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Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor Mediated pri- let-7 miRNAs processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593372. [PMID: 38766155 PMCID: PMC11100773 DOI: 10.1101/2024.05.09.593372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
miRNA biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryo-EM and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has structural plasticity to accommodate different pri-miRNAs. These also revealed key structural features of the 5' UG sequence motif, more comprehensively represented as the "fUN" motif. Our analysis explains how the bulged nucleotide in class-II pri-let-7 members alters Drosha cleavage, generating a noncanonical precursor with 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 interacts with the CNNC motif and Drosha's PAZ-like domain, to promote proper Drosha loading onto the basal hairpin junction. Overall, our work illuminates the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
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2
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Mihaylov SR, Castelli LM, Lin YH, Gül A, Soni N, Hastings C, Flynn HR, Păun O, Dickman MJ, Snijders AP, Goldstone R, Bandmann O, Shelkovnikova TA, Mortiboys H, Ultanir SK, Hautbergue GM. The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function. Nat Commun 2023; 14:5496. [PMID: 37679383 PMCID: PMC10485026 DOI: 10.1038/s41467-023-41304-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and an RNA recognition motif, however the RNA-processing function(s) were poorly investigated over the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that its RNA/NXF1-binding activity is required for the nuclear export of some canonical mitochondrial-related mRNAs and mitochondrial homeostasis. Genome-wide investigations reveal that the nuclear export function is not strictly linked to promoter-binding, identifying in turn novel regulatory targets of PGC-1α in non-homologous end-joining and nucleocytoplasmic transport. These findings provide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, aging and neurodegeneration.
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Affiliation(s)
- Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Aytac Gül
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Nikita Soni
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher Hastings
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oana Păun
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Life Science Mass Spectrometry, Bruker Daltonics, Banner Lane, Coventry, CV4 9GH, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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3
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Li D, Yu W, Lai M. Targeting serine- and arginine-rich splicing factors to rectify aberrant alternative splicing. Drug Discov Today 2023; 28:103691. [PMID: 37385370 DOI: 10.1016/j.drudis.2023.103691] [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: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Serine- and arginine-rich splicing factors are pivotal modulators of constitutive splicing and alternative splicing that bind to the cis-acting elements in precursor mRNAs and facilitate the recruitment and assembly of the spliceosome. Meanwhile, SR proteins shuttle between the nucleus and cytoplasm with a broad implication in multiple RNA-metabolizing events. Recent studies have demonstrated the positive correlation of overexpression and/or hyperactivation of SR proteins and development of the tumorous phenotype, indicating the therapeutic potentials of targeting SR proteins. In this review, we highlight key findings concerning the physiological and pathological roles of SR proteins. We have also investigated small molecules and oligonucleotides that effectively modulate the functions of SR proteins, which could benefit future studies of SR proteins.
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Affiliation(s)
- Dianyang Li
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China.
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
| | - Maode Lai
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Science (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China.
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4
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Jia R, Zheng ZM. Oncogenic SRSF3 in health and diseases. Int J Biol Sci 2023; 19:3057-3076. [PMID: 37416784 PMCID: PMC10321290 DOI: 10.7150/ijbs.83368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Serine/arginine rich splicing factor 3 (SRSF3) is an important multi-functional splicing factor, and has attracted increasing attentions in the past thirty years. The importance of SRSF3 is evidenced by its impressively conserved protein sequences in all animals and alternative exon 4 which represents an autoregulatory mechanism to maintain its proper cellular expression level. New functions of SRSF3 have been continuously discovered recently, especially its oncogenic function. SRSF3 plays essential roles in many cellular processes by regulating almost all aspects of RNA biogenesis and processing of many target genes, and thus, contributes to tumorigenesis when overexpressed or disregulated. This review updates and highlights the gene, mRNA, and protein structure of SRSF3, the regulatory mechanisms of SRSF3 expression, and the characteristics of SRSF3 targets and binding sequences that contribute to SRSF3's diverse molecular and cellular functions in tumorigenesis and human diseases.
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Affiliation(s)
- Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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Le MN, Nguyen TD, Nguyen TA. SRSF7 and SRSF3 depend on RNA sequencing motifs and secondary structures to regulate Microprocessor. Life Sci Alliance 2023; 6:e202201779. [PMID: 36750366 PMCID: PMC9905709 DOI: 10.26508/lsa.202201779] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Human Microprocessor cleaves pri-miRNAs to initiate miRNA biogenesis. The accuracy and efficiency of Microprocessor cleavage ensure appropriate miRNA sequence and expression and thus its proper gene regulation. However, Microprocessor cleaves many pri-miRNAs incorrectly, so it requires assistance from many cofactors. For example, SRSF3 enhances Microprocessor cleavage by interacting with the CNNC motif in pri-miRNAs. However, whether SRSF3 can function with other motifs and/or requires the motifs in a certain secondary structure is unknown. In addition, the function of SRSF7 (a paralog of SRSF3) in miRNA biogenesis still needs to be discovered. Here, we demonstrated that SRSF7 could stimulate Microprocessor cleavage. In addition, by conducting high-throughput pri-miRNA cleavage assays for Microprocessor and SRSF7 or SRSF3, we demonstrated that SRSF7 and SRSF3 function with the CRC and CNNC motifs, adopting certain secondary structures. In addition, SRSF7 and SRSF3 affect the Microprocessor cleavage sites in human cells. Our findings demonstrate the roles of SRSF7 in miRNA biogenesis and provide a comprehensive view of the molecular mechanism of SRSF7 and SRSF3 in enhancing Microprocessor cleavage.
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Affiliation(s)
- Minh Ngoc Le
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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6
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Cooperative Binding of SRSF3 to Structured 3'ss-α Exon RNA during α Exon Inclusion in the ZO-1 mRNA. Curr Issues Mol Biol 2023; 45:593-603. [PMID: 36661525 PMCID: PMC9857539 DOI: 10.3390/cimb45010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
ZO-1α+ and ZO-1α- proteins are expressed in hermetic and leaky tight junctions, respectively. Two cis-acting distant exonic elements partly activate the 240 nucleotide-long α exon producing the ZO-1α+ isoform. However, the elements within and around the α exon and their respective factors involved in its splicing are unknown. To study the dynamic interaction between SRSF3 and its bioinformatically predicted target sites around the 3'ss upstream of the α exon during its activation, we performed EMSA, crosslinking, and in vivo splicing assays by ZO-1 minigene expression and siRNA-mediated silencing in transfected cells. Using V1 RNase, we probed the possible formation of a hairpin RNA structure between the intronic and proximal exonic SRSF3 binding sites. The hairpin sufficed for complex formations in the EMSA. The interaction of SRSF3 with the intronic site promoted the cooperative binding of SRSF3 to the exonic site. Finally, SRSF3 restored α exon activation in SRSF3 knockdown transfectants. Altogether, our results show that SRSF3-hairpin RNA interaction is crucial in the early recognition of 3'ss for α exon activation. It remains to be explored whether SRSF3 recruits or stabilizes the binding of other factors or brings separate splice sites into proximity.
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Shi W, Yang J, Chen D, Yin C, Zhang H, Xu X, Pan X, Wang R, Fei L, Li M, Qi L, Bhadauria V, Liu J, Peng YL. The rice blast fungus SR protein 1 regulates alternative splicing with unique mechanisms. PLoS Pathog 2022; 18:e1011036. [PMID: 36480554 PMCID: PMC9767378 DOI: 10.1371/journal.ppat.1011036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/20/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are well known as splicing factors in humans, model animals and plants. However, they are largely unknown in regulating pre-mRNA splicing of filamentous fungi. Here we report that the SR protein MoSrp1 enhances and suppresses alternative splicing in a model fungal plant pathogen Magnaporthe oryzae. Deletion of MoSRP1 caused multiple defects, including reduced virulence and thousands of aberrant alternative splicing events in mycelia, most of which were suppressed or enhanced intron splicing. A GUAG consensus bound by MoSrp1 was identified in more than 94% of the intron or/and proximate exons having the aberrant splicing. The dual functions of regulating alternative splicing of MoSrp1 were exemplified in enhancing and suppressing the consensus-mediated efficient splicing of the introns in MoATF1 and MoMTP1, respectively, which both were important for mycelial growth, conidiation, and virulence. Interestingly, MoSrp1 had a conserved sumoylation site that was essential to nuclear localization and enhancing GUAG binding. Further, we showed that MoSrp1 interacted with a splicing factor and two components of the exon-joining complex via its N-terminal RNA recognition domain, which was required to regulate mycelial growth, development and virulence. In contrast, the C-terminus was important only for virulence and stress responses but not for mycelial growth and development. In addition, only orthologues from Pezizomycotina species could completely rescue defects of the deletion mutants. This study reveals that the fungal conserved SR protein Srp1 regulates alternative splicing in a unique manner.
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Affiliation(s)
- Wei Shi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jun Yang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Deng Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Changfa Yin
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Huixia Zhang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaozhou Xu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiao Pan
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ruijin Wang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Liwang Fei
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Mengfei Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Linlu Qi
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Vijai Bhadauria
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junfeng Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- * E-mail:
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circSMARCA5 Is an Upstream Regulator of the Expression of miR-126-3p, miR-515-5p, and Their mRNA Targets, Insulin-like Growth Factor Binding Protein 2 ( IGFBP2) and NRAS Proto-Oncogene, GTPase ( NRAS) in Glioblastoma. Int J Mol Sci 2022; 23:ijms232213676. [PMID: 36430152 PMCID: PMC9690846 DOI: 10.3390/ijms232213676] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022] Open
Abstract
The involvement of non-coding RNAs (ncRNAs) in glioblastoma multiforme (GBM) pathogenesis and progression has been ascertained but their cross-talk within GBM cells remains elusive. We previously demonstrated the role of circSMARCA5 as a tumor suppressor (TS) in GBM. In this paper, we explore the involvement of circSMARCA5 in the control of microRNA (miRNA) expression in GBM. By using TaqMan® low-density arrays, the expression of 748 miRNAs was assayed in U87MG overexpressing circSMARCA5. Differentially expressed (DE) miRNAs were validated through single TaqMan® assays in: (i) U87MG overexpressing circSMARCA5; (ii) four additional GBM cell lines (A172; CAS-1; SNB-19; U251MG); (iii) thirty-eight GBM biopsies; (iv) twenty biopsies of unaffected brain parenchyma (UC). Validated targets of DE miRNAs were selected from the databases TarBase and miRTarbase, and the literature; their expression was inferred from the GBM TCGA dataset. Expression was assayed in U87MG overexpressing circSMARCA5, GBM cell lines, and biopsies through real-time PCR. TS miRNAs 126-3p and 515-5p were upregulated following circSMARCA5 overexpression in U87MG and their expression was positively correlated with that of circSMARCA5 (r-values = 0.49 and 0.50, p-values = 9 × 10-5 and 7 × 10-5, respectively) in GBM biopsies. Among targets, IGFBP2 (target of miR-126-3p) and NRAS (target of miR-515-5p) mRNAs were positively correlated (r-value = 0.46, p-value = 0.00027), while their expression was negatively correlated with that of circSMARCA5 (r-values = -0.58 and -0.30, p-values = 0 and 0.019, respectively), miR-126-3p (r-value = -0.36, p-value = 0.0066), and miR-515-5p (r-value = -0.34, p-value = 0.010), respectively. Our data identified a new GBM subnetwork controlled by circSMARCA5, which regulates downstream miRNAs 126-3p and 515-5p, and their mRNA targets IGFBP2 and NRAS.
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The Role of RNA-Binding Proteins in Hematological Malignancies. Int J Mol Sci 2022; 23:ijms23179552. [PMID: 36076951 PMCID: PMC9455611 DOI: 10.3390/ijms23179552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Hematological malignancies comprise a plethora of different neoplasms, such as leukemia, lymphoma, and myeloma, plus a myriad of dysplasia, such as myelodysplastic syndromes or anemias. Despite all the advances in patient care and the development of new therapies, some of these malignancies remain incurable, mainly due to resistance and refractoriness to treatment. Therefore, there is an unmet clinical need to identify new biomarkers and potential therapeutic targets that play a role in treatment resistance and contribute to the poor outcomes of these tumors. RNA-binding proteins (RBPs) are a diverse class of proteins that interact with transcripts and noncoding RNAs and are involved in every step of the post-transcriptional processing of transcripts. Dysregulation of RBPs has been associated with the development of hematological malignancies, making them potential valuable biomarkers and potential therapeutic targets. Although a number of dysregulated RBPs have been identified in hematological malignancies, there is a critical need to understand the biology underlying their contribution to pathology, such as the spatiotemporal context and molecular mechanisms involved. In this review, we emphasize the importance of deciphering the regulatory mechanisms of RBPs to pinpoint novel therapeutic targets that could drive or contribute to hematological malignancy biology.
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Müller L, Ptok J, Nisar A, Antemann J, Grothmann R, Hillebrand F, Brillen AL, Ritchie A, Theiss S, Schaal H. Modeling splicing outcome by combining 5'ss strength and splicing regulatory elements. Nucleic Acids Res 2022; 50:8834-8851. [PMID: 35947702 PMCID: PMC9410876 DOI: 10.1093/nar/gkac663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/23/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
Correct pre-mRNA processing in higher eukaryotes vastly depends on splice site recognition. Beyond conserved 5'ss and 3'ss motifs, splicing regulatory elements (SREs) play a pivotal role in this recognition process. Here, we present in silico designed sequences with arbitrary a priori prescribed splicing regulatory HEXplorer properties that can be concatenated to arbitrary length without changing their regulatory properties. We experimentally validated in silico predictions in a massively parallel splicing reporter assay on more than 3000 sequences and exemplarily identified some SRE binding proteins. Aiming at a unified 'functional splice site strength' encompassing both U1 snRNA complementarity and impact from neighboring SREs, we developed a novel RNA-seq based 5'ss usage landscape, mapping the competition of pairs of high confidence 5'ss and neighboring exonic GT sites along HBond and HEXplorer score coordinate axes on human fibroblast and endothelium transcriptome datasets. These RNA-seq data served as basis for a logistic 5'ss usage prediction model, which greatly improved discrimination between strong but unused exonic GT sites and annotated highly used 5'ss. Our 5'ss usage landscape offers a unified view on 5'ss and SRE neighborhood impact on splice site recognition, and may contribute to improved mutation assessment in human genetics.
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Affiliation(s)
| | | | - Azlan Nisar
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany,Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen 45665, Germany
| | - Jennifer Antemann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Ramona Grothmann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | | | - Heiner Schaal
- To whom correspondence should be addressed. Tel: +49 211 81 12393; Fax: +49 211 81 10856;
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11
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Conformational effects of a cancer-linked mutation in pri-miR-30c RNA. J Mol Biol 2022; 434:167705. [PMID: 35760371 DOI: 10.1016/j.jmb.2022.167705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that mediate post-transcriptional downregulation of specific target genes. These transcripts are the products of a two-step processing pathway; primary miRNAs (pri-miRNAs) are processed by Drosha into individual precursor miRNA (pre-miRNA) hairpins, which are subsequently processed by Dicer into mature miRNAs. Single nucleotide polymorphisms (SNPs) that occur in pri-miRNAs, pre-miRNAs and mature miRNAs have been shown to affect the processing of specific target genes by modulating Drosha and Dicer processing or interactions with RNA binding proteins (RBPs). Using NMR and single-molecule optical tweezer experiments, we have investigated the conformational effects of a cancer-linked G/A mutation in the terminal loop of pri-miR-30c RNA, and how this influences binding by the SRSF3 and hnRNP A1 RBPs, which are implicated in its processing. Our results reveal that the wildtype and G/A variant pri-miR-30c RNAs adopt very similar elongated stem-loop structures, both of which are bound by SRSF3. However, while both wildtype and G/A pri-miR-30c RNAs can form dimeric kissing hairpin structures, the G to A mutation results in partial destabilization of the dimer in the variant transcript. This promotes recognition and binding by hnRNP A1, an RBP that enhances pri-miR-30c processing. Our data provide structural insight into the conformational effects of a G/A mutation in pri-miR-30c RNA and how this could affect processing and promote cancer.
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12
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SRSF3 facilitates replication of influenza A virus via binding and promoting the transport of viral mRNA. Vet Microbiol 2022; 266:109343. [DOI: 10.1016/j.vetmic.2022.109343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/11/2022] [Accepted: 01/16/2022] [Indexed: 12/17/2022]
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13
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Kubina J, Geldreich A, Gales JP, Baumberger N, Bouton C, Ryabova LA, Grasser KD, Keller M, Dimitrova M. Nuclear export of plant pararetrovirus mRNAs involves the TREX complex, two viral proteins and the highly structured 5' leader region. Nucleic Acids Res 2021; 49:8900-8922. [PMID: 34370034 PMCID: PMC8421220 DOI: 10.1093/nar/gkab653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, the major nuclear export pathway for mature mRNAs uses the dimeric receptor TAP/p15, which is recruited to mRNAs via the multisubunit TREX complex, comprising the THO core and different export adaptors. Viruses that replicate in the nucleus adopt different strategies to hijack cellular export factors and achieve cytoplasmic translation of their mRNAs. No export receptors are known in plants, but Arabidopsis TREX resembles the mammalian complex, with a conserved hexameric THO core associated with ALY and UIEF proteins, as well as UAP56 and MOS11. The latter protein is an orthologue of mammalian CIP29. The nuclear export mechanism for viral mRNAs has not been described in plants. To understand this process, we investigated the export of mRNAs of the pararetrovirus CaMV in Arabidopsis and demonstrated that it is inhibited in plants deficient in ALY, MOS11 and/or TEX1. Deficiency for these factors renders plants partially resistant to CaMV infection. Two CaMV proteins, the coat protein P4 and reverse transcriptase P5, are important for nuclear export. P4 and P5 interact and co-localise in the nucleus with the cellular export factor MOS11. The highly structured 5′ leader region of 35S RNAs was identified as an export enhancing element that interacts with ALY1, ALY3 and MOS11 in vitro.
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Affiliation(s)
- Julie Kubina
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Angèle Geldreich
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jón Pol Gales
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Nicolas Baumberger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Clément Bouton
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lyubov A Ryabova
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93053 Regensburg, Germany
| | - Mario Keller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Maria Dimitrova
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
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14
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Haward F, Maslon MM, Yeyati PL, Bellora N, Hansen JN, Aitken S, Lawson J, von Kriegsheim A, Wachten D, Mill P, Adams IR, Caceres JF. Nucleo-cytoplasmic shuttling of splicing factor SRSF1 is required for development and cilia function. eLife 2021; 10:e65104. [PMID: 34338635 PMCID: PMC8352595 DOI: 10.7554/elife.65104] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
Shuttling RNA-binding proteins coordinate nuclear and cytoplasmic steps of gene expression. The SR family proteins regulate RNA splicing in the nucleus and a subset of them, including SRSF1, shuttles between the nucleus and cytoplasm affecting post-splicing processes. However, the physiological significance of this remains unclear. Here, we used genome editing to knock-in a nuclear retention signal (NRS) in Srsf1 to create a mouse model harboring an SRSF1 protein that is retained exclusively in the nucleus. Srsf1NRS/NRS mutants displayed small body size, hydrocephalus, and immotile sperm, all traits associated with ciliary defects. We observed reduced translation of a subset of mRNAs and decreased abundance of proteins involved in multiciliogenesis, with disruption of ciliary ultrastructure and motility in cells and tissues derived from this mouse model. These results demonstrate that SRSF1 shuttling is used to reprogram gene expression networks in the context of high cellular demands, as observed here, during motile ciliogenesis.
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Affiliation(s)
- Fiona Haward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Patricia L Yeyati
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Nicolas Bellora
- Institute of Nuclear Technologies for Health (Intecnus), National Scientific and Technical Research Council (CONICET)BarilocheArgentina
| | - Jan N Hansen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Jennifer Lawson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Alex von Kriegsheim
- Edinburgh Cancer Research United Kingdom Centre, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Javier F Caceres
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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15
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Khan M, Hou S, Azam S, Lei H. Sequence-dependent recruitment of SRSF1 and SRSF7 to intronless lncRNA NKILA promotes nuclear export via the TREX/TAP pathway. Nucleic Acids Res 2021; 49:6420-6436. [PMID: 34096602 PMCID: PMC8216466 DOI: 10.1093/nar/gkab445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022] Open
Abstract
The TREX-TAP pathway is vital for mRNA export. For spliced mRNA, the TREX complex is recruited during splicing; however, for intronless mRNA, recruitment is sequence dependent. However, the export of cytoplasmic long noncoding RNA (lncRNA) is poorly characterized. We report the identification of a cytoplasmic accumulation region (CAR-N) in the intronless lncRNA, NKILA. CAR-N removal led to strong nuclear retention of NKILA, and CAR-N insertion promoted the export of cDNA transcripts. In vitro RNP purification via CAR-N, mass spectrometry, and siRNA screening revealed that SRSF1 and SRSF7 were vital to NKILA export, and identified a cluster of SRSF1/7 binding sites within a 55 nucleotide sequence in CAR-N. Significant nuclear enrichment of NKILA was observed for NKILA lacking CAR-N or the cluster of binding sites in knock-in models. Depletion of TREX-TAP pathway components resulted in strong nuclear retention of NKILA. RNA and protein immunoprecipitation verified that SRSF1/7 were bound to NKILA and interacted with UAP56 and ALYREF. Moreover, NKILA lacking CAR-N was unable to inhibit breast cancer cell migration. We concluded that the binding of SRSF1/7 to clustered motifs in CAR-N facilitated TREX recruitment, promoting the export of NKILA, and confirmed the importance of NKILA localization to its function.
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Affiliation(s)
- Misbah Khan
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, 9 West Section, Lvshun South Rd, Dalian 116044, P.R. China
| | - Shuai Hou
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, 9 West Section, Lvshun South Rd, Dalian 116044, P.R. China.,School of Food Science and Technology, Dalian Polytechnic University, Dalian 1160343, P.R. China
| | - Sikandar Azam
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, 9 West Section, Lvshun South Rd, Dalian 116044, P.R. China.,Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, USA
| | - Haixin Lei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, 9 West Section, Lvshun South Rd, Dalian 116044, P.R. China
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16
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Abstract
After human immunodeficiency virus type 1 (HIV-1) was identified in the early 1980s, intensive work began to understand the molecular basis of HIV-1 gene expression. Subgenomic HIV-1 RNA regions, spread throughout the viral genome, were described to have a negative impact on the nuclear export of some viral transcripts. Those studies revealed an intrinsic RNA code as a new form of nuclear export regulation. Since such regulatory regions were later also identified in other viruses, as well as in cellular genes, it can be assumed that, during evolution, viruses took advantage of them to achieve more sophisticated replication mechanisms. Here, we review HIV-1 cis-acting repressive sequences that have been identified, and we discuss their possible underlying mechanisms and importance. Additionally, we show how current bioinformatic tools might allow more predictive approaches to identify and investigate them.
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17
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Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genet Sel Evol 2021; 53:43. [PMID: 33947333 PMCID: PMC8097994 DOI: 10.1186/s12711-021-00632-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. RESULTS By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3'UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. CONCLUSIONS Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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18
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Wang H, Jiang Y. SRp20: A potential therapeutic target for human tumors. Pathol Res Pract 2021; 224:153444. [PMID: 34126370 DOI: 10.1016/j.prp.2021.153444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/11/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022]
Abstract
As an important member of SR protein family, SRp20 plays a crucial role in alternative splicing. It not only participates in cell cycle regulation, export of mRNA, cleaving of primary microRNAs, homologous recombination-mediated DNA repair, cellular senescence and apoptosis, but also gets involved in the integrity and pluripotency of genome. Alternative splicing maintains a strict balance in the body to ensure the normal physiological function of cells. Once the balance is broken, diseases, even tumors, will follow. Through the analysis of SRp20-related articles, we found that Alzheimer's disease, glaucoma, bipolar disorder and other diseases have a certain relationship with SRp20. More importantly, SRp20 is closely related to the occurrence, proliferation, invasion and metastasis of various tumors, as well as chemotherapy resistance. Some SRp20 inhibitors have shown significant anticancer efficacy, suggesting a potential therapeutic strategy for tumors.
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Affiliation(s)
- Han Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China.
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19
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Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRDL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M. SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol 2021; 22:82. [PMID: 33706811 PMCID: PMC7948361 DOI: 10.1186/s13059-021-02298-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Results Here we combine iCLIP and 3′-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3′UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3′UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3′UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3′UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3′UTRs. Conclusions We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02298-y.
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Affiliation(s)
- Oliver Daniel Schwich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Marius Wegener
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Samarth Thonta Setty
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Melinda Elaine Brunstein
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | | | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - François McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Michaela Müller-McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.
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20
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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21
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Guha S, Bhaumik SR. Viral regulation of mRNA export with potentials for targeted therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194655. [PMID: 33246183 DOI: 10.1016/j.bbagrm.2020.194655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Eukaryotic gene expression begins with transcription in the nucleus to synthesize mRNA (messenger RNA), which is subsequently exported to the cytoplasm for translation to protein. Like transcription and translation, mRNA export is an important regulatory step of eukaryotic gene expression. Various factors are involved in regulating mRNA export, and thus gene expression. Intriguingly, some of these factors interact with viral proteins, and such interactions interfere with mRNA export of the host cell, favoring viral RNA export. Hence, viruses hijack host mRNA export machinery for export of their own RNAs from nucleus to cytoplasm for translation to proteins for viral life cycle, suppressing host mRNA export (and thus host gene expression and immune/antiviral response). Therefore, the molecules that can impair the interactions of these mRNA export factors with viral proteins could emerge as antiviral therapeutic agents to suppress viral RNA transport and enhance host mRNA export, thereby promoting host gene expression and immune response. Thus, there has been a number of studies to understand how virus hijacks mRNA export machinery in suppressing host gene expression and promoting its own RNA export to the cytoplasm for translation to proteins required for viral replication/assembly/life cycle towards developing targeted antiviral therapies, as concisely described here.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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22
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Zhou Z, Gong Q, Lin Z, Wang Y, Li M, Wang L, Ding H, Li P. Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. Front Oncol 2020; 10:577636. [PMID: 33072610 PMCID: PMC7544984 DOI: 10.3389/fonc.2020.577636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
Ser/Arg-rich (SR) proteins are RNA-binding proteins known as constitutive and alternative splicing (AS) regulators that regulate multiple aspects of the gene expression program. Ser/Arg-rich splicing factor 3 (SRSF3) is the smallest member of the SR protein family, and its level is controlled by multiple factors and involves complex mechanisms in eukaryote cells, whereas the aberrant expression of SRSF3 is associated with many human diseases, including cancer. Here, we review state-of-the-art research on SRSF3 in terms of its function, expression, and misregulation in human cancers. We emphasize the negative consequences of the overexpression of the SRSF3 oncogene in cancers, the pathways underlying SRSF3-mediated transformation, and implications of potential anticancer drugs by downregulation of SRSF3 expression for cancer therapy. Cumulative research on SRSF3 provides critical insight into its essential part in maintaining cellular processes, offering potential new targets for anti-cancer therapy.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Qi Gong
- Departments of Pediatrics, Second Clinical Medical College of Qingdao University, Qingdao, China
| | - Zhijuan Lin
- Key Laboratory for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Mengkun Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hongfei Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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23
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Janowski R, Niessing D. The large family of PC4-like domains - similar folds and functions throughout all kingdoms of life. RNA Biol 2020; 17:1228-1238. [PMID: 32476604 PMCID: PMC7549692 DOI: 10.1080/15476286.2020.1761639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved β-β-β-β-α-linker-β-β-β-β-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a β-β-β-β-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.
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Affiliation(s)
- Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University , Ulm, Germany
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24
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Kundinger SR, Bishof I, Dammer EB, Duong DM, Seyfried NT. Middle-Down Proteomics Reveals Dense Sites of Methylation and Phosphorylation in Arginine-Rich RNA-Binding Proteins. J Proteome Res 2020; 19:1574-1591. [PMID: 31994892 DOI: 10.1021/acs.jproteome.9b00633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Post-translational modifications (PTMs) within arginine (Arg)-rich RNA-binding proteins, such as phosphorylation and methylation, regulate multiple steps in RNA metabolism. However, the identification of PTMs within Arg-rich domains with complete trypsin digestion is extremely challenging due to the high density of Arg residues within these proteins. Here, we report a middle-down proteomic approach coupled with electron-transfer dissociation (ETD) mass spectrometry to map previously unknown sites of phosphorylation and methylation within the Arg-rich domains of U1-70K and structurally similar RNA-binding proteins from nuclear extracts of human embryonic kidney (HEK)-293T cells. Notably, the Arg-rich domains in RNA-binding proteins are densely modified by methylation and phosphorylation compared with the remainder of the proteome, with methylation and phosphorylation favoring RSRS motifs. Although they favor a common motif, analysis of combinatorial PTMs within RSRS motifs indicates that phosphorylation and methylation do not often co-occur, suggesting that they may functionally oppose one another. Furthermore, we show that phosphorylation may modify interactions between Arg-rich proteins, as serine-arginine splicing factor 2 (SRSF2) has a stronger association with U1-70K and LUC7L3 upon dephosphorylation. Collectively, these findings suggest that the level of PTMs within Arg-rich domains may be among the highest in the proteome and a possible unexplored regulator of RNA-binding protein interactions.
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25
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Integrative Structural Biology of Protein-RNA Complexes. Structure 2020; 28:6-28. [DOI: 10.1016/j.str.2019.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
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26
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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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27
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Scott DD, Aguilar LC, Kramar M, Oeffinger M. It's Not the Destination, It's the Journey: Heterogeneity in mRNA Export Mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:33-81. [PMID: 31811630 DOI: 10.1007/978-3-030-31434-7_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The process of creating a translation-competent mRNA is highly complex and involves numerous steps including transcription, splicing, addition of modifications, and, finally, export to the cytoplasm. Historically, much of the research on regulation of gene expression at the level of the mRNA has been focused on either the regulation of mRNA synthesis (transcription and splicing) or metabolism (translation and degradation). However, in recent years, the advent of new experimental techniques has revealed the export of mRNA to be a major node in the regulation of gene expression, and numerous large-scale and specific mRNA export pathways have been defined. In this chapter, we will begin by outlining the mechanism by which most mRNAs are homeostatically exported ("bulk mRNA export"), involving the recruitment of the NXF1/TAP export receptor by the Aly/REF and THOC5 components of the TREX complex. We will then examine various mechanisms by which this pathway may be controlled, modified, or bypassed in order to promote the export of subset(s) of cellular mRNAs, which include the use of metazoan-specific orthologs of bulk mRNA export factors, specific cis RNA motifs which recruit mRNA export machinery via specific trans-acting-binding factors, posttranscriptional mRNA modifications that act as "inducible" export cis elements, the use of the atypical mRNA export receptor, CRM1, and the manipulation or bypass of the nuclear pore itself. Finally, we will discuss major outstanding questions in the field of mRNA export heterogeneity and outline how cutting-edge experimental techniques are providing new insights into and tools for investigating the intriguing field of mRNA export heterogeneity.
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Affiliation(s)
- Daniel D Scott
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | | | - Mathew Kramar
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada. .,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada. .,Faculté de Médecine, Département de Biochimie, Université de Montréal, Montréal, QC, Canada.
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28
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Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nat Chem Biol 2019; 16:150-159. [PMID: 31768034 PMCID: PMC6982592 DOI: 10.1038/s41589-019-0404-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022]
Abstract
Covalent probes serve as valuable tools for global investigation of protein function and ligand binding capacity. Despite efforts to expand coverage of residues available for chemical proteomics (e.g. cysteine and lysine), a large fraction of the proteome remains inaccessible with current activity-based probes. Here, we introduce sulfur-triazole exchange (SuTEx) chemistry as a tunable platform for developing covalent probes with broad applications for chemical proteomics. We show modifications to the triazole leaving group can furnish sulfonyl probes with ~5-fold enhanced chemoselectivity for tyrosines over other nucleophilic amino acids to investigate, for the first time, more than 10,000 tyrosine sites in lysates and live cells. We discover that tyrosines with enhanced nucleophilicity are enriched in enzymatic, protein-protein interaction, and nucleotide recognition domains. We apply SuTEx as a chemical phosphoproteomics strategy to monitor activation of phosphotyrosine sites. Collectively, we describe SuTEx as a biocompatible chemistry for chemical biology investigations of the human proteome.
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29
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Jia R, Ajiro M, Yu L, McCoy P, Zheng ZM. Oncogenic splicing factor SRSF3 regulates ILF3 alternative splicing to promote cancer cell proliferation and transformation. RNA (NEW YORK, N.Y.) 2019; 25:630-644. [PMID: 30796096 PMCID: PMC6467003 DOI: 10.1261/rna.068619.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/28/2023]
Abstract
Alternative RNA splicing is an important focus in molecular and clinical oncology. We report here that SRSF3 regulates alternative RNA splicing of interleukin enhancer binding factor 3 (ILF3) and production of this double-strand RNA-binding protein. An increased coexpression of ILF3 isoforms and SRSF3 was found in various types of cancers. ILF3 isoform-1 and isoform-2 promote cell proliferation and transformation. Tumor cells with reduced SRSF3 expression produce aberrant isoform-5 and -7 of ILF3. By binding to RNA sequence motifs, SRSF3 regulates the production of various ILF3 isoforms by exclusion/inclusion of ILF3 exon 18 or by selection of an alternative 3' splice site within exon 18. ILF3 isoform-5 and isoform-7 suppress tumor cell proliferation and the isoform-7 induces cell apoptosis. Our data indicate that ILF3 isoform-1 and isoform-2 are two critical factors for cell proliferation and transformation. The increased SRSF3 expression in cancer cells plays an important role in maintaining the steady status of ILF3 isoform-1 and isoform-2.
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Affiliation(s)
- Rong Jia
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Ke Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Masahiko Ajiro
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Lulu Yu
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Philip McCoy
- Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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30
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The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition. J Mol Biol 2019; 431:498-510. [DOI: 10.1016/j.jmb.2018.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 01/26/2023]
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31
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View from an mRNP: The Roles of SR Proteins in Assembly, Maturation and Turnover. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:83-112. [PMID: 31811631 DOI: 10.1007/978-3-030-31434-7_3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Serine- and arginine-rich proteins (SR proteins) are a family of multitasking RNA-binding proteins (RBPs) that are key determinants of messenger ribonucleoprotein (mRNP) formation, identity and fate. Apart from their essential functions in pre-mRNA splicing, SR proteins display additional pre- and post-splicing activities and connect nuclear and cytoplasmic gene expression machineries. Through changes in their post-translational modifications (PTMs) and their subcellular localization, they provide functional specificity and adjustability to mRNPs. Transcriptome-wide UV crosslinking and immunoprecipitation (CLIP-Seq) studies revealed that individual SR proteins are present in distinct mRNPs and act in specific pairs to regulate different gene expression programmes. Adopting an mRNP-centric viewpoint, we discuss the roles of SR proteins in the assembly, maturation, quality control and turnover of mRNPs and describe the mechanisms by which they integrate external signals, coordinate their multiple tasks and couple subsequent mRNA processing steps.
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32
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Erkelenz S, Theiss S, Kaisers W, Ptok J, Walotka L, Müller L, Hillebrand F, Brillen AL, Sladek M, Schaal H. Ranking noncanonical 5' splice site usage by genome-wide RNA-seq analysis and splicing reporter assays. Genome Res 2018; 28:1826-1840. [PMID: 30355602 PMCID: PMC6280755 DOI: 10.1101/gr.235861.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/20/2018] [Indexed: 01/01/2023]
Abstract
Most human pathogenic mutations in 5' splice sites affect the canonical GT in positions +1 and +2, leading to noncanonical dinucleotides. On the other hand, noncanonical dinucleotides are observed under physiological conditions in ∼1% of all human 5'ss. It is therefore a challenging task to understand the pathogenic mutation mechanisms underlying the conditions under which noncanonical 5'ss are used. In this work, we systematically examined noncanonical 5' splice site selection, both experimentally using splicing competition reporters and by analyzing a large RNA-seq data set of 54 fibroblast samples from 27 subjects containing a total of 2.4 billion gapped reads covering 269,375 exon junctions. From both approaches, we consistently derived a noncanonical 5'ss usage ranking GC > TT > AT > GA > GG > CT. In our competition splicing reporter assay, noncanonical splicing was strictly dependent on the presence of upstream or downstream splicing regulatory elements (SREs), and changes in SREs could be compensated by variation of U1 snRNA complementarity in the competing 5'ss. In particular, we could confirm splicing at different positions (i.e., -1, +1, +5) of a splice site for all noncanonical dinucleotides "weaker" than GC. In our comprehensive RNA-seq data set analysis, noncanonical 5'ss were preferentially detected in weakly used exon junctions of highly expressed genes. Among high-confidence splice sites, they were 10-fold overrepresented in clusters with a neighboring, more frequently used 5'ss. Conversely, these more frequently used neighbors contained only the dinucleotides GT, GC, and TT, in accordance with the above ranking.
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Affiliation(s)
- Steffen Erkelenz
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Center for Biological and Medical Research (BMFZ), Center of Bioinformatics and Biostatistics (CBiBs), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lara Walotka
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Michael Sladek
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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33
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Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I, Wilson SA. The m 6A-methylase complex recruits TREX and regulates mRNA export. Sci Rep 2018; 8:13827. [PMID: 30218090 PMCID: PMC6138711 DOI: 10.1038/s41598-018-32310-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/04/2018] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modification has previously been shown to alter the export kinetics for mRNAs though the molecular details surrounding this phenomenon remain poorly understood. Recruitment of the TREX mRNA export complex to mRNA is driven by transcription, 5' capping and pre-mRNA splicing. Here we identify a fourth mechanism in human cells driving the association of TREX with mRNA involving the m6A methylase complex. We show that the m6A complex recruits TREX to m6A modified mRNAs and this process is essential for their efficient export. TREX also stimulates recruitment of the m6A reader protein YTHDC1 to the mRNA and the m6A complex influences the interaction of TREX with YTHDC1. Together our studies reveal a key role for TREX in the export of m6A modified mRNAs.
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Affiliation(s)
- Simon Lesbirel
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Matthew Parker
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Jacob Parker
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Catherine Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK.
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34
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Kim K, Nguyen TD, Li S, Nguyen TA. SRSF3 recruits DROSHA to the basal junction of primary microRNAs. RNA (NEW YORK, N.Y.) 2018; 24:892-898. [PMID: 29615481 PMCID: PMC6004053 DOI: 10.1261/rna.065862.118] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/29/2018] [Indexed: 05/22/2023]
Abstract
The Microprocessor complex, consisting of an RNase III DROSHA and the DGCR8 dimer, cleaves primary microRNA transcripts (pri-miRNAs) to initiate microRNA (miRNA) maturation. Pri-miRNAs are stem-loop RNAs, and ∼79% of them contain at least one of the three major and conserved RNA motifs, UG, UGU, and CNNC. We recently demonstrated that the basal UG and apical UGU motifs of pri-miRNAs interact with DROSHA and DGCR8, respectively. They help orient Microprocessor on pri-miRNA in a proper direction in which DROSHA and DGCR8 localize to the basal and apical pri-miRNA junctions, respectively. In addition, CNNC, located at ∼17 nucleotides (nt) from the Microprocessor cleavage site, interacts with SRSF3 (SRp20) to stimulate Microprocessor to process pri-miRNAs. The mechanism underlying this stimulation, however, is unknown. In this study, we discovered that SRSF3 recruits DROSHA to the basal junction in a CNNC-dependent manner, thereby enhancing Microprocessor activity. Furthermore, by generating various pri-miRNA substrates containing CNNC at different locations, we demonstrated that such stimulation only occurs when CNNC is located at ∼17 nt from the Microprocessor cleavage site. Our findings reveal the molecular mechanism of SRSF3 in pri-miRNA processing and support the previously proposed explanation for the highly conserved position of CNNC in SRSF3-enhanced pri-miRNA processing.
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Affiliation(s)
- Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Trung Duc Nguyen
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- HKUST Shenzhen Research Institute, Shenzhen 518057, China
| | - Shaohua Li
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- HKUST Shenzhen Research Institute, Shenzhen 518057, China
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35
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Ratnadiwakara M, Archer SK, Dent CI, Ruiz De Los Mozos I, Beilharz TH, Knaupp AS, Nefzger CM, Polo JM, Anko ML. SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program. eLife 2018; 7:37419. [PMID: 29741478 PMCID: PMC5963917 DOI: 10.7554/elife.37419] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/05/2018] [Indexed: 12/28/2022] Open
Abstract
The establishment and maintenance of pluripotency depend on precise coordination of gene expression. We establish serine-arginine-rich splicing factor 3 (SRSF3) as an essential regulator of RNAs encoding key components of the mouse pluripotency circuitry, SRSF3 ablation resulting in the loss of pluripotency and its overexpression enhancing reprogramming. Strikingly, SRSF3 binds to the core pluripotency transcription factor Nanog mRNA to facilitate its nucleo-cytoplasmic export independent of splicing. In the absence of SRSF3 binding, Nanog mRNA is sequestered in the nucleus and protein levels are severely downregulated. Moreover, SRSF3 controls the alternative splicing of the export factor Nxf1 and RNA regulators with established roles in pluripotency, and the steady-state levels of mRNAs encoding chromatin modifiers. Our investigation links molecular events to cellular functions by demonstrating how SRSF3 regulates the pluripotency genes and uncovers SRSF3-RNA interactions as a critical means to coordinate gene expression during reprogramming, stem cell self-renewal and early development.
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Affiliation(s)
- Madara Ratnadiwakara
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Stuart K Archer
- Bioinformatics Platform, Monash University, Clayton, Australia
| | - Craig I Dent
- School of Biological Sciences, Monash University, Melbourne, Australia
| | | | - Traude H Beilharz
- Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Minna-Liisa Anko
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
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36
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Abstract
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.
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37
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Saijo S, Kuwano Y, Masuda K, Nishikawa T, Rokutan K, Nishida K. Serine/arginine-rich splicing factor 7 regulates p21-dependent growth arrest in colon cancer cells. THE JOURNAL OF MEDICAL INVESTIGATION 2017; 63:219-26. [PMID: 27644562 DOI: 10.2152/jmi.63.219] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Serine/arginine-rich splicing factors (SRSFs) play wide-ranging roles in gene expression through post-transcriptional regulation as well as pre-mRNA splicing. SRSF7 was highly expressed in colon cancer tissues, and its knockdown inhibited cell growth in colon cancer cells (HCT116) in association with altered expression of 4,499 genes. The Ingenuity Pathway Analysis revealed that cell cycle-related canonical pathways were ranked as the highly enriched category in the affected genes. Western blotting confirmed that p21, a master regulator in cell cycle, was increased without any induction of p53 in SRSF7 knockdown cells. Furthermore, cyclin-dependent kinase 2 and retinoblastoma protein were remained in the hypophosphorylated state. In addition, the SRSF7 knockdown-induced cell growth inhibition was observed in p53-null HCT116 cells, suggesting that p53-independent pathways were involved in the SRSF7 knockdown-induced cell growth inhibition. The reduction of SRSF7 stabilized cyclin-dependent kinase inhibitor 1A (CDKN1A) mRNA without any activation of the CDKN1A promoter. Interestingly, SRSF7 knockdown also blocked p21 degradation. These results suggest that the reduction of SRSF7 post-transcriptionally regulates p21 induction at the multistep processes. Thus, the present findings disclose a novel, important role of SRSF7 in cell proliferation through regulating p21 levels. J. Med. Invest. 63: 219-226, August, 2016.
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Affiliation(s)
- Saki Saijo
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School
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38
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Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. Cellular differentiation state modulates the mRNA export activity of SR proteins. J Cell Biol 2017; 216:1993-2009. [PMID: 28592444 PMCID: PMC5496613 DOI: 10.1083/jcb.201610051] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/22/2017] [Accepted: 04/24/2017] [Indexed: 01/22/2023] Open
Abstract
SR proteins connect nuclear pre-mRNA processing to mRNA export and translation. Botti et al. develop a quantitative nucleocytoplasmic shuttling assay and show that SR proteins are differentially modified and active in differentiated and pluripotent cells. SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein–protein and protein–RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.
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Affiliation(s)
- Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - François McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michaela C Steiner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Florian M Richter
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anfisa Solovyeva
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marius Wegener
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Oliver D Schwich
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Michaela Müller-McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
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Kamina AD, Williams N. Non-canonical binding interactions of the RNA recognition motif (RRM) domains of P34 protein modulate binding within the 5S ribonucleoprotein particle (5S RNP). PLoS One 2017; 12:e0177890. [PMID: 28542332 PMCID: PMC5436847 DOI: 10.1371/journal.pone.0177890] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 05/04/2017] [Indexed: 11/18/2022] Open
Abstract
RNA binding proteins are involved in many aspects of RNA metabolism. In Trypanosoma brucei, our laboratory has identified two trypanosome-specific RNA binding proteins P34 and P37 that are involved in the maturation of the 60S subunit during ribosome biogenesis. These proteins are part of the T. brucei 5S ribonucleoprotein particle (5S RNP) and P34 binds to 5S ribosomal RNA (rRNA) and ribosomal protein L5 through its N-terminus and its RNA recognition motif (RRM) domains. We generated truncated P34 proteins to determine these domains’ interactions with 5S rRNA and L5. Our analyses demonstrate that RRM1 of P34 mediates the majority of binding with 5S rRNA and the N-terminus together with RRM1 contribute the most to binding with L5. We determined that the consensus ribonucleoprotein (RNP) 1 and 2 sequences, characteristic of canonical RRM domains, are not fully conserved in the RRM domains of P34. However, the aromatic amino acids previously described to mediate base stacking interactions with their RNA target are conserved in both of the RRM domains of P34. Surprisingly, mutation of these aromatic residues did not disrupt but instead enhanced 5S rRNA binding. However, we identified four arginine residues located in RRM1 of P34 that strongly impact L5 binding. These mutational analyses of P34 suggest that the binding site for 5S rRNA and L5 are near each other and specific residues within P34 regulate the formation of the 5S RNP. These studies show the unique way that the domains of P34 mediate binding with the T. brucei 5S RNP.
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Affiliation(s)
- Anyango D. Kamina
- Department of Microbiology and Immunology and Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, Buffalo, New York, United States of America
| | - Noreen Williams
- Department of Microbiology and Immunology and Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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Schubert M. Insights into Carbohydrate Recognition by 3D Structure Determination of Protein–Carbohydrate Complexes Using NMR. NMR IN GLYCOSCIENCE AND GLYCOTECHNOLOGY 2017:101-122. [DOI: 10.1039/9781782623946-00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This chapter provides an overview of protein–carbohydrate complex structures determined with NMR spectroscopy and deposited in the Protein Data Bank (PDB). These 14 structures include protein–carbohydrate interactions ranging from nanomolar to millimolar affinities. Two complexes are discussed in detail, one representing a tightly bound complex and one a weak but specific interaction. This review illustrates that NMR spectroscopy is a competitive method for three-dimensional structure determination of protein–carbohydrate complexes, especially in the case of weak interactions. The number of biological functions in which protein–carbohydrate interactions are involved is steadily growing. Essential functions of the immune system such as the distinction between self and non-self, or the resolution of inflammation, involve critical protein–carbohydrate recognition events. It is therefore expected that by providing atomic details, NMR spectroscopy can make a significant contribution in the near future to unexplored pathways of the immune system and of many other biological processes.
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Affiliation(s)
- Mario Schubert
- Department of Molecular Biology, University of Salzburg 5020 Salzburg Austria
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41
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Fernandez N, Cordiner RA, Young RS, Hug N, Macias S, Cáceres JF. Genetic variation and RNA structure regulate microRNA biogenesis. Nat Commun 2017; 8:15114. [PMID: 28466845 PMCID: PMC5418625 DOI: 10.1038/ncomms15114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast and gastric cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing. Our results are compatible with a model whereby a genetic variant in pri-mir-30c-1 leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 resulting in increased levels of miR-30c. These data highlight that primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.
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Affiliation(s)
- Noemi Fernandez
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ross A. Cordiner
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert S. Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Javier F. Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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Abstract
Serine and arginine-rich (SR) proteins are RNA-binding proteins (RBPs) known as constitutive and alternative splicing regulators. As splicing is linked to transcriptional and post-transcriptional steps, SR proteins are implicated in the regulation of multiple aspects of the gene expression program. Recent global analyses of SR-RNA interaction maps have advanced our understanding of SR-regulated gene expression. Diverse SR proteins play partially overlapping but distinct roles in transcription-coupled splicing and mRNA processing in the nucleus. In addition, shuttling SR proteins act as adaptors for mRNA export and as regulators for translation in the cytoplasm. This mini-review will summarize the roles of SR proteins as RNA binders, regulators, and connectors from transcription in the nucleus to translation in the cytoplasm.
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Affiliation(s)
- Sunjoo Jeong
- Department of Bioconvergent Science and Technology, Dankook University, Yongin 16890,
Korea
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Serine/Arginine-Rich Splicing Factor 3 and Heterogeneous Nuclear Ribonucleoprotein A1 Regulate Alternative RNA Splicing and Gene Expression of Human Papillomavirus 18 through Two Functionally Distinguishable cis Elements. J Virol 2016; 90:9138-52. [PMID: 27489271 DOI: 10.1128/jvi.00965-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/25/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Human papillomavirus 18 (HPV18) is the second most common oncogenic HPV type associated with cervical, anogenital, and oropharyngeal cancers. Like other oncogenic HPVs, HPV18 encodes two major (one early and one late) polycistronic pre-mRNAs that are regulated by alternative RNA splicing to produce a repertoire of viral transcripts for the expression of individual viral genes. However, RNA cis-regulatory elements and trans-acting factors contributing to HPV18 alternative RNA splicing remain unknown. In this study, an exonic splicing enhancer (ESE) in the nucleotide (nt) 3520 to 3550 region in the HPV18 genome was identified and characterized for promotion of HPV18 929^3434 splicing and E1^E4 production through interaction with SRSF3, a host oncogenic splicing factor differentially expressed in epithelial cells and keratinocytes. Introduction of point mutations in the SRSF3-binding site or knockdown of SRSF3 expression in cells reduces 929^3434 splicing and E1^E4 production but activates other, minor 929^3465 and 929^3506 splicing. Knockdown of SRSF3 expression also enhances the expression of E2 and L1 mRNAs. An exonic splicing silencer (ESS) in the HPV18 nt 612 to 639 region was identified as being inhibitory to the 233^416 splicing of HPV18 E6E7 pre-mRNAs via binding to hnRNP A1, a well-characterized, abundantly and ubiquitously expressed RNA-binding protein. Introduction of point mutations into the hnRNP A1-binding site or knockdown of hnRNP A1 expression promoted 233^416 splicing and reduced E6 expression. These data provide the first evidence that the alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host trans-acting splicing factors. IMPORTANCE Expression of HPV18 genes is regulated by alternative RNA splicing of viral polycistronic pre-mRNAs to produce a repertoire of viral early and late transcripts. RNA cis elements and trans-acting factors contributing to HPV18 alternative RNA splicing have been discovered in this study for the first time. The identified ESS at the E7 open reading frame (ORF) prevents HPV18 233^416 splicing in the E6 ORF through interaction with a host splicing factor, hnRNP A1, and regulates E6 and E7 expression of the early E6E7 polycistronic pre-mRNA. The identified ESE at the E1^E4 ORF promotes HPV18 929^3434 splicing of both viral early and late pre-mRNAs and E1^E4 production through interaction with SRSF3. This study provides important observations on how alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host splicing factors and offers potential therapeutic targets to overcome HPV-related cancer.
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Müller-McNicoll M, Botti V, de Jesus Domingues AM, Brandl H, Schwich OD, Steiner MC, Curk T, Poser I, Zarnack K, Neugebauer KM. SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes Dev 2016; 30:553-66. [PMID: 26944680 PMCID: PMC4782049 DOI: 10.1101/gad.276477.115] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this study, Müller-McNicoll et al. investigate how export machinery assembles on mRNA and how it senses mRNA maturity before exporting mRNAs from the nucleus. They show that SR proteins act as NXF1 adaptors by connecting alternative splicing and 3′ end formation to mRNA export in vivo and propose that SR proteins and NXF1 form a ternary complex on mRNAs, particularly in last exons, and shuttle together to the cytoplasm. Nuclear export factor 1 (NXF1) exports mRNA to the cytoplasm after recruitment to mRNA by specific adaptor proteins. How and why cells use numerous different export adaptors is poorly understood. Here we critically evaluate members of the SR protein family (SRSF1–7) for their potential to act as NXF1 adaptors that couple pre-mRNA processing to mRNA export. Consistent with this proposal, >1000 endogenous mRNAs required individual SR proteins for nuclear export in vivo. To address the mechanism, transcriptome-wide RNA-binding profiles of NXF1 and SRSF1–7 were determined in parallel by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP). Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. Interestingly, SRSF3 and SRSF7 were shown to bind different sites in last exons and regulate 3′ untranslated region length in an opposing manner. Both SRSF3 and SRSF7 promoted NXF1 recruitment to mRNA. Thus, SRSF3 and SRSF7 couple alternative splicing and polyadenylation to NXF1-mediated mRNA export, thereby controlling the cytoplasmic abundance of transcripts with alternative 3′ ends.
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Affiliation(s)
- Michaela Müller-McNicoll
- RNA Regulation Group, Institute of Cell Biology and Neuroscience, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | | | - Holger Brandl
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Oliver D Schwich
- RNA Regulation Group, Institute of Cell Biology and Neuroscience, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany; Buchmann Institute for Life Sciences (BMLS), 60438 Frankfurt/Main, Germany
| | - Michaela C Steiner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Kathi Zarnack
- Buchmann Institute for Life Sciences (BMLS), 60438 Frankfurt/Main, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A. Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches. J Proteome Res 2016; 15:1659-69. [PMID: 27049334 DOI: 10.1021/acs.jproteome.6b00126] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cells' compartments. NCL plays important roles in a variety of essential functions, among which are ribosome biogenesis, gene expression, and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 proteins co-purified with NCL, among which 100 of them were specifically found to be associated with NCL after RNase digestion. The functional classification of these proteins confirmed the prominent role of NCL in ribosome biogenesis and additionally revealed the possible involvement of nuclear NCL in several pre-mRNA processing pathways through its interaction with RNA helicases and proteins participating in pre-mRNA splicing, transport, or stability. NCL knockdown experiments revealed that NCL regulates the localization of EXOSC10 and the amount of ZC3HAV1, two components of the RNA exosome, further suggesting its involvement in the control of mRNA stability. Altogether, this study describes the first nuclear interactome of human NCL and provides the basis for further understanding the mechanisms underlying the essential functions of this nucleolar protein.
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Affiliation(s)
- Anna Salvetti
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Labex Ecofect Université de Lyon , 69007 Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes , 38000 Grenoble, France
- CEA, BIG-BGE , 38000 Grenoble, France
- INSERM, BGE , 38000 Grenoble, France
| | - Alberto Epstein
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Labex Ecofect Université de Lyon , 69007 Lyon, France
| | - Loredana Arata
- Subdepartment of Molecular Genetics, Public Health Institute of Chile , Santiago, Chile
| | - Alexandra Kraut
- Université Grenoble Alpes , 38000 Grenoble, France
- CEA, BIG-BGE , 38000 Grenoble, France
- INSERM, BGE , 38000 Grenoble, France
| | - Vincent Navratil
- Pôle Rhône Alpes de Bioinformatique (PRABI), Université Lyon 1 , 69100 Villeurbanne, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286 , 69003 Lyon, France
| | - Anna Greco
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308 , 69007 Lyon, France
- Ecole Normale Supérieure de Lyon , 69007 Lyon, France
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46
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Efficient large-scale preparation and purification of short single-stranded RNA oligonucleotides. Biotechniques 2016; 60:75-83. [PMID: 26842352 DOI: 10.2144/000114383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/12/2015] [Indexed: 11/23/2022] Open
Abstract
Sequence-specific RNA recognition by RNA-binding proteins plays a crucial role in the post-translational regulation of gene expression. Biophysical and biochemical studies help to unravel the principles of sequence-specific RNA recognition, but the methods used require large amounts of single-stranded RNA (ssRNA). Here we present a fast and robust method for large-scale preparation and purification of short ssRNA oligonucleotides for biochemical, biophysical, and structural studies. We designed an efficiently folding, self-cleaving hammerhead (HH) ribozyme to prepare ssRNA oligonucleotides. Hammerhead ribozyme RNAs self-cleave with over 95% efficiency during in vitro transcription as a function of magnesium concentration to produce high yields of the desired ssRNA products. The resulting ssRNAs can be purified from crude transcription reactions by denaturing anion-exchange chromatography and then desalted by weak anion-exchange chromatography using volatile ammonium bicarbonate buffer solutions. The ssRNA oligonucleotides produced this way are homogenous, as judged by mass spectrometry (MS), and are suitable for biochemical and biophysical studies. Moreover, for high-resolution NMR structure determination of RNA-protein complexes, our protocol enables efficient preparation of ssRNA oligonucleotides with various isotope-labeling schemes which are not commercially available.
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47
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Stankovic N, Schloesser M, Joris M, Sauvage E, Hanikenne M, Motte P. Dynamic Distribution and Interaction of the Arabidopsis SRSF1 Subfamily Splicing Factors. PLANT PHYSIOLOGY 2016; 170:1000-13. [PMID: 26697894 PMCID: PMC4734559 DOI: 10.1104/pp.15.01338] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/19/2015] [Indexed: 05/19/2023]
Abstract
Ser/Arg-rich (SR) proteins are essential nucleus-localized splicing factors. Our prior studies showed that Arabidopsis (Arabidopsis thaliana) RSZ22, a homolog of the human SRSF7 SR factor, exits the nucleus through two pathways, either dependent or independent on the XPO1 receptor. Here, we examined the expression profiles and shuttling dynamics of the Arabidopsis SRSF1 subfamily (SR30, SR34, SR34a, and SR34b) under control of their endogenous promoter in Arabidopsis and in transient expression assay. Due to its rapid nucleocytoplasmic shuttling and high expression level in transient assay, we analyzed the multiple determinants that regulate the localization and shuttling dynamics of SR34. By site-directed mutagenesis of SR34 RNA-binding sequences and Arg/Ser-rich (RS) domain, we further show that functional RRM1 or RRM2 are dispensable for the exclusive protein nuclear localization and speckle-like distribution. However, mutations of both RRMs induced aggregation of the protein whereas mutation in the RS domain decreased the stability of the protein and suppressed its nuclear accumulation. Furthermore, the RNA-binding motif mutants are defective for their export through the XPO1 (CRM1/Exportin-1) receptor pathway, but retain nucleocytoplasmic mobility. We performed a yeast two hybrid screen with SR34 as bait and discovered SR45 as a new interactor. SR45 is an unusual SR splicing factor bearing two RS domains. These interactions were confirmed in planta by FLIM-FRET and BiFC and the roles of SR34 domains in protein-protein interactions were further studied. Altogether, our report extends our understanding of shuttling dynamics of Arabidopsis SR splicing factors.
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Affiliation(s)
- Nancy Stankovic
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Marie Schloesser
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Marine Joris
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Eric Sauvage
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Marc Hanikenne
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Patrick Motte
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
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48
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Perea W, Schroeder KT, Bryant AN, Greenbaum NL. Interaction between the Spliceosomal Pre-mRNA Branch Site and U2 snRNP Protein p14. Biochemistry 2016; 55:629-32. [PMID: 26784522 DOI: 10.1021/acs.biochem.5b01036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have probed the molecular basis of recognition between human spliceosomal U2 snRNP protein p14 and RNA targets representing the intron branch site region. Interaction of an RNA duplex representing the branch site helix perturbed at least 10 nuclear magnetic resonance cross-peaks of (15)N-labeled p14. However, similar chemical shift changes were observed upon interaction with a duplex without the bulged branch site residue, suggesting that binding of p14 to RNA is nonspecific and does not recognize the branch site. We propose that the p14-RNA interaction screens charges on the backbone of the branch site during spliceosome assembly.
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Affiliation(s)
- William Perea
- Department of Chemistry & Biochemistry, Hunter College of the City University of New York , New York, New York 10065, United States.,The Graduate Group in Chemistry, The Graduate Center, City University of New York , New York, New York 10016, United States
| | - Kersten T Schroeder
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Amy N Bryant
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Nancy L Greenbaum
- Department of Chemistry & Biochemistry, Hunter College of the City University of New York , New York, New York 10065, United States.,The Graduate Group in Chemistry, The Graduate Center, City University of New York , New York, New York 10016, United States
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49
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Hennig J, Sattler M. Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology. Bioessays 2015; 37:899-908. [DOI: 10.1002/bies.201500033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
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50
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Abstract
RRM-containing proteins are involved in most of the RNA metabolism steps. Their functions are closely related to their mode of RNA recognition, which has been studied by structural biologists for more than 20 years. In this chapter, we report on high-resolution structures of single and multi RRM-RNA complexes to explain the numerous strategies used by these domains to interact specifically with a large repertoire of RNA sequences. We show that multiple variations of their canonical fold can be used to adapt to different single-stranded sequences with a large range of affinities. Furthermore, we describe the consequences on RNA binding of the different structural arrangements found in tandem RRMs and higher order RNPs. Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. Finally, we show how structural and cellular biology can benefit from each other and pave a way for understanding, defining, and predicting a code of RNA recognition by the RRMs.
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