1
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Fronk AD, Manzanares MA, Zheng P, Geier A, Anderson K, Stanton S, Zumrut H, Gera S, Munch R, Frederick V, Dhingra P, Arun G, Akerman M. Development and validation of AI/ML derived splice-switching oligonucleotides. Mol Syst Biol 2024; 20:676-701. [PMID: 38664594 PMCID: PMC11148135 DOI: 10.1038/s44320-024-00034-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 06/05/2024] Open
Abstract
Splice-switching oligonucleotides (SSOs) are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of functional, verifiable, and therapeutic SSOs. We trained XGboost tree models using splicing factor (SF) pre-mRNA binding profiles and spliceosome assembly information to identify modulatory SSO binding sites on pre-mRNA. Using Shapley and out-of-bag analyses we also predicted the identity of specific SFs whose binding to pre-mRNA is blocked by SSOs. This step adds considerable transparency to AI/ML-driven drug discovery and informs biological insights useful in further validation steps. We applied this approach to previously established functional SSOs to retrospectively identify the SFs likely to regulate those events. We then took a prospective validation approach using a novel target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13). Targeting NEDD4Le13 with an AI/ML-designed SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGFβ pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data.
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Affiliation(s)
| | | | - Paulina Zheng
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Adam Geier
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Hasan Zumrut
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Sakshi Gera
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Robin Munch
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Gayatri Arun
- Envisagenics, Inc., Long Island City, NY, 11101, USA
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2
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Shirokikh NE, Jensen KB, Thakor N. Editorial: RNA machines. Front Genet 2023; 14:1290420. [PMID: 37829284 PMCID: PMC10565666 DOI: 10.3389/fgene.2023.1290420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Affiliation(s)
- Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kirk Blomquist Jensen
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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3
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Lu S, Ye J, Li H, He F, Qi Y, Wang T, Wang W, Zheng L. The Splicing Factor OsSCL26 Regulates Phosphorus Homeostasis in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2326. [PMID: 37375951 DOI: 10.3390/plants12122326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth. However, its deficiency poses a significant challenge for crop production. To overcome the low P availability, plants have developed various strategies to regulate their P uptake and usage. In this study, we identified a splicing factor, OsSCL26, belonging to the Serine/arginine-rich (SR) proteins, that plays a crucial role in regulating P homeostasis in rice. OsSCL26 is expressed in the roots, leaves, and base nodes, with higher expression levels observed in the leaf blades during the vegetative growth stage. The OsSCL26 protein is localized in the nucleus. Mutation of OsSCL26 resulted in the accumulation of P in the shoot compared to the wild-type, and the dwarf phenotype of the osscl26 mutant was alleviated under low P conditions. Further analysis revealed that the accumulated P concentrations in the osscl26 mutant were higher in the old leaves and lower in the new leaves. Furthermore, the P-related genes, including the PHT and SPX family genes, were upregulated in the osscl26 mutant, and the exclusion/inclusion ratio of the two genes, OsSPX-MFS2 and OsNLA2, was increased compared to wild-type rice. These findings suggest that the splicing factor OsSCL26 plays a pivotal role in maintaining P homeostasis in rice by influencing the absorption and distribution of P through the regulation of the transcription and splicing of the P transport genes.
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Affiliation(s)
- Shanshan Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Ye
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengyu He
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yue Qi
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wujian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luqing Zheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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4
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Sertznig H, Roesmann F, Wilhelm A, Heininger D, Bleekmann B, Elsner C, Santiago M, Schuhenn J, Karakoese Z, Benatzy Y, Snodgrass R, Esser S, Sutter K, Dittmer U, Widera M. SRSF1 acts as an IFN-I-regulated cellular dependency factor decisively affecting HIV-1 post-integration steps. Front Immunol 2022; 13:935800. [PMID: 36458014 PMCID: PMC9706209 DOI: 10.3389/fimmu.2022.935800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 08/24/2023] Open
Abstract
Efficient HIV-1 replication depends on balanced levels of host cell components including cellular splicing factors as the family of serine/arginine-rich splicing factors (SRSF, 1-10). Type I interferons (IFN-I) play a crucial role in the innate immunity against HIV-1 by inducing the expression of IFN-stimulated genes (ISGs) including potent host restriction factors. The less well known IFN-repressed genes (IRepGs) might additionally affect viral replication by downregulating host dependency factors that are essential for the viral life cycle; however, so far, the knowledge about IRepGs involved in HIV-1 infection is very limited. In this work, we could demonstrate that HIV-1 infection and the associated ISG induction correlated with low SRSF1 levels in intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs) during acute and chronic HIV-1 infection. In HIV-1-susceptible cell lines as well as primary monocyte-derived macrophages (MDMs), expression levels of SRSF1 were transiently repressed upon treatment with specific IFNα subtypes in vitro. Mechanically, 4sU labeling of newly transcribed mRNAs revealed that IFN-mediated SRSF1 repression is regulated on early RNA level. SRSF1 knockdown led to an increase in total viral RNA levels, but the relative proportion of the HIV-1 viral infectivity factor (Vif) coding transcripts, which is essential to counteract APOBEC3G-mediated host restriction, was significantly reduced. In the presence of high APOBEC3G levels, however, increased LTR activity upon SRSF1 knockdown facilitated the overall replication, despite decreased vif mRNA levels. In contrast, SRSF1 overexpression significantly impaired HIV-1 post-integration steps including LTR transcription, alternative splice site usage, and virus particle production. Since balanced SRSF1 levels are crucial for efficient viral replication, our data highlight the so far undescribed role of SRSF1 acting as an IFN-modulated cellular dependency factor decisively regulating HIV-1 post-integration steps.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Delia Heininger
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Barbara Bleekmann
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Mario Santiago
- Department of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Jonas Schuhenn
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Zehra Karakoese
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Yvonne Benatzy
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Ryan Snodgrass
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Stefan Esser
- Clinic of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
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5
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Sun M, Jin Y, Zhang Y, Gregorich ZR, Ren J, Ge Y, Guo W. SR Protein Kinases Regulate the Splicing of Cardiomyopathy-Relevant Genes via Phosphorylation of the RSRSP Stretch in RBM20. Genes (Basel) 2022; 13:1526. [PMID: 36140694 PMCID: PMC9498672 DOI: 10.3390/genes13091526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: RNA binding motif 20 (RBM20) regulates mRNA splicing specifically in muscle tissues. Missense mutations in the arginine/serine (RS) domain of RBM20 lead to abnormal gene splicing and have been linked to severe dilated cardiomyopathy (DCM) in human patients and animal models. Interestingly, many of the reported DCM-linked missense mutations in RBM20 are in a highly conserved RSRSP stretch within the RS domain. Recently, it was found that the two Ser residues within this stretch are constitutively phosphorylated, yet the identity of the kinase(s) responsible for phosphorylating these residues, as well as the function of RSRSP phosphorylation, remains unknown. (2) Methods: The ability of three known SR protein kinases (SRPK1, CLK1, and AKT2) to phosphorylate the RBM20 RSRSP stretch and regulate target gene splicing was evaluated by using both in vitro and in vivo approaches. (3) Results: We found that all three kinases phosphorylated S638 and S640 in the RSRSP stretch and regulated RBM20 target gene splicing. While SRPK1 and CLK1 were both capable of directly phosphorylating the RS domain in RBM20, whether AKT2-mediated control of the RS domain phosphorylation is direct or indirect could not be determined. (4) Conclusions: Our results indicate that SR protein kinases regulate the splicing of a cardiomyopathy-relevant gene by modulating phosphorylation of the RSRSP stretch in RBM20. These findings suggest that SR protein kinases may be potential targets for the treatment of RBM20 cardiomyopathy.
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Affiliation(s)
- Mingming Sun
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yanghai Zhang
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachery R Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Ren
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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6
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Mendes FC, de Paiva JC, da Silva EQG, Santos MR, de Almeida Lima GD, Moreira GA, Silva LVG, de Melo Agripino J, de Souza APM, de Oliveira Mendes TA, Machado-Neves M, Teixeira RR, Silva-Júnior A, Fietto JLR, de Oliveira LL, Bressan GC. Immunomodulatory activity of trifluoromethyl arylamides derived from the SRPK inhibitor SRPIN340 and their potential use as vaccine adjuvant. Life Sci 2022; 307:120849. [PMID: 35926588 DOI: 10.1016/j.lfs.2022.120849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 02/08/2023]
Abstract
The serine/arginine-rich protein kinases (SRPK) specifically phosphorylate their substrates at RS-rich dipeptides, which are abundantly found in SR splicing factors. SRPK are classically known for their ability to affect the splicing and expression of gene isoforms commonly implicated in cancer and diseases associated with infectious processes. Non-splicing functions have also been attributed to SRPK, which highlight their functional plasticity and relevance as therapeutic targets for pharmacological intervention. In this sense, different SRPK inhibitors have been developed, such as the well-known SRPIN340 and its derivatives, with anticancer and antiviral activities. Here we evaluated the potential immunomodulatory activity of SRPIN340 and three trifluoromethyl arylamide derivatives. In in vitro analysis with RAW 264.7 macrophages and primary splenocytes, all the compounds modulated the expression of immune response mediators and antigen-presentation molecules related to a tendency for M2 macrophage polarization. Immunization experiments were carried out in mice to evaluate their potential as vaccine immunostimulants. When administrated alone, the compounds altered the expression of immune factors at the injection site and did not produce macroscopic or microscopic local reactions. In addition, when prepared as an adjuvant with inactivated EHV-1 antigens, all the compounds increased the anti-EHV-1 neutralizing antibody titers, a change that is consistent with an increased Th2 response. These findings demonstrate that SRPIN340 and its derivatives exhibit a noticeable capacity to modulate innate and adaptative immune cells, disclosing their potential to be used as vaccine adjuvants or in immunotherapies.
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Affiliation(s)
- Flávia Carneiro Mendes
- Universidade Federal de Viçosa, Departamento de Bioquímica e Biologia Molecular, Viçosa, MG, Brazil
| | | | | | | | | | - Gabriela Alves Moreira
- Universidade Federal de Viçosa, Departamento de Bioquímica e Biologia Molecular, Viçosa, MG, Brazil
| | - Lucas Viana Gomes Silva
- Universidade Federal de Viçosa, Departamento de Bioquímica e Biologia Molecular, Viçosa, MG, Brazil
| | - Joice de Melo Agripino
- Universidade Federal de Viçosa, Departamento de Bioquímica e Biologia Molecular, Viçosa, MG, Brazil
| | | | | | | | | | | | | | | | - Gustavo Costa Bressan
- Universidade Federal de Viçosa, Departamento de Bioquímica e Biologia Molecular, Viçosa, MG, Brazil.
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7
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A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
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8
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Zhang Y, Wang C, Sun M, Jin Y, Braz CU, Khatib H, Hacker TA, Liss M, Gotthardt M, Granzier H, Ge Y, Guo W. RBM20 phosphorylation and its role in nucleocytoplasmic transport and cardiac pathogenesis. FASEB J 2022; 36:e22302. [PMID: 35394688 PMCID: PMC9233413 DOI: 10.1096/fj.202101811rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022]
Abstract
Arginine-serine (RS) domain(s) in splicing factors are critical for protein-protein interaction in pre-mRNA splicing. Phosphorylation of RS domain is important for splicing control and nucleocytoplasmic transport in the cell. RNA-binding motif 20 (RBM20) is a splicing factor primarily expressed in the heart. A previous study using phospho-antibody against RS domain showed that RS domain can be phosphorylated. However, its actual phosphorylation sites and function have not been characterized. Using middle-down mass spectrometry, we identified 16 phosphorylation sites, two of which (S638 and S640 in rats, or S637 and S639 in mice) were located in the RSRSP stretch in the RS domain. Mutations on S638 and S640 regulated splicing, promoted nucleocytoplasmic transport and protein-RNA condensates. Phosphomimetic mutations on S638 and S640 indicated that phosphorylation was not the major cause for RBM20 nucleocytoplasmic transport and condensation in vitro. We generated a S637A knock-in (KI) mouse model (Rbm20S637A ) and observed the reduced RBM20 phosphorylation. The KI mice exhibited aberrant gene splicing, protein condensates, and a dilated cardiomyopathy (DCM)-like phenotype. Transcriptomic profiling demonstrated that KI mice had altered expression and splicing of genes involving cardiac dysfunction, protein localization, and condensation. Our in vitro data showed that phosphorylation was not a direct cause for nucleocytoplasmic transport and protein condensation. Subsequently, the in vivo results reveal that RBM20 mutations led to cardiac pathogenesis. However, the role of phosphorylation in vivo needs further investigation.
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Affiliation(s)
- Yanghai Zhang
- Department of Animal and Dairy SciencesUniversity of Wisconsin‐MadisonWisconsinUSA
| | - Chunyan Wang
- Department of Animal and Dairy SciencesUniversity of Wisconsin‐MadisonWisconsinUSA
| | - Mingming Sun
- Department of Animal ScienceUniversity of WyomingLaramieWyomingUSA
| | - Yutong Jin
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Camila Urbano Braz
- Department of Animal and Dairy SciencesUniversity of Wisconsin‐MadisonWisconsinUSA
| | - Hasan Khatib
- Department of Animal and Dairy SciencesUniversity of Wisconsin‐MadisonWisconsinUSA
| | - Timothy A. Hacker
- Division of Cardiovascular MedicineDepartment of MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Martin Liss
- Neuromuscular and Cardiovascular Cell BiologyMax Delbrueck Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell BiologyMax Delbrueck Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Charité UniversitätsmedizinBerlinGermany
| | - Henk Granzier
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonArizonaUSA
| | - Ying Ge
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Department of Cell and Regenerative BiologySchool of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Human Proteomics ProgramSchool of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Wei Guo
- Department of Animal and Dairy SciencesUniversity of Wisconsin‐MadisonWisconsinUSA
- Department of Animal ScienceUniversity of WyomingLaramieWyomingUSA
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9
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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10
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Habib EB, Mathavarajah S, Dellaire G. Tinker, Tailor, Tumour Suppressor: The Many Functions of PRP4K. Front Genet 2022; 13:839963. [PMID: 35281802 PMCID: PMC8912934 DOI: 10.3389/fgene.2022.839963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Pre-mRNA processing factor 4 kinase (PRP4K, also known as PRPF4B) is an essential kinase first identified in the fission yeast Schizosaccharomyces pombe that is evolutionarily conserved from amoebae to animals. During spliceosomal assembly, PRP4K interacts with and phosphorylates PRPF6 and PRPF31 to facilitate the formation of the spliceosome B complex. However, over the past decade additional evidence has emerged that PRP4K has many diverse cellular roles beyond splicing that contribute to tumour suppression and chemotherapeutic responses in mammals. For example, PRP4K appears to play roles in regulating transcription and the spindle assembly checkpoint (SAC), a key pathway in maintaining chromosomes stability and the response of cancer cells to taxane-based chemotherapy. In addition, PRP4K has been revealed to be a haploinsufficient tumour suppressor that promotes aggressive cancer phenotypes when partially depleted. PRP4K is regulated by both the HER2 and estrogen receptor, and its partial loss increases resistance to the taxanes in multiple malignancies including cervical, breast and ovarian cancer. Moreover, ovarian and triple negative breast cancer patients harboring tumours with low PRP4K expression exhibit worse overall survival. The depletion of PRP4K also enhances both Yap and epidermal growth factor receptor (EGFR) signaling, the latter promoting anoikis resistance in breast and ovarian cancer. Finally, PRP4K is negatively regulated during epithelial-to-mesenchymal transition (EMT), a process that promotes increased cell motility, drug resistance and cancer metastasis. Thus, as we discuss in this review, PRP4K likely plays evolutionarily conserved roles not only in splicing but in a number of cellular pathways that together contribute to tumour suppression.
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Affiliation(s)
- Elias B. Habib
- Dalhousie University, Department of Pathology, Halifax, NS, Canada
| | | | - Graham Dellaire
- Dalhousie University, Department of Pathology, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- *Correspondence: Graham Dellaire,
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11
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Chen CB, Li J, Deng X, Liu LL, Deng J, Zha XF. Effects of Serine/Arginine Enriched Protein BmUP on the Development of Male Silkworm Reproductive Organs. Curr Issues Mol Biol 2022; 44:928-941. [PMID: 35723346 PMCID: PMC8929119 DOI: 10.3390/cimb44020061] [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: 12/02/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/23/2022] Open
Abstract
Serine/arginine-rich proteins are a class of highly conserved splicing factor proteins involved in constitutive and alternative splicing. We screened a low molecular weight serine/arginine rich protein from silkworms and named it BmUP. Temporal and spatial expression analysis indicated that the BmUP gene was specifically expressed in the silkworm testis, and the highest expression occurred in the pre-pupa stage from the fifth instar to the moth stages. Here, we generated BmUP knockout individuals with the CRISPR/Cas9 system. Both the internal and external genitalia of knockout individuals were abnormal in knockout compared with wild-type male silkworms. In transgenic silkworms overexpressing BmUP, male silkworms showed a phenotype similar to that of the knockout individuals, whereas female individuals showed no significant differences from the wild type. In addition, by conducting promoter analysis, we identified Bmachi, a transcription factor that regulates the BmUP gene. Gel migration experiments revealed that BmAchi specifically binds the BmUP promoter. Quantitative real-time PCR showed that an increase in Bmachi expression up-regulated the expression of BmUP. In contrast, when the expression of Bmachi decreased, the expression of BmUP also downregulated in the experimental group compared with the control group. These results provide new insights for studying the effects of serine/arginine-rich proteins on the development of silkworm genitals.
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Affiliation(s)
- Chun-Bing Chen
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; (C.-B.C.); (J.L.); (X.D.); (L.-L.L.); (J.D.)
| | - Juan Li
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; (C.-B.C.); (J.L.); (X.D.); (L.-L.L.); (J.D.)
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuan Deng
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; (C.-B.C.); (J.L.); (X.D.); (L.-L.L.); (J.D.)
| | - Lian-Lian Liu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; (C.-B.C.); (J.L.); (X.D.); (L.-L.L.); (J.D.)
| | - Jing Deng
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; (C.-B.C.); (J.L.); (X.D.); (L.-L.L.); (J.D.)
| | - Xing-Fu Zha
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China; (C.-B.C.); (J.L.); (X.D.); (L.-L.L.); (J.D.)
- Correspondence: ; Tel.: +86-23-68251573
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12
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Ren S, Chen X, Tian X, Yang D, Dong Y, Chen F, Fang X. The expression, function, and utilization of Protamine1: a literature review. Transl Cancer Res 2022; 10:4947-4957. [PMID: 35116345 PMCID: PMC8799248 DOI: 10.21037/tcr-21-1582] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
Objective Protamine 1 (PRM1) is specific in sperm and plays essential roles in fertilization, also a member of cancer testis antigen (CTA) family. This study aims to summarize the expression and function of PRM1 in spermatogenesis, and to broaden the current knowledge and inspire future development of PRM1-based therapeutic strategies in cancer treatment and nanomedicine. Background The protamine proteins, are characterized by an arginine-rich core and cysteine residues. Humans express two types of protamine: PRM1 and PRM2. The abnormal expression or proportion of PRM1 and PRM2 is known to be associated with subfertility and infertility, especially for PRM1 which is highly evolutionary conserved in mammalians and expressed in all vertebrates. Biological functions of PRM1 have been unveiled in diverse cellular processes, such as tumorigenesis, somatic cell nucleus transfer, and drug delivery systems. Moreover, PRM1 is identified as a CTA in chronic leukemia (CLL) and colorectal cancer (CRC). Methods Literature was obtained using PubMed and the keywords protamine 1, PRM1, or P1, from January 1, 1980, through July 20, 2021. We also collect the additional evidence through screening references of articles identified through the PubMed searches. Conclusions PRM1 is well-studied in male infertility, and further researches and attempts to develop PRM1 as novel tumor marker, as well as drug delivery vector, will be of important clinical significance.
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Affiliation(s)
- Shengnan Ren
- Department of Breast, Thyroid, Hepatobiliary and Pancreatic Surgery, Xinmin Division of China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuebo Chen
- Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Xiaofeng Tian
- Department of Breast, Thyroid, Hepatobiliary and Pancreatic Surgery, Xinmin Division of China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dingquan Yang
- Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yongli Dong
- Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Fangfang Chen
- Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.,Nanomedicine Translational Research Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuedong Fang
- Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
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13
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Zeke A, Schád É, Horváth T, Abukhairan R, Szabó B, Tantos A. Deep structural insights into RNA-binding disordered protein regions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1714. [PMID: 35098694 PMCID: PMC9539567 DOI: 10.1002/wrna.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
Abstract
Recent efforts to identify RNA binding proteins in various organisms and cellular contexts have yielded a large collection of proteins that are capable of RNA binding in the absence of conventional RNA recognition domains. Many of the recently identified RNA interaction motifs fall into intrinsically disordered protein regions (IDRs). While the recognition mode and specificity of globular RNA binding elements have been thoroughly investigated and described, much less is known about the way IDRs can recognize their RNA partners. Our aim was to summarize the current state of structural knowledge on the RNA binding modes of disordered protein regions and to propose a classification system based on their sequential and structural properties. Through a detailed structural analysis of the complexes that contain disordered protein regions binding to RNA, we found two major binding modes that represent different recognition strategies and, most likely, functions. We compared these examples with DNA binding disordered proteins and found key differences stemming from the nucleic acids as well as similar binding strategies, implying a broader substrate acceptance by these proteins. Due to the very limited number of known structures, we integrated molecular dynamics simulations in our study, whose results support the proposed structural preferences of specific RNA‐binding IDRs. To broaden the scope of our review, we included a brief analysis of RNA‐binding small molecules and compared their structural characteristics and RNA recognition strategies to the RNA‐binding IDRs. This article is categorized under:RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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14
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Xu W, Zhang Y, Qin D, Gui Y, Wang S, Du G, Yang F, Li L, Yuan S, Wang M, Wu X. Transcription factor-like 5 is a potential DNA/RNA-binding protein essential for maintaining male fertility in mice. J Cell Sci 2021; 135:273810. [PMID: 34931239 DOI: 10.1242/jcs.259036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Transcription factor-like 5 (TCFL5) is a testis-specific protein that contains the basic helix-loop-helix domain, but the in vivo functions of TCFL5 remain unknown. Herein, we generated CRISPR/Cas9-mediated knockout mice to dissect the function of TCFL5 in mouse testes. Surprisingly, we found that it was difficult to generate homozygous mice with the Tcfl5 deletion since the heterozygous males (Tcfl5+/-) were infertile. We did; however, observe markedly abnormal phenotypes of spermatids and spermatozoa in the testes and epididymides of Tcfl5+/- mice. Mechanistically, we demonstrated that TCFL5 transcriptionally and post-transcriptionally regulated a set of genes participating in male germ cell development via TCFL5 ChIP-DNA and eCLIP-RNA high-throughput sequencing. We also identified a known RBP, FXR1 as an interacting partner of TCFL5 that may coordinate the transition and localization of TCFL5 in the nucleus. Collectively, we herein report for the first time that Tcfl5 is haploinsufficient in vivo and acts as a dual-function protein that mediates DNA and RNA to regulate spermatogenesis.
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Affiliation(s)
- Weiya Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yiyun Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Dongdong Qin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shu Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Guihua Du
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Fan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lufan Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mei Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China.,Centre for Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
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15
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Speckles and paraspeckles coordinate to regulate HSV-1 genes transcription. Commun Biol 2021; 4:1207. [PMID: 34675360 PMCID: PMC8531360 DOI: 10.1038/s42003-021-02742-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Numbers of nuclear speckles and paraspeckles components have been demonstrated to regulate herpes simplex virus 1 (HSV-1) replication. However, how HSV-1 infection affects the two nuclear bodies, and whether this influence facilitates the expression of viral genes, remains elusive. In the current study, we found that HSV-1 infection leads to a redistribution of speckles and paraspeckles components. Serine/arginine-rich splicing factor 2 (SRSF2), the core component of speckles, was associated with multiple paraspeckles components, including nuclear paraspeckles assembly transcript 1 (NEAT1), PSPC1, and P54nrb, in HSV-1 infected cells. This association coordinates the transcription of viral genes by binding to the promoters of these genes. By association with the enhancer of zeste homolog 2 (EZH2) and P300/CBP complex, NEAT1 and SRSF2 influenced the histone modifications located near viral genes. This study elucidates the interplay between speckles and paraspeckles following HSV-1 infection and provides insight into the mechanisms by which HSV-1 utilizes host cellular nuclear bodies to facilitate its life cycle. Li & Wang report that components of nuclear speckles and paraspeckles are redistributed upon HSV-1 infection. They show that the association of Serine/arginine-rich splicing factor 2 (SRSF2) with nuclear paraspeckles assembly transcript 1 (NEAT1) coordinates the transcription of viral genes
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16
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RBM20-Related Cardiomyopathy: Current Understanding and Future Options. J Clin Med 2021; 10:jcm10184101. [PMID: 34575212 PMCID: PMC8468976 DOI: 10.3390/jcm10184101] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
Splice regulators play an essential role in the transcriptomic diversity of all eukaryotic cell types and organ systems. Recent evidence suggests a contribution of splice-regulatory networks in many diseases, such as cardiomyopathies. Adaptive splice regulators, such as RNA-binding motif protein 20 (RBM20) determine the physiological mRNA landscape formation, and rare variants in the RBM20 gene explain up to 6% of genetic dilated cardiomyopathy (DCM) cases. With ample knowledge from RBM20-deficient mice, rats, swine and induced pluripotent stem cells (iPSCs), the downstream targets and quantitative effects on splicing are now well-defined and the prerequisites for corrective therapeutic approaches are set. This review article highlights some of the recent advances in the field, ranging from aspects of granule formation to 3D genome architectures underlying RBM20-related cardiomyopathy. Promising therapeutic strategies are presented and put into context with the pathophysiological characteristics of RBM20-related diseases.
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17
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Li Y, Wang X, Qi S, Gao L, Huang G, Ren Z, Li K, Peng Y, Yi G, Guo J, Yang R, Wang H, Zhang X, Liu Y. Spliceosome-regulated RSRP1-dependent NF-κB activation promotes the glioblastoma mesenchymal phenotype. Neuro Oncol 2021; 23:1693-1708. [PMID: 34042961 DOI: 10.1093/neuonc/noab126] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The glioblastoma (GBM) mesenchymal (MES) phenotype, induced by NF-κB activation, is characterized by aggressive tumour progression and poor clinical outcomes. Our previous analysis indicated that MES GBM has a unique alternative splicing (AS) pattern; however, the underlying mechanism remains obscure. We aimed to reveal how splicing regulation contributes to MES phenotype promotion in GBM. METHODS We screened novel candidate splicing factors that participate in NF-κB activation and MES phenotype promotion in GBM. In vitro and in vivo assays were used to explore the function of RSRP1 in MES GBM. RESULTS Here, we identified that arginine/serine-rich protein 1 (RSRP1) promotes the MES phenotype by facilitating GBM cell invasion and apoptosis resistance. Proteomic, transcriptomic and functional analyses confirmed that RSRP1 regulates AS in MES GBM through mediating spliceosome assembly. One RSRP1-regulated AS event resulted in skipping PARP6 exon 18 to form truncated, oncogenic PARP6-s. This isoform was unable to effectively suppress NF-κB. Co-treatment of cultured GBM cells and GBM tumour-bearing mice with spliceosome and NF-κB inhibitors exerted a synergistic effect on MES GBM growth. CONCLUSION We identified a novel mechanism through which RSRP1-dependent splicing promotes the GBM MES phenotype. Targeting AS via RSRP1-related spliceosomal factors might constitute a promising treatment for GBM.
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Affiliation(s)
- Yaomin Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiran Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Gao
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Guanglong Huang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhonglu Ren
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Kaishu Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuping Peng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Guozhong Yi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinglin Guo
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Runwei Yang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Hai Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xian Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yawei Liu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
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18
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Ka HI, Seo H, Choi Y, Kim J, Cho M, Choi SY, Park S, Han S, An J, Chung HS, Yang Y, Kim MJ. Loss of splicing factor IK impairs normal skeletal muscle development. BMC Biol 2021; 19:44. [PMID: 33789631 PMCID: PMC8015194 DOI: 10.1186/s12915-021-00980-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND IK is a splicing factor that promotes spliceosome activation and contributes to pre-mRNA splicing. Although the molecular mechanism of IK has been previously reported in vitro, the physiological role of IK has not been fully understood in any animal model. Here, we generate an ik knock-out (KO) zebrafish using the CRISPR/Cas9 system to investigate the physiological roles of IK in vivo. RESULTS The ik KO embryos display severe pleiotropic phenotypes, implying an essential role of IK in embryonic development in vertebrates. RNA-seq analysis reveals downregulation of genes involved in skeletal muscle differentiation in ik KO embryos, and there exist genes having improper pre-mRNA splicing among downregulated genes. The ik KO embryos display impaired neuromuscular junction (NMJ) and fast-twitch muscle development. Depletion of ik reduces myod1 expression and upregulates pax7a, preventing normal fast muscle development in a non-cell-autonomous manner. Moreover, when differentiation is induced in IK-depleted C2C12 myoblasts, myoblasts show a reduced ability to form myotubes. However, inhibition of IK does not influence either muscle cell proliferation or apoptosis in zebrafish and C2C12 cells. CONCLUSION This study provides that the splicing factor IK contributes to normal skeletal muscle development in vivo and myogenic differentiation in vitro.
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Affiliation(s)
- Hye In Ka
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea.,Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Hyemin Seo
- Howard Hughes Medical Institute and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Youngsook Choi
- Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Joohee Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Mina Cho
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Sujeong Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Sora Han
- Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Jinsu An
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Hak Suk Chung
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea. .,Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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19
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Li L, Miao H, Chang Y, Yao H, Zhao Y, Wu F, Song X. Multidimensional crosstalk between RNA-binding proteins and noncoding RNAs in cancer biology. Semin Cancer Biol 2021; 75:84-96. [PMID: 33722631 DOI: 10.1016/j.semcancer.2021.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 02/09/2023]
Abstract
RNA-binding proteins (RBPs) are well-known to bind RNA via a set of RNA-binding domains (RBDs) and determine the fate and function of their RNA targets; inversely, some RBPs, in certain cases, may be modulated by the bound RNAs rather than regulate their RNA partners. Current proteome-wide studies reveal that almost half of RBPs have no canonical RBDs, and the discovery of tens of thousands of noncoding RNAs (ncRNAs), especially those with the size larger than 200 nt (namely long noncoding RNAs, lncRNAs), makes the crosstalk between RBPs and RNAs more complicated. It is clear that macromolecular complexes formed by RBP and RNA are not only a form of existence of their RBP and RNA components in cells, but also represent a functional entity through which those RBPs and regulatory ncRNAs participate in the construction of regulatory networks in organism. In this review, we summarize the multidimensional crosstalk between RBPs and ncRNAs in cancer and discuss how RBPs achieve their function via the bound ncRNAs in different aspects of gene expression as well as how RBPs direct modification and processing of ncRNAs, in order to better understand tumor biology and provide new insights into development of strategies for cancer therapy and early detection.
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Affiliation(s)
- Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Hui Miao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yanbo Chang
- Sichuan Institute for Food and Drug Control, Department of Forensic Analytical Toxicology, West China School of Basic Medical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Hong Yao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yongyun Zhao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Fan Wu
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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20
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The splicing factor SRSF1 stabilizes the mRNA of TSLP to enhance acute lung injury. Cell Immunol 2021; 362:104299. [PMID: 33607522 DOI: 10.1016/j.cellimm.2021.104299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/24/2022]
Abstract
Acute lung injury (ALI) is a severe disease with a high rate of morbidity and mortality, characterized by excessive and uncontrolled inflammatory response in lung. Recent studies demonstrated that serine arginine-rich splicing factor 1 (SRSF1) is involved in inflammation. However, whether SRSF1 modulates ALI remains to be determined. In this study, we established an ALI mouse model that induced by lipopolysaccharide (LPS), with or without the treatment of SRSF1 antibody. Our result showed that SRSF1 expression was elevated in LPS-induced ALI. Importantly, treatment with SRSF1 antibody notably ameliorated ALI in mice, as determined by reduction in lung W/D ratios, histopathological changes, lung inflammation and TSLP expression. Besides, exposure of human alveolar epithelial A549 cells to LPS enhanced the expression of both SRSF1 and TSLP, while knockdown or overexpression of SRSF1 significantly lowered or upregulated the expression of TSLP induced by LPS. Interestingly, the expression of SRSF1 and TSLP showed a positive correlation in normal human lung tissues. Mechanistically, we found that SRSF1 directly bound with the mRNA of TSLP and may exert its function by stabilizing the mRNA of TSLP in LPS-induced ALI. Therefore, our results indicated that SRSF1 may be an important contributor in lung inflammation of LPS-induced ALI and SRSF1 signaling blocking may serve as a potential treatment of ALI.
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21
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Abstract
U1 snRNP is one of the most abundant ribonucleoprotein (RNP) complexes in eukaryotic cells and is estimated to be approximately 1 million copies per cell. Apart from its canonical role in mRNA splicing, this complex has emerged as a key regulator of eukaryotic mRNA length via inhibition of mRNA 3'-end processing at numerous intronic polyadenylation sites, in a process that is also termed 'U1 snRNP telescripting'. Several reviews have extensively described the concept of U1 telescripting and subsequently highlighted its potential impacts in mRNA metabolism. Here, we review what is currently known regarding the underlying mechanisms of this important phenomenon and discuss open questions and future challenges.
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Affiliation(s)
- Yi Ran
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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22
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Costa R, Rodia MT, Zini N, Pegoraro V, Marozzo R, Capanni C, Angelini C, Lattanzi G, Santi S, Cenacchi G. Morphological study of TNPO3 and SRSF1 interaction during myogenesis by combining confocal, structured illumination and electron microscopy analysis. Mol Cell Biochem 2021; 476:1797-1811. [PMID: 33452620 PMCID: PMC7940345 DOI: 10.1007/s11010-020-04023-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Transportin3 (TNPO3) shuttles the SR proteins from the cytoplasm to the nucleus. The SR family includes essential splicing factors, such as SRSF1, that influence alternative splicing, controlling protein diversity in muscle and satellite cell differentiation. Given the importance of alternative splicing in the myogenic process and in the maintenance of healthy muscle, alterations in the splicing mechanism might contribute to the development of muscle disorders. Combining confocal, structured illumination and electron microscopy, we investigated the expression of TNPO3 and SRSF1 during myogenesis, looking at nuclear and cytoplasmic compartments. We investigated TNPO3 and its interaction with SRSF1 and we observed that SRSF1 remained mainly localized in the nucleus, while TNPO3 decreased in the cytoplasm and was strongly clustered in the nuclei of differentiated myotubes. In conclusion, combining different imaging techniques led us to describe the behavior of TNPO3 and SRSF1 during myogenesis, showing that their dynamics follow the myogenic process and could influence the proteomic network necessary during myogenesis. The combination of different high-, super- and ultra-resolution imaging techniques led us to describe the behavior of TNPO3 and its interaction with SRSF1, looking at nuclear and cytoplasmic compartments. These observations represent a first step in understanding the role of TNPO3 and SRFSF1 in complex mechanisms, such as myogenesis.
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Affiliation(s)
- Roberta Costa
- Department of Biomedical and Neuromotor Sciences-DIBINEM, Alma Mater Studiorum University of Bologna, via Massarenti 9, 40138, Bologna, Italy.,Center of Applied Biomedical Research-CRBA, Alma Mater Studiorum University of Bologna, St. Orsola Hospital, via Massarenti 9, 40138, Bologna, Italy
| | - Maria Teresa Rodia
- Department of Biomedical and Neuromotor Sciences-DIBINEM, Alma Mater Studiorum University of Bologna, via Massarenti 9, 40138, Bologna, Italy.,Center of Applied Biomedical Research-CRBA, Alma Mater Studiorum University of Bologna, St. Orsola Hospital, via Massarenti 9, 40138, Bologna, Italy
| | - Nicoletta Zini
- CNR-National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, via di Barbiano 1/10, 40136, Bologna, Italy.,IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Valentina Pegoraro
- Neuromuscular Unit, Neurobiology Research group, IRCCS San Camillo Hospital, via Alberoni 70, 30126, Venice, Italy
| | - Roberta Marozzo
- Neuromuscular Unit, Neurobiology Research group, IRCCS San Camillo Hospital, via Alberoni 70, 30126, Venice, Italy
| | - Cristina Capanni
- CNR-National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, via di Barbiano 1/10, 40136, Bologna, Italy.,IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Corrado Angelini
- Neuromuscular Unit, Neurobiology Research group, IRCCS San Camillo Hospital, via Alberoni 70, 30126, Venice, Italy
| | - Giovanna Lattanzi
- CNR-National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, via di Barbiano 1/10, 40136, Bologna, Italy.,IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Spartaco Santi
- CNR-National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, via di Barbiano 1/10, 40136, Bologna, Italy.,IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and Neuromotor Sciences-DIBINEM, Alma Mater Studiorum University of Bologna, via Massarenti 9, 40138, Bologna, Italy. .,Center of Applied Biomedical Research-CRBA, Alma Mater Studiorum University of Bologna, St. Orsola Hospital, via Massarenti 9, 40138, Bologna, Italy.
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23
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Wang Z, Li K, Chen W, Wang X, Huang Y, Wang W, Wu W, Cai Z, Huang W. Modulation of SRSF2 expression reverses the exhaustion of TILs via the epigenetic regulation of immune checkpoint molecules. Cell Mol Life Sci 2020; 77:3441-3452. [PMID: 31838573 PMCID: PMC7426320 DOI: 10.1007/s00018-019-03362-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 10/15/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023]
Abstract
The elevated expression of immune checkpoints by the tumor microenvironment is associated with poor prognosis in several cancers due to the exhaustion of tumor-infiltrating lymphocytes (TILs), and the effective suppression of the expression of these genes is key to reversing the exhaustion of TILs. Herein, we determined that serine/arginine-rich splicing factor 2 (SRSF2) is a target for blocking the tumor microenvironment-associated immunosuppressive effects. We found that the expression of SRSF2 was increased in exhausted T cells and that SRSF2 was involved in multiple immune checkpoint molecules mediating TILs' exhaustion. Furthermore, SRSF2 was revealed to regulate the transcription of these immune checkpoint genes by associating with an acyl-transferases P300/CBP complex and altering the H3K27Ac level near these genes, thereafter influencing the recruitment of signal transducer and activator of transcription 3 (STAT3) to these gene promoters. Collectively, our data indicated that SRSF2 functions as a modulator of the anti-tumor response of T cells and may be a therapeutic target for reversing the exhaustion of TILs.
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Affiliation(s)
- Ziqiang Wang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Kun Li
- Department of Nuclear Medicine, Shandong Provincial Qianfoshan Hospital, The First Hospital Affiliated with Shandong First Medical University, Jinan, 250014, China
| | - Wei Chen
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Xiaoxia Wang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Yikun Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Weiming Wang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Wanjun Wu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Zhiming Cai
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China.
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China.
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China.
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China.
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24
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Zhang Z, Yao M, Zhu G, Chen Y, Chen Y, Sun F, Zhang Y, Wang Q, Shen Z. Identification and subcellular localization of splicing factor arginine/serine-rich 10 in the microsporidian Nosema bombycis. J Invertebr Pathol 2020; 174:107441. [PMID: 32659232 DOI: 10.1016/j.jip.2020.107441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
Splicing factors are important components of RNA editing in eukaryotic organisms and can produce many functional and coding genes, which is an indispensable step for the correct expression of corresponding proteins. In this study, we identified splicing factor arginine/serine-rich 10 protein in the microsporidian Nosema bombycis and named it NbSRSF10. The NbSRSF10 gene contains a complete ORF of 1449 bp in length that encodes a 482-amino acid polypeptide. The isoelectric point (pI) of the protein encoded by NbSRSF10 gene was 4.94. NbSRSF10 has a molecular weight of 54.6 kD and has no signal peptide. NbSRSF10 is comprised of arginine (11.41%), glutamic acid (11.41%) and serine (9.54%) among the total amino acids, and 7 α-helix, 7 β-sheet and 15 random coils in secondary structure, and contains 71 phosphorylation sites, 22 N-glycosylation sites and 20 O-glycosylation sites. The three-dimensional structure of NbSRSF10 is similar to that of transformer-2 beta of Homo sapiens (hTra2-β). Indirect immunofluorescence showed that the NbSRSF10 is localized in the cytoplasm of the dormant microsporidian spore and is transferred to the nuclei when N. bombycis develops into the proliferative and sporogonic phase. qPCR revealed that the relative expression of NbSRSF10 increased in the meronts stage and was found at a relatively low level in the sporogonic phase of development of N. bombycis, and was up-regulated again during infection in the host cell and early proliferative phase of second life cycle. These results suggested that the NbSRSF10 may participate in the whole life cycle and play an important role in transcription regulation of N. bombycis.
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Affiliation(s)
- Zhilin Zhang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Mingshuai Yao
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Guanyu Zhu
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Yong Chen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Ying Chen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Fuzhen Sun
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Yiling Zhang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Qiang Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Zhongyuan Shen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China.
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25
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Rahman MA, Nasrin F, Bhattacharjee S, Nandi S. Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel) 2020; 12:cancers12061381. [PMID: 32481522 PMCID: PMC7352608 DOI: 10.3390/cancers12061381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.
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26
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Sebbag-Sznajder N, Brody Y, Hochberg-Laufer H, Shav-Tal Y, Sperling J, Sperling R. Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State. Front Genet 2020; 11:409. [PMID: 32499811 PMCID: PMC7243799 DOI: 10.3389/fgene.2020.00409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Splicing and alternative splicing of pre-mRNA are key sources in the formation of diversity in the human proteome. These processes have a central role in the regulation of the gene expression pathway. Yet, how spliceosomes are assembled on a multi-intronic pre-mRNA is at present not well understood. To study the spliceosomes assembled in vivo on transcripts with variable number of introns, we examined a series of three related transcripts derived from the β-globin gene, where two transcript types contained increasing number of introns, while one had only an exon. Each transcript had multiple MS2 sequence repeats that can be bound by the MS2 coat protein. Using our protocol for isolation of endogenous spliceosomes under native conditions from cell nuclei, we show that all three transcripts are found in supraspliceosomes – 21 MDa dynamic complexes, sedimenting at 200S in glycerol gradients, and composed of four native spliceosomes connected by the transcript. Affinity purification of complexes assembled on the transcript with most introns (termed E6), using the MS2 tag, confirmed the assembly of E6 in supraspliceosomes with components such as Sm proteins and PSF. Furthermore, splicing inhibition by spliceostatin A did not inhibit the assembly of supraspliceosomes on the E6 transcript, yet increased the percentage of E6 pre-mRNA supraspliceosomes. These findings were corroborated in intact cells, using RNA FISH to detect the MS2-tagged E6 mRNA, together with GFP-tagged splicing factors, showing the assembly of splicing factors SRSF2, U1-70K, and PRP8 onto the E6 transcripts under normal conditions and also when splicing was inhibited. This study shows that different transcripts with different number of introns, or lacking an intron, are assembled in supraspliceosomes even when splicing is inhibited. This assembly starts at the site of transcription and can continue during the life of the transcript in the nucleoplasm. This study further confirms the dynamic and universal nature of supraspliceosomes that package RNA polymerase II transcribed pre-mRNAs into complexes composed of four native spliceosomes connected by the transcript, independent of their length, number of introns, or splicing state.
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Affiliation(s)
| | - Yehuda Brody
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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27
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Zhang X, Xu Y, Chen B, Kang L. Long noncoding RNA PAHAL modulates locust behavioural plasticity through the feedback regulation of dopamine biosynthesis. PLoS Genet 2020; 16:e1008771. [PMID: 32348314 PMCID: PMC7241820 DOI: 10.1371/journal.pgen.1008771] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/21/2020] [Accepted: 04/09/2020] [Indexed: 11/24/2022] Open
Abstract
Some long noncoding RNAs (lncRNAs) are specifically expressed in brain cells, implying their neural and behavioural functions. However, how lncRNAs contribute to neural regulatory networks governing the precise behaviour of animals is less explored. Here, we report the regulatory mechanism of the nuclear-enriched lncRNA PAHAL for dopamine biosynthesis and behavioural adjustment in migratory locusts (Locusta migratoria), a species with extreme behavioral plasticity. PAHAL is transcribed from the sense (coding) strand of the gene encoding phenylalanine hydroxylase (PAH), which is responsible for the synthesis of dopamine from phenylalanine. PAHAL positively regulates PAH expression resulting in dopamine production in the brain. In addition, PAHAL modulates locust behavioral aggregation in a population density-dependent manner. Mechanistically, PAHAL mediates PAH transcriptional activation by recruiting serine/arginine-rich splicing factor 2 (SRSF2), a transcription/splicing factor, to the PAH proximal promoter. The co-activation effect of PAHAL requires the interaction of the PAHAL/SRSF2 complex with the promoter-associated nascent RNA of PAH. Thus, the data support a model of feedback modulation of animal behavioural plasticity by an lncRNA. In this model, the lncRNA mediates neurotransmitter metabolism through orchestrating a local transcriptional loop. The neurotransmitter dopamine is crucial for the neuronal and behavioral response in animals. Phenylalanine hydroxylase (PAH) is involved in dopamine biosynthesis and behavioral regulation in the migratory locust. However, the molecular mechanism for the fine tuning of PAH expression in behavioral response remains ambiguous. Here we discovered a nuclear-enriched lncRNA PAHAL that is transcribed from the coding strand of the PAH gene in the locust (i.e., sense lncRNA). PAHAL positively regulated PAH expression and dopamine production in the brain. In addition, PAHAL modulated behavioral aggregation of the locust. Mechanistically, PAHAL mediated the transcriptional activation of PAH by recruiting SRSF2, a transcription/splicing factor, to the promoter-associated nascent RNA of PAH. These data support a model of feedback modulation of dopamine biosynthesis and behavioral plasticity via a sense lncRNA in the catecholamine metabolic pathway.
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Affiliation(s)
- Xia Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Ya'nan Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bing Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Hebei University, Baoding, China
- * E-mail: (BC); (KL)
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Hebei University, Baoding, China
- * E-mail: (BC); (KL)
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28
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Gou LT, Lim DH, Ma W, Aubol BE, Hao Y, Wang X, Zhao J, Liang Z, Shao C, Zhang X, Meng F, Li H, Zhang X, Xu R, Li D, Rosenfeld MG, Mellon PL, Adams JA, Liu MF, Fu XD. Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine Phosphorylation. Cell 2020; 180:1212-1227.e14. [PMID: 32169215 DOI: 10.1016/j.cell.2020.02.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/04/2019] [Accepted: 02/07/2020] [Indexed: 01/15/2023]
Abstract
The paternal genome undergoes a massive exchange of histone with protamine for compaction into sperm during spermiogenesis. Upon fertilization, this process is potently reversed, which is essential for parental genome reprogramming and subsequent activation; however, it remains poorly understood how this fundamental process is initiated and regulated. Here, we report that the previously characterized splicing kinase SRPK1 initiates this life-beginning event by catalyzing site-specific phosphorylation of protamine, thereby triggering protamine-to-histone exchange in the fertilized oocyte. Interestingly, protamine undergoes a DNA-dependent phase transition to gel-like condensates and SRPK1-mediated phosphorylation likely helps open up such structures to enhance protamine dismissal by nucleoplasmin (NPM2) and enable the recruitment of HIRA for H3.3 deposition. Remarkably, genome-wide assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis reveals that selective chromatin accessibility in both sperm and MII oocytes is largely erased in early pronuclei in a protamine phosphorylation-dependent manner, suggesting that SRPK1-catalyzed phosphorylation initiates a highly synchronized reorganization program in both parental genomes.
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Affiliation(s)
- Lan-Tao Gou
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Do-Hwan Lim
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brandon E Aubol
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Zhao
- Transgenic and Knockout Mouse Core, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuan Zhang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fan Meng
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaorong Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruiming Xu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dangsheng Li
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pamela L Mellon
- Transgenic and Knockout Mouse Core, University of California, San Diego, La Jolla, CA 92093, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph A Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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29
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Movassat M, Forouzmand E, Reese F, Hertel KJ. Exon size and sequence conservation improves identification of splice-altering nucleotides. RNA (NEW YORK, N.Y.) 2019; 25:1793-1805. [PMID: 31554659 PMCID: PMC6859846 DOI: 10.1261/rna.070987.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Pre-mRNA splicing is regulated through multiple trans-acting splicing factors. These regulators interact with the pre-mRNA at intronic and exonic positions. Given that most exons are protein coding, the evolution of exons must be modulated by a combination of selective coding and splicing pressures. It has previously been demonstrated that selective splicing pressures are more easily deconvoluted when phylogenetic comparisons are made for exons of identical size, suggesting that exon size-filtered sequence alignments may improve identification of nucleotides evolved to mediate efficient exon ligation. To test this hypothesis, an exon size database was created, filtering 76 vertebrate sequence alignments based on exon size conservation. In addition to other genomic parameters, such as splice-site strength, gene position, or flanking intron length, this database permits the identification of exons that are size- and/or sequence-conserved. Highly size-conserved exons are always sequence-conserved. However, sequence conservation does not necessitate exon size conservation. Our analysis identified evolutionarily young exons and demonstrated that length conservation is a strong predictor of alternative splicing. A published data set of approximately 5000 exonic SNPs associated with disease was analyzed to test the hypothesis that exon size-filtered sequence comparisons increase detection of splice-altering nucleotides. Improved splice predictions could be achieved when mutations occur at the third codon position, especially when a mutation decreases exon inclusion efficiency. The results demonstrate that coding pressures dominate nucleotide composition at invariable codon positions and that exon size-filtered sequence alignments permit identification of splice-altering nucleotides at wobble positions.
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Affiliation(s)
- Maliheh Movassat
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Elmira Forouzmand
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Fairlie Reese
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
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30
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DeLigio JT, Stevens SC, Nazario-Muñoz GS, MacKnight HP, Doe KK, Chalfant CE, Park MA. Serine/Arginine-Rich Splicing Factor 3 Modulates the Alternative Splicing of Cytoplasmic Polyadenylation Element Binding Protein 2. Mol Cancer Res 2019; 17:1920-1930. [PMID: 31138601 PMCID: PMC6726571 DOI: 10.1158/1541-7786.mcr-18-1291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/17/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023]
Abstract
Triple negative breast cancer (TNBC) has an unusually low 5-year survival rate linked to higher metastatic rates. Our laboratory recently delineated a role for the alternative RNA splicing (AS) of cytoplasmic polyadenylation element binding protein 2 (CPEB2), via inclusion/exclusion of exon 4, in the metastasis of TNBC. In these studies, the mechanism governing the inclusion/exclusion of exon 4 was examined. Specifically, the RNA trans-factor, SRSF3, was found to be explicitly associated with CPEB2 exon 4. A SRSF3 consensus sequence was identified in exon 4, and mutation of this sequence abolished the association of SRSF3. The expression of SRSF3 was upregulated in TNBC cells upon the acquisition of anoikis resistance correlating with a reduction in the CPEB2A/B ratio. Importantly, downregulation of SRSF3 in these cells by siRNA induced the exclusion of exon 4 in cells increasing the ratio of CPEB2A (exon 4 excluded) to CPEB2B (exon 4 included). Downregulation of SRSF3 also reversed the CPEB2A/B ratio of a wild-type CPEB2 exon 4 minigene and endogenous CPEB2 pre-mRNA, but not a mutant CPEB2 minigene with the SRSF3 RNA cis-element ablated. SRSF3 downregulation ablated the anoikis resistance of TNBC cells, which was "rescued" by ectopic expression of CPEB2B. Finally, analysis of The Cancer Genome Atlas database showed a positive relationship between SRSF3 expression and lower CPEB2A/B ratios in aggressive breast cancers. IMPLICATIONS: These findings demonstrate that SRSF3 modulates CPEB2 AS to induce the expression of the CPEB2B isoform that drives TNBC phenotypes correlating with aggressive human breast cancer. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/17/9/1920/F1.large.jpg.
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Affiliation(s)
- James T DeLigio
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Shaun C Stevens
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - Gina S Nazario-Muñoz
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - H Patrick MacKnight
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Keli K Doe
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Charles E Chalfant
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia.
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
- VCU Massey Cancer Center, Cancer Cell Signaling Program, VCU, Richmond Virginia
- Research Service, Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia
- VCU Institute of Molecular Medicine, Richmond, Virginia
- VCU Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia
- Research Service, James A. Haley Veterans Hospital, Tampa, Florida
- The Moffitt Cancer Center, Tampa, Florida
| | - Margaret A Park
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia.
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
- VCU Massey Cancer Center, Cancer Cell Signaling Program, VCU, Richmond Virginia
- VCU Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia
- Research Service, James A. Haley Veterans Hospital, Tampa, Florida
- The Moffitt Cancer Center, Tampa, Florida
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31
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Sperling R. Small non-coding RNA within the endogenous spliceosome and alternative splicing regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194406. [PMID: 31323432 DOI: 10.1016/j.bbagrm.2019.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Splicing and alternative splicing (AS), which occur in the endogenous spliceosome, play major roles in regulating gene expression, and defects in them are involved in numerous human diseases including cancer. Although the mechanism of the splicing reaction is well understood, the regulation of AS remains to be elucidated. A group of essential regulatory factors in gene expression are small non-coding RNAs (sncRNA): e.g. microRNA, mainly known for their inhibitory role in translation in the cytoplasm; and small nucleolar RNA, known for their role in methylating non-coding RNA in the nucleolus. Here I highlight a new aspect of sncRNAs found within the endogenous spliceosome. Assembled in non-canonical complexes and through different base pairing than their canonical ones, spliceosomal sncRNAs can potentially target different RNAs. Examples of spliceosomal sncRNAs regulating AS, regulating gene expression, and acting in a quality control of AS are reviewed, suggesting novel functions for spliceosomal sncRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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32
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Driller JH, Lützkendorf J, Depner H, Siebert M, Kuropka B, Weise C, Piao C, Petzoldt AG, Lehmann M, Stelzl U, Zahedi R, Sickmann A, Freund C, Sigrist SJ, Wahl MC. Phosphorylation of the Bruchpilot N-terminus in Drosophila unlocks axonal transport of active zone building blocks. J Cell Sci 2019; 132:jcs.225151. [PMID: 30745339 DOI: 10.1242/jcs.225151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Protein scaffolds at presynaptic active zone membranes control information transfer at synapses. For scaffold biogenesis and maintenance, scaffold components must be safely transported along axons. A spectrum of kinases has been suggested to control transport of scaffold components, but direct kinase-substrate relationships and operational principles steering phosphorylation-dependent active zone protein transport are presently unknown. Here, we show that extensive phosphorylation of a 150-residue unstructured region at the N-terminus of the highly elongated Bruchpilot (BRP) active zone protein is crucial for ordered active zone precursor transport in Drosophila Point mutations that block SRPK79D kinase-mediated phosphorylation of the BRP N-terminus interfered with axonal transport, leading to BRP-positive axonal aggregates that also contain additional active zone scaffold proteins. Axonal aggregates formed only in the presence of non-phosphorylatable BRP isoforms containing the SRPK79D-targeted N-terminal stretch. We assume that specific active zone proteins are pre-assembled in transport packages and are thus co-transported as functional scaffold building blocks. Our results suggest that transient post-translational modification of a discrete unstructured domain of the master scaffold component BRP blocks oligomerization of these building blocks during their long-range transport.
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Affiliation(s)
- Jan H Driller
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Janine Lützkendorf
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Harald Depner
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Matthias Siebert
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Benno Kuropka
- Laboratory of Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Christoph Weise
- Laboratory of Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Chengji Piao
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Astrid G Petzoldt
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany.,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin Lehmann
- Cellular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, D-13125 Berlin, Germany
| | - Ulrich Stelzl
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, A-8010 Graz, Austria
| | - René Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, D-44139 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, D-44139 Dortmund, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Stephan J Sigrist
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany .,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany .,Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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33
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Huang W, Chen X, Guan Q, Zhong Z, Ma J, Yang B, Wang T, Zhu W, Tian J. Changes of alternative splicing in Arabidopsis thaliana grown under different CO2 concentrations. Gene 2019; 689:43-50. [DOI: 10.1016/j.gene.2018.11.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
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34
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Filatova EN, Utkin OV. The Role of Noncoding mRNA Isoforms in the Regulation of Gene Expression. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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35
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Liu X, Klein PS. Glycogen synthase kinase-3 and alternative splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1501. [PMID: 30118183 DOI: 10.1002/wrna.1501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
Glycogen synthase kinase-3 (GSK-3) is a highly conserved negative regulator of receptor tyrosine kinase, cytokine, and Wnt signaling pathways. Stimulation of these pathways inhibits GSK-3 to modulate diverse downstream effectors that include transcription factors, nutrient sensors, glycogen synthesis, mitochondrial function, circadian rhythm, and cell fate. GSK-3 also regulates alternative splicing in response to T-cell receptor activation, and recent phosphoproteomic studies have revealed that multiple splicing factors and regulators of RNA biosynthesis are phosphorylated in a GSK-3-dependent manner. Furthermore, inhibition of GSK-3 alters the splicing of hundreds of mRNAs, indicating a broad role for GSK-3 in the regulation of RNA processing. GSK-3-regulated phosphoproteins include SF3B1, SRSF2, PSF, RBM8A, nucleophosmin 1 (NPM1), and PHF6, many of which are mutated in leukemia and myelodysplasia. As GSK-3 is inhibited by pathways that are pathologically activated in leukemia and loss of Gsk3 in hematopoietic cells causes a severe myelodysplastic neoplasm in mice, these findings strongly implicate GSK-3 as a critical regulator of mRNA processing in normal and malignant hematopoiesis. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Xiaolei Liu
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S Klein
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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36
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Preußner M, Heyd F. Temperature‐controlled Rhythmic Gene Expression in Endothermic Mammals: All Diurnal Rhythms are Equal, but Some are Circadian. Bioessays 2018; 40:e1700216. [DOI: 10.1002/bies.201700216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 05/03/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Marco Preußner
- Laboratory of RNA BiochemistryInstitute of Chemistry and BiochemistryFreie Universität Berlin Takustrasse 6Berlin14195Germany
| | - Florian Heyd
- Laboratory of RNA BiochemistryInstitute of Chemistry and BiochemistryFreie Universität Berlin Takustrasse 6Berlin14195Germany
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37
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Lee AR, Che N, Lovnicki JM, Dong X. Development of Neuroendocrine Prostate Cancers by the Ser/Arg Repetitive Matrix 4-Mediated RNA Splicing Network. Front Oncol 2018; 8:93. [PMID: 29666783 PMCID: PMC5891588 DOI: 10.3389/fonc.2018.00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/16/2018] [Indexed: 12/19/2022] Open
Abstract
While the use of next-generation androgen receptor pathway inhibition (ARPI) therapy has significantly increased the survival of patients with metastatic prostate adenocarcinoma (AdPC), several groups have reported a treatment-resistant mechanism, whereby cancer cells can become androgen receptor (AR) indifferent and gain a neuroendocrine (NE)-like phenotype. This subtype of castration-resistant prostate cancer has been termed "treatment-induced castration-resistant neuroendocrine prostate cancer" (CRPC-NE). Recent reports indicate that the overall genomic landscapes of castration-resistant tumors with AdPC phenotypes and CRPC-NE are not significantly altered. However, CRPC-NE tumors have been found to contain a NE-specific pattern throughout their epigenome and splicing transcriptome, which are significantly modified. The molecular mechanisms by which CRPC-NE develops remain unclear, but several factors have been implicated in the progression of the disease. Recently, Ser/Arg repetitive matrix 4 (SRRM4), a neuronal-specific RNA splicing factor that is upregulated in CRPC-NE tumors, has been shown to establish a CRPC-NE-unique splicing transcriptome, to induce a NE-like morphology in AdPC cells, and, most importantly, to transform AdPC cells into CRPC-NE xenografts under ARPI. Moreover, the SRRM4-targeted splicing genes are highly enriched in various neuronal processes, suggesting their roles in facilitating a CRPC-NE program. This article will address the importance of SRRM4-mediated alternative RNA splicing in reprogramming translated proteins to facilitate NE differentiation, survival, and proliferation of cells to establish CRPC-NE tumors. In addition, we will discuss the potential roles of SRRM4 in conjunction with other known pathways and factors important for CRPC-NE development, such as the AR pathway, TP53 and RB1 genes, the FOXA family of proteins, and environmental factors. This study aims to explore the multifaceted functions of SRRM4 and SRRM4-mediated splicing in driving a CRPC-NE program as a coping mechanism for therapy resistance, as well as define future SRRM4-targeted therapeutic approaches for treating CRPC-NE or mitigating its development.
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Affiliation(s)
- Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Che
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jessica M Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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38
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Suess B, Kemmerer K, Weigand JE. Splicing and Alternative Splicing Impact on Gene Design. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Katrin Kemmerer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Julia E. Weigand
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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39
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Guo W, Zhu C, Yin Z, Wang Q, Sun M, Cao H, Greaser ML. Splicing Factor RBM20 Regulates Transcriptional Network of Titin Associated and Calcium Handling Genes in The Heart. Int J Biol Sci 2018; 14:369-380. [PMID: 29725258 PMCID: PMC5930469 DOI: 10.7150/ijbs.24117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/27/2018] [Indexed: 01/28/2023] Open
Abstract
RNA binding motif 20 (RBM20) regulates pre-mRNA splicing of over thirty genes, among which titin is a major target. With RBM20 expression, titin expresses a larger isoform at fetal stage to a smaller isoform at adult resulting from alternative splicing, while, without RBM20, titin expresses exclusively a larger isoform throughout all ages. In addition to splicing regulation, it is unknown whether RBM20 also regulates gene expression. In this study, we employed Rbm20 knockout rats to investigate gene expression profile using Affymetrix expression array. We compared wild type to Rbm20 knockout at day1, 20 and 49. Bioinformatics analysis showed RBM20 regulates fewer genes expression at younger age and more at older age and commonly expressed genes have the same trends. GSEA indicated up-regulated genes are associated with heart failure. We examined titin binding partners. All titin direct binding partners are up-regulated and their increased expression is associated with dilated cardiomyopathy. Particularly, we found that genes involving calcium handling and muscle contraction are changed by RBM20. Intracellular calcium level measurement with individual cardiomyocytes further confirmed that changes of these proteins impact calcium handling. Selected genes from titin binding partners and calcium handling were validated with QPCR and western blotting. These data demonstrate that RBM20 regulates gene splicing as well as gene expression. Altered gene expression by RBM20 influences protein-protein interaction, calcium releasing and thus muscle contraction. Our results first reported gene expression impacted by RBM20 with heart maturation, and provided new insights into the role of RBM20 in the progression of heart failure.
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Affiliation(s)
- Wei Guo
- Animal Science, University of Wyoming, Laramie, WY 82071, USA.,Center for Cardiovascular Research and Alternative Medicine, University of Wyoming, Laramie, WY 82071, USA
| | - Chaoqun Zhu
- Animal Science, University of Wyoming, Laramie, WY 82071, USA.,Center for Cardiovascular Research and Alternative Medicine, University of Wyoming, Laramie, WY 82071, USA
| | - Zhiyong Yin
- Animal Science, University of Wyoming, Laramie, WY 82071, USA.,Department of Cardiology, Xi Jing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Qiurong Wang
- Animal Science, University of Wyoming, Laramie, WY 82071, USA.,Center for Cardiovascular Research and Alternative Medicine, University of Wyoming, Laramie, WY 82071, USA
| | - Mingming Sun
- Animal Science, University of Wyoming, Laramie, WY 82071, USA.,Center for Cardiovascular Research and Alternative Medicine, University of Wyoming, Laramie, WY 82071, USA
| | - Huojun Cao
- Iowa Institute for Oral Health Research, College of Dentistry.,Craniofacial Anomalies Research Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Marion L Greaser
- Animal Science, University of Wisconsin-Madison, Madison, WI 53705, USA
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40
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Yin X, Chen C, Xu T, Li L, Zhang L. Tetrahydroxystilbene glucoside modulates amyloid precursor protein processing via activation of AKT-GSK3β pathway in cells and in APP/PS1 transgenic mice. Biochem Biophys Res Commun 2018; 495:672-678. [DOI: 10.1016/j.bbrc.2017.11.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 11/08/2017] [Indexed: 11/26/2022]
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41
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Ohno K, Takeda JI, Masuda A. Rules and tools to predict the splicing effects of exonic and intronic mutations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [DOI: 10.1002/wrna.1451] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Jun-ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
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42
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Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell 2017; 65:539-553.e7. [PMID: 28157508 DOI: 10.1016/j.molcel.2017.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulatory events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one-third of the regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large "missing cache" of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.
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Affiliation(s)
- Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | | | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Calley L Hirsch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Juli Wang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frederick Vizeacoumar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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43
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Shkreta L, Blanchette M, Toutant J, Wilhelm E, Bell B, Story BA, Balachandran A, Cochrane A, Cheung PK, Harrigan PR, Grierson DS, Chabot B. Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication. Nucleic Acids Res 2017; 45:4051-4067. [PMID: 27928057 PMCID: PMC5397194 DOI: 10.1093/nar/gkw1223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
We recently identified the 4-pyridinone-benzisothiazole carboxamide compound 1C8 as displaying strong anti-HIV-1 potency against a variety of clinical strains in vitro. Here we show that 1C8 decreases the expression of HIV-1 and alters splicing events involved in the production of HIV-1 mRNAs. Although 1C8 was designed to be a structural mimic of the fused tetracyclic indole compound IDC16 that targets SRSF1, it did not affect the splice site shifting activity of SRSF1. Instead, 1C8 altered splicing regulation mediated by SRSF10. Depleting SRSF10 by RNA interference affected viral splicing and, like 1C8, decreased expression of Tat, Gag and Env. Incubating cells with 1C8 promoted the dephosphorylation of SRSF10 and increased its interaction with hTra2β, a protein previously implicated in the control of HIV-1 RNA splicing. While 1C8 affects the alternative splicing of cellular transcripts controlled by SRSF10 and hTra2β, concentrations greater than those needed to inhibit HIV-1 replication were required to elicit significant alterations. Thus, the ability of 1C8 to alter the SRSF10-dependent splicing of HIV-1 transcripts, with minor effects on cellular splicing, supports the view that SRSF10 may be used as a target for the development of new anti-viral agents.
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Affiliation(s)
- Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Johanne Toutant
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Emmanuelle Wilhelm
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Brendan Bell
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Benjamin A Story
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Peter K Cheung
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David S Grierson
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
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44
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Zhou J, Gao G, Hou P, Li CM, Guo D. Regulation of the Alternative Splicing and Function of Cyclin T1 by the Serine-Arginine-Rich Protein ASF/SF2. J Cell Biochem 2017; 118:4020-4032. [PMID: 28422315 DOI: 10.1002/jcb.26058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/11/2017] [Indexed: 02/04/2023]
Abstract
Positive transcription elongation factor-b (P-TEFb) is required for the release of RNA polymerase II (RNAPII) from its pause near the gene promoters and thus for efficient proceeding to the transcription elongation. It consists of two core subunits-CDK9 and one of T-typed or K-typed cyclin, of which, cyclin T1/CDK9 is the major and most studied combination. We have previously identified a novel splice variant of cyclin T1, cyclin T1b, which negatively regulates the transcription elongation of HIV-1 genes as well as several host genes. In this study, we revealed the serine-arginine-rich protein, ASF/SF2, as a regulatory factor of the alternative splicing of cyclin T1 gene. ASF/SF2 promotes the production of cyclin T1b versus cyclin T1a and regulates the expression of cyclin T1-depedent genes at the transcription level. We further found that a cis-element on exon 8 is responsible for the skipping of exon 7 mediated by ASF/SF2. Collectively, ASF/SF2 is identified as a splicing regulator of cyclin T1, which contributes to the control of the subsequent transcription events. J. Cell. Biochem. 118: 4020-4032, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Jieqiong Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guozhen Gao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Panpan Hou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chun-Mei Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Deyin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.,School of Basic Medical Sciences, Wuhan University, Wuhan, China
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45
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Liu Z, Yuan G, Liu S, Jia J, Cheng L, Qi D, Shen S, Peng X, Liu G. Identified of a novel cis-element regulating the alternative splicing of LcDREB2. Sci Rep 2017; 7:46106. [PMID: 28383047 PMCID: PMC5382683 DOI: 10.1038/srep46106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/08/2017] [Indexed: 01/26/2023] Open
Abstract
Alternative splicing (AS) is an important gene regulation mechanism in plants. Despite the widespread use of AS in plant gene expression regulation, the identification of the cis-elements involved in the AS mechanism is rarely reported in plants. To explore the regulation mechanism of the AS of LcDREB2, a DREB2 ortholog from Sheepgrass (Leymus chinensis), the genomic sequences of LcDREB2 and its homologs in Poaceae were aligned, and six mutations were introduced in the conserved sequence of LcDREB2. By analyzing the distinct transcript patterns of the LcDREB2 mutants in transgenic Oryza sativa, a novel cis-element that affected the AS of LcDREB2 was identified as Exonic Splicing Enhancer 1 (ESE1). In addition, five serine-arginine rich (SR) proteins were confirmed to interact with ESE1 by electrophoretic mobility shift assay (EMSA). To further explore the expression regulation mechanism of the DREB subfamily, phylogenetic analysis of DREB2 paralogous genes was performed. The results strongly supported the hypothesis that AS is conserved in Poaceae plants and that it is an evolutionary strategy for the regulation of the functional expression of genes. The findings and methods of our study will promote a substantial step forward in understanding of the plant AS regulation mechanism.
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Affiliation(s)
- Zhujiang Liu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Guangxiao Yuan
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shu Liu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Junting Jia
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Liqin Cheng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Dongmei Qi
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Gongshe Liu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
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46
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Wu W, Zong J, Wei N, Cheng J, Zhou X, Cheng Y, Chen D, Guo Q, Zhang B, Feng Y. CASH: a constructing comprehensive splice site method for detecting alternative splicing events. Brief Bioinform 2017; 19:905-917. [DOI: 10.1093/bib/bbx034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/03/2023] Open
Affiliation(s)
- Wenwu Wu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Hangzhou, China
| | - Jie Zong
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ning Wei
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuexia Zhou
- Tianjin Medical University General Hospital, China
| | - Yuanming Cheng
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Dai Chen
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Qinghua Guo
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Bo Zhang
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ying Feng
- Institute for Nutritional Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
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47
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Chen J, Li N, Lian P, Wang J, Li P, Gong Z, Jiang L. Interaction of cyclophilin A with a novel binding protein, SR-25, and characterization of their expression pattern in Chinese hepatocellular carcinoma patients. Oncol Lett 2017; 12:5254-5260. [PMID: 28105234 DOI: 10.3892/ol.2016.5357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/18/2016] [Indexed: 11/06/2022] Open
Abstract
Cyclophilin (Cyp) A has been reported to be overexpressed in the majority of cancer cells, including hepatocellular carcinoma (HCC). However, the biological functions of CypA in HCC are far from being understood. To determine the biological functions of CypA in HCC, the present study screened human fetal liver complementary DNA for proteins interacting with CypA using the yeast two-hybrid system. A nuclear protein, serine/arginine-rich (SR)-25, was isolated as a novel CypA-binding protein that is distinct from those previously described in the literature. Binding assays and co-immunoprecipitation confirmed the physical association between CypA and SR-25. The present study demonstrated that CypA may interact with SR-25 through its peptidyl-prolyl isomerase domain. In addition, CypA may induce the expression of SR-25 in Hep3B cells. The messenger RNA levels of CypA and SR-25 in HCC indicated that there was a significant correlation between the expression of CypA and the expression of SR-25 in HCC. It can be speculated that the interaction between CypA and SR-25 proteins may be involved in potential carcinogenic functions of CypA in HCC. Further studies will focus on elucidating in detail the molecular mechanisms of the interaction between CypA and SR-25.
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Affiliation(s)
- Jian Chen
- Department of Oncology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China; Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Ning Li
- Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Peiwen Lian
- Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Jiahui Wang
- Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Peng Li
- Department of Oncology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Zhaohua Gong
- Department of Oncology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Lixin Jiang
- Department of Gastrointestinal Surgery, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
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48
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Ohnishi T, Shirane M, Nakayama KI. SRRM4-dependent neuron-specific alternative splicing of protrudin transcripts regulates neurite outgrowth. Sci Rep 2017; 7:41130. [PMID: 28106138 PMCID: PMC5247714 DOI: 10.1038/srep41130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/15/2016] [Indexed: 11/09/2022] Open
Abstract
Alternative splicing gives rise to diversity of the proteome, and it is especially prevalent in the mammalian nervous system. Indeed, many factors that control the splicing process govern nervous system development. Among such factors, SRRM4 is an important regulator of aspects of neural differentiation including neurite outgrowth. The mechanism by which SRRM4 regulates neurite outgrowth has remained poorly understood, however. We now show that SRRM4 regulates the splicing of protrudin gene (Zfyve27) transcripts in neuronal cells. SRRM4 was found to promote splicing of protrudin pre-mRNA so as to include a microexon (exon L) encoding seven amino acids in a neuron-specific manner. The resulting protein (protrudin-L) promotes neurite outgrowth during neurogenesis. Depletion of SRRM4 in Neuro2A cells impaired inclusion of exon L in protrudin mRNA, resulting in the generation of a shorter protein isoform (protrudin-S) that is less effective at promoting neurite extension. SRRM4 was found to recognize a UGC motif that is located immediately upstream of exon L and is necessary for inclusion of exon L in the mature transcript. Deletion of exon L in Neuro2A or embryonic stem cells inhibited neurite outgrowth. Our results suggest that SRRM4 controls neurite outgrowth through regulation of alternative splicing of protrudin transcripts.
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Affiliation(s)
- Takafumi Ohnishi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Michiko Shirane
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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49
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Wang Z, Liu Q, Lu J, Fan P, Xie W, Qiu W, Wang F, Hu G, Zhang Y. Serine/Arginine-rich Splicing Factor 2 Modulates Herpes Simplex Virus Type 1 Replication via Regulating Viral Gene Transcriptional Activity and Pre-mRNA Splicing. J Biol Chem 2016; 291:26377-26387. [PMID: 27784784 DOI: 10.1074/jbc.m116.753046] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/17/2016] [Indexed: 11/06/2022] Open
Abstract
Once it enters the host cell, herpes simplex virus type 1 (HSV-1) recruits a series of host cell factors to facilitate its life cycle. Here, we demonstrate that serine/arginine-rich splicing factor 2 (SRSF2), which is an important component of the splicing speckle, mediates HSV-1 replication by regulating viral gene expression at the transcriptional and posttranscriptional levels. Our results indicate that SRSF2 functions as a transcriptional activator by directly binding to infected cell polypeptide 0 (ICP0), infected cell polypeptide 27 (ICP27), and thymidine kinase promoters. Moreover, SRSF2 participates in ICP0 pre-mRNA splicing by recognizing binding sites in ICP0 exon 3. These findings provide insight into the functions of SRSF2 in HSV-1 replication and gene expression.
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Affiliation(s)
- Ziqiang Wang
- From the School of Life Sciences, Tsinghua University, Beijing 100084, China.,the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Qing Liu
- From the School of Life Sciences, Tsinghua University, Beijing 100084, China.,the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Jinhua Lu
- Shenzhen South China Pharmaceutical Co., Ltd., Shenzhen 518055, China, and
| | - Ping Fan
- From the School of Life Sciences, Tsinghua University, Beijing 100084, China.,the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Weidong Xie
- the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Wei Qiu
- From the School of Life Sciences, Tsinghua University, Beijing 100084, China.,the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Fan Wang
- From the School of Life Sciences, Tsinghua University, Beijing 100084, China.,the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Guangnan Hu
- the Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Yaou Zhang
- the Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China,
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50
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Liu B, Bossing T. Single neuron transcriptomics identify SRSF/SR protein B52 as a regulator of axon growth and Choline acetyltransferase splicing. Sci Rep 2016; 6:34952. [PMID: 27725692 PMCID: PMC5057162 DOI: 10.1038/srep34952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/21/2016] [Indexed: 01/14/2023] Open
Abstract
We removed single identified neurons from living Drosophila embryos to gain insight into the transcriptional control of developing neuronal networks. The microarray analysis of the transcriptome of two sibling neurons revealed seven differentially expressed transcripts between both neurons (threshold: log21.4). One transcript encodes the RNA splicing factor B52. Loss of B52 increases growth of axon branches. B52 function is also required for Choline acetyltransferase (ChAT ) splicing. At the end of embryogenesis, loss of B52 function impedes splicing of ChAT, reduces acetylcholine synthesis, and extends the period of uncoordinated muscle twitches during larval hatching. ChAT regulation by SRSF proteins may be a conserved feature since changes in SRSF5 expression and increased acetylcholine levels in brains of bipolar disease patients have been reported recently.
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Affiliation(s)
- Boyin Liu
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Torsten Bossing
- School of Biomedical and Healthcare Sciences, Plymouth University, John Bull Building, Plymouth, PL6 8BU, U.K
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