.gde.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 12/15/2022]
Abstract
Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity.
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Affiliation(s)
- Nade Abazova
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany.
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Despic V, Dejung M, Butter F, Neugebauer KM. Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches. Methods 2017; 126:44-53. [DOI: 10.1016/j.ymeth.2017.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/15/2017] [Accepted: 07/15/2017] [Indexed: 02/06/2023] Open
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