1
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Xie X, Chen X, Wang C, Sun L, Yu W, Lv Z, Tian S, Yao X, Wang F, Ding D, Chen J, Liu J. PARN Maintains RNA Stability to Regulate Insulin Maturation and GSIS in Pancreatic β Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2407774. [PMID: 39297407 PMCID: PMC11558150 DOI: 10.1002/advs.202407774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/09/2024] [Indexed: 11/14/2024]
Abstract
Diabetes, a metabolic disorder characterized by hyperglycemia, underscores the importance of normal pancreatic β-cell development and function in maintaining glucose homeostasis. Poly(A)-specific ribonuclease (PARN) serves as the principal regulator of messenger RNA (mRNA) stability, yet its specific role in pancreatic β cells remains unclear. This study utilizes mice with targeted PARN deficiency in β cells to elucidate this role. Notably, Parn conditional knockout mice present unaltered β-cell development and insulin sensitivity but reduced glucose-stimulated insulin secretion (GSIS). The observed outcomes are corroborated in NIT-1 cells. Furthermore, transcriptomic analyses reveal aberrant mRNA expression of genes crucial for insulin secretion in PARN-deficient β cells. Insights from linear amplification of complementary DNA ends and sequencing and coimmunoprecipitation experiments reveal an interaction between PARN and polypyrimidine tract-binding protein 1 (PTBP1), regulating the RNA stability of solute carrier family 30, member 8 (Slc30a8) and carbohydrate sulfotransferase 3 (Chst3). Interference with either PARN or PTBP1 disrupts this stability. These data indicate that PARN deficiency hampers GSIS and insulin maturation by destabilizing Slc30a8 and Chst3 RNAs. These findings provide compelling evidence indicating that PARN is a potential therapeutic target for enhancing insulin maturation and secretion.
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Affiliation(s)
- Xiaomei Xie
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
- College of Food and BioengineeringFujian Polytechnic Normal UniversityLongjiang StreetFuqingFujian310300China
| | - Xuexue Chen
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Chaofan Wang
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Longjie Sun
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Weiru Yu
- Key Laboratory of Precision Nutrition and Food QualityDepartment of Nutrition and HealthChina Agricultural UniversityBeijing100190China
| | - Zheng Lv
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Shuang Tian
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Xiaohong Yao
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Fengchao Wang
- National Institute of Biological SciencesBeijing102206China
- Tsinghua Institute of Multidisciplinary Biomedical ResearchTsinghua UniversityBeijing102206China
| | - Deqiang Ding
- Shanghai Key Laboratory of Maternal Fetal MedicineClinical and Translational Research CenterShanghai First Maternity and Infant HospitalFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai200092China
| | - Juan Chen
- Key Laboratory of Precision Nutrition and Food QualityDepartment of Nutrition and HealthChina Agricultural UniversityBeijing100190China
| | - Jiali Liu
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
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2
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Guo Y, Shang X, Ma L, Cao Y. RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants. Int J Mol Sci 2024; 25:10548. [PMID: 39408875 PMCID: PMC11477454 DOI: 10.3390/ijms251910548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 09/28/2024] [Accepted: 09/29/2024] [Indexed: 10/20/2024] Open
Abstract
The alternative splicing of pre-mRNA generates distinct mRNA variants from a pre-mRNA, thereby modulating a gene's function. The splicing of pre-mRNA depends on splice sites and regulatory elements in pre-mRNA, as well as the snRNA and proteins that recognize these sequences. Among these, RNA-binding proteins (RBPs) are the primary regulators of pre-mRNA splicing and play a critical role in the regulation of alternative splicing by recognizing the elements in pre-mRNA. However, little is known about the function of RBPs in stress response in plants. Here, we summarized the RBPs involved in the alternative splicing of pre-mRNA and their recognizing elements in pre-mRNA, and the recent advance in the role of RBP-mediated alternative splicing in response to abiotic stresses in plants. This review proposes that the regulation of pre-mRNA alternative splicing by RBPs is an important way for plants to adapt to abiotic stresses, and the regulation of alternative splicing by RBPs is a promising direction for crop breeding.
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Affiliation(s)
| | | | | | - Ying Cao
- College of Life Sciences, Capital Normal University, Beijing 100048, China; (Y.G.); (X.S.); (L.M.)
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3
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Truong A, Barton M, Tran U, Mellody M, Berger D, Madory D, Hitch E, Jibrael B, Nikolaidis N, Luchko T, Keppetipola N. Unstructured linker regions play a role in the differential splicing activities of paralogous RNA binding proteins PTBP1 and PTBP2. J Biol Chem 2024; 300:105733. [PMID: 38336291 PMCID: PMC10914480 DOI: 10.1016/j.jbc.2024.105733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
RNA Binding Proteins regulate, in part, alternative pre-mRNA splicing and, in turn, gene expression patterns. Polypyrimidine tract binding proteins PTBP1 and PTBP2 are paralogous RNA binding proteins sharing 74% amino acid sequence identity. Both proteins contain four structured RNA-recognition motifs (RRMs) connected by linker regions and an N-terminal region. Despite their similarities, the paralogs have distinct tissue-specific expression patterns and can regulate discrete sets of target exons. How two highly structurally similar proteins can exert different splicing outcomes is not well understood. Previous studies revealed that PTBP2 is post-translationally phosphorylated in the unstructured N-terminal, Linker 1, and Linker 2 regions that share less sequence identity with PTBP1 signifying a role for these regions in dictating the paralog's distinct splicing activities. To this end, we conducted bioinformatics analysis to determine the evolutionary conservation of RRMs versus linker regions in PTBP1 and PTBP2 across species. To determine the role of PTBP2 unstructured regions in splicing activity, we created hybrid PTBP1-PTBP2 constructs that had counterpart PTBP1 regions swapped to an otherwise PTBP2 protein and assayed on differentially regulated exons. We also conducted molecular dynamics studies to investigate how negative charges introduced by phosphorylation in PTBP2 unstructured regions can alter their physical properties. Collectively, results from our studies reveal an important role for PTBP2 unstructured regions and suggest a role for phosphorylation in the differential splicing activities of the paralogs on certain regulated exons.
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Affiliation(s)
- Anthony Truong
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California, USA
| | - Michael Barton
- Department of Physics and Astronomy, California State University, Northridge, Northridge, California, USA
| | - Uyenphuong Tran
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California, USA
| | - Montana Mellody
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California, USA
| | - Devon Berger
- Department of Biological Sciences, California State University Fullerton, Fullerton, California, USA
| | - Dean Madory
- Department of Biological Science, Santa Ana College, Santa Ana, California, USA
| | - Elizabeth Hitch
- Department of Biological Sciences, California State University Fullerton, Fullerton, California, USA
| | - Basma Jibrael
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California, USA
| | - Nikolas Nikolaidis
- Department of Biological Sciences, California State University Fullerton, Fullerton, California, USA
| | - Tyler Luchko
- Department of Physics and Astronomy, California State University, Northridge, Northridge, California, USA.
| | - Niroshika Keppetipola
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California, USA.
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4
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Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet 2023; 39:672-685. [PMID: 37236814 PMCID: PMC10524715 DOI: 10.1016/j.tig.2023.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Transcription of eukaryotic genes by RNA polymerase II (Pol II) yields RNA precursors containing introns that must be spliced out and the flanking exons ligated together. Splicing is catalyzed by a dynamic ribonucleoprotein complex called the spliceosome. Recent evidence has shown that a large fraction of splicing occurs cotranscriptionally as the RNA chain is extruded from Pol II at speeds of up to 5 kb/minute. Splicing is more efficient when it is tethered to the transcription elongation complex, and this linkage permits functional coupling of splicing with transcription. We discuss recent progress that has uncovered a network of connections that link splicing to transcript elongation and other cotranscriptional RNA processing events.
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Affiliation(s)
- Hossein Shenasa
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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5
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Iosub IA, Klobučar T, Ule J. Looping in on splicing: CRIC-seq uncovers PTBP1's long-range RNA regulatory rules. Mol Cell 2023; 83:1206-1207. [PMID: 37084712 DOI: 10.1016/j.molcel.2023.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/23/2023]
Abstract
RNA looping adds crucial information to understanding the position-dependent regulatory mechanisms of protein-RNA interactions. In this issue, Xue et al.1 present CRIC-seq, which comprehensively identifies RNA loops mediated by specific proteins and demonstrates their value for interpreting disease-causing mutations.
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Affiliation(s)
- Ira Alexandra Iosub
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UK Dementia Research Institute at King's College London, London, UK
| | - Tajda Klobučar
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; Biosciences PhD Program, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UK Dementia Research Institute at King's College London, London, UK; National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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6
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Ye R, Hu N, Cao C, Su R, Xu S, Yang C, Zhou X, Xue Y. Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation. Mol Cell 2023; 83:1311-1327.e7. [PMID: 36958328 DOI: 10.1016/j.molcel.2023.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/10/2023] [Accepted: 02/27/2023] [Indexed: 03/25/2023]
Abstract
RNA-binding proteins (RBPs) bind at different positions of the pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These "positional rules" can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease.
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Affiliation(s)
- Rong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruibao Su
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihan Xu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Chen Yang
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Xiangtian Zhou
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Dai S, Wang C, Zhang C, Feng L, Zhang W, Zhou X, He Y, Xia X, Chen B, Song W. PTB: Not just a polypyrimidine tract-binding protein. J Cell Physiol 2022; 237:2357-2373. [PMID: 35288937 DOI: 10.1002/jcp.30716] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
Polypyrimidine tract-binding protein (PTB), as a member of the heterogeneous nuclear ribonucleoprotein family, functions by rapidly shuttling between the nucleus and the cytoplasm. PTB is involved in the alternative splicing of pre-messenger RNA (mRNA) and almost all steps of mRNA metabolism. PTB regulation is organ-specific; brain- or muscle-specific microRNAs and long noncoding RNAs partially contribute to regulating PTB, thereby modulating many physiological and pathological processes, such as embryonic development, cell development, spermatogenesis, and neuron growth and differentiation. Previous studies have shown that PTB knockout can inhibit tumorigenesis and development. The knockout of PTB in glial cells can be reprogrammed into functional neurons, which shows great promise in the field of nerve regeneration but is controversial.
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Affiliation(s)
- Shirui Dai
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China.,Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Chao Wang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Cheng Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Lemeng Feng
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Wulong Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xuezhi Zhou
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Ye He
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xiaobo Xia
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Baihua Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Weitao Song
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
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8
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Zheng X, Zhu J, Liu J, Wang H, Qin Y, Jiang P, Xiao L, Gong T, Li Y, Peng X, Xu X, Cheng L, Huang L, Chen Q, Zhou X, Margolskee RF. Sweet taste perception in mice is blunted by PTBP1-regulated skipping of Tas1r2 exon 4. Chem Senses 2022; 47:6884719. [PMID: 36484118 DOI: 10.1093/chemse/bjac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Taste perception, initiated by activation of taste receptors in taste bud cells, is crucial for regulating nutrient intake. Genetic polymorphisms in taste receptor genes cannot fully explain the wide individual variations of taste sensitivity. Alternative splicing (AS) is a ubiquitous posttranscriptional mode of gene regulation that enriches the functional diversity of proteins. Here, we report the identification of a novel splicing variant of sweet taste receptor gene Tas1r2 (Tas1r2_∆e4) in mouse taste buds and the mechanism by which it diminishes sweet taste responses in vitro and in vivo. Skipping of Tas1r2 exon 4 in Tas1r2_∆e4 led to loss of amino acids in the extracellular Venus flytrap domain, and the truncated isoform reduced the response of sweet taste receptors (STRs) to all sweet compounds tested by generating nonfunctional T1R2/T1R3 STR heterodimers. The splicing factor PTBP1 (polypyrimidine tract-binding protein 1) promoted Tas1r2_∆e4 generation through binding to a polypyrimidine-rich splicing silencer in Tas1r2 exon 4, thus decreasing STR function and sweet taste perception in mice. Taken together, these data reveal the existence of a regulated AS event in Tas1r2 expression and its effect on sweet taste perception, providing a novel mechanism for modulating taste sensitivity at the posttranscriptional level.
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Affiliation(s)
- Xin Zheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Jianhui Zhu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Jiaxin Liu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Hong Wang
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | - Yumei Qin
- School of Food Science and Bioengineering, Zhejiang Gongshang University, Hangzhou 310006, P. R. China
| | - Peihua Jiang
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | - Li Xiao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Tao Gong
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Xian Peng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Xin Xu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Liquan Huang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qianming Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
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9
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RNA-binding protein 39: a promising therapeutic target for cancer. Cell Death Discov 2021; 7:214. [PMID: 34389703 PMCID: PMC8363639 DOI: 10.1038/s41420-021-00598-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/04/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022] Open
Abstract
RNA-binding motif protein 39 (RBM39), as a key factor in tumor-targeted mRNA and protein expression, not only plays a vital role in tumorigenesis, but also has broad development prospects in clinical treatment and drug research. Moreover, since RBM39 was identified as a target of sulfonamides, it has played a key role in the emerging field of molecule drug development. Hence, it is of great significance to study the interaction between RBM39 and tumors and the clinical application of drug-targeted therapy. In this paper, we describe the possible multi-level regulation of RBM39, including gene transcription, protein translation, and alternative splicing. Importantly, the molecular function of RBM39 as an important splicing factor in most common tumors is systematically outlined. Furthermore, we briefly introduce RBM39’s tumor-targeted drug research and its clinical application, hoping to give reference significance for the molecular mechanism of RBM39 in tumors, and provide reliable ideas for in-depth research for future therapeutic strategies.
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10
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Martelly W, Fellows B, Kang P, Vashisht A, Wohlschlegel JA, Sharma S. Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing. RNA Biol 2021; 18:2576-2593. [PMID: 34105434 DOI: 10.1080/15476286.2021.1932360] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
During spliceosome assembly, interactions that bring the 5' and 3' ends of an intron in proximity are critical for the production of mature mRNA. Here, we report synergistic roles for the stem-loops 3 (SL3) and 4 (SL4) of the human U1 small nuclear RNA (snRNA) in maintaining the optimal U1 snRNP function, and formation of cross-intron contact with the U2 snRNP. We find that SL3 and SL4 bind distinct spliceosomal proteins and combining a U1 snRNA activity assay with siRNA-mediated knockdown, we demonstrate that SL3 and SL4 act through the RNA helicase UAP56 and the U2 protein SF3A1, respectively. In vitro analysis using UV crosslinking and splicing assays indicated that SL3 likely promotes the SL4-SF3A1 interaction leading to enhancement of A complex formation and pre-mRNA splicing. Overall, these results highlight the vital role of the distinct contacts of SL3 and SL4 in bridging the pre-mRNA bound U1 and U2 snRNPs during the early steps of human spliceosome assembly.
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Affiliation(s)
- William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Bernice Fellows
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Paul Kang
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
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11
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Vilys L, Peciuliene I, Jakubauskiene E, Zinkeviciute R, Makino Y, Kanopka A. U2AF - Hypoxia-induced fas alternative splicing regulator. Exp Cell Res 2020; 399:112444. [PMID: 33347855 DOI: 10.1016/j.yexcr.2020.112444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023]
Abstract
The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia are involved in large-scale alterations in alternative pre-mRNA splicing. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. In the present study we show that U2AF is involved in hypoxia dependent anti-apoptotic Fas mRNA isoform formation. Our performed studies show that U2AF-RNA interaction is reduced in hypoxic cells, leading to reduction of Fas and increased sFas mRNAs formation. Efficient U2AF-RNA interactions of both subunits are important for Fas exon 6 inclusion into forming mRNA in normoxic and hypoxic cells.
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Affiliation(s)
- Laurynas Vilys
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Inga Peciuliene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ruta Zinkeviciute
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yuichi Makino
- Division of Metabolism and Biosystemic Science, Department of Medicine, Asahikawa Medical College, Asahikawa, Hokkaido, Japan
| | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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12
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Ontiveros RJ, Hernandez L, Nguyen H, Hernandez Lopez AL, Shankar A, Kim E, Keppetipola NM. Identification and Characterization of a Minimal Functional Splicing Regulatory Protein, PTBP1. Biochemistry 2020; 59:4766-4774. [PMID: 33284593 DOI: 10.1021/acs.biochem.0c00664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polypyrimidine tract binding protein 1 (PTBP1) is a well-studied RNA binding protein that serves as an important model for understanding molecular mechanisms underlying alternative splicing regulation. PTBP1 has four RNA binding domains (RBDs) connected via linker regions. Additionally, PTBP1 has an N-terminal unstructured region that contains nuclear import and export sequences. Each RBD can bind to pyrimidine rich elements with high affinity to mediate splicing activity. Studies support a variety of models for how PTBP1 can mediate splicing regulation on target exons. Obtaining a detailed atomic view hinges on determining a crystal structure of PTBP1 bound to a target RNA transcript. Here, we created a minimal functional PTBP1 with deletions in both linker 1 and linker 2 regions and assayed for activity on certain regulated exons, including the c-Src N1 exon. We show that for a subset of PTBP1-regulated exons the linker regions are not necessary for splicing repression activity. Gel mobility shift assays reveal the linker deletion mutant binds with 12-fold higher affinity to a target RNA sequence compared to wild-type PTBP1. A minimal PTBP1 that also contains an N-terminal region deletion binds to a target RNA with an affinity higher than that of wild-type PTBP1. Moreover, this minimal protein oligomerizes readily to form a distinct higher-order complex previously shown to be required for mediating splicing repression. This minimal functional PTBP1 protein can serve as a candidate for future structure studies to understand the mechanism of splicing repression for certain regulated exons.
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Affiliation(s)
- Robert J Ontiveros
- Department of Biological Sciences, California State University Fullerton, Fullerton, California 92831, United States
| | - Luis Hernandez
- Department of Biological Sciences, California State University Fullerton, Fullerton, California 92831, United States
| | - Haylena Nguyen
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California 92831, United States
| | - Adrian Lino Hernandez Lopez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90035, United States
| | - Archana Shankar
- Department of Biological Sciences, California State University Fullerton, Fullerton, California 92831, United States
| | - Enoch Kim
- Department of Biological Sciences, California State University Fullerton, Fullerton, California 92831, United States
| | - Niroshika M Keppetipola
- Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, California 92831, United States
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13
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Developmental Attenuation of Neuronal Apoptosis by Neural-Specific Splicing of Bak1 Microexon. Neuron 2020; 107:1180-1196.e8. [PMID: 32710818 DOI: 10.1016/j.neuron.2020.06.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/29/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022]
Abstract
Continuous neuronal survival is vital for mammals because mammalian brains have limited regeneration capability. After neurogenesis, suppression of apoptosis is needed to ensure a neuron's long-term survival. Here we describe a robust genetic program that intrinsically attenuates apoptosis competence in neurons. Developmental downregulation of the splicing regulator PTBP1 in immature neurons allows neural-specific splicing of the evolutionarily conserved Bak1 microexon 5. Exon 5 inclusion triggers nonsense-mediated mRNA decay (NMD) and unproductive translation of Bak1 transcripts (N-Bak mRNA), leading to suppression of pro-apoptotic BAK1 proteins and allowing neurons to reduce apoptosis. Germline heterozygous ablation of exon 5 increases BAK1 proteins exclusively in the brain, inflates neuronal apoptosis, and leads to early postnatal mortality. Therefore, neural-specific exon 5 splicing and depletion of BAK1 proteins uniquely repress neuronal apoptosis. Although apoptosis is important for development, attenuation of apoptosis competence through neural-specific splicing of the Bak1 microexon is essential for neuronal and animal survival.
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14
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Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr Opin Genet Dev 2020; 65:22-33. [PMID: 32535349 DOI: 10.1016/j.gde.2020.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of a network of highly conserved neuronal microexons has provided fundamental new insight into mechanisms underlying nervous system development and function, as well as an important basis for pathway convergence in autism spectrum disorder. In the past few years, considerable progress has been made in comprehensively determining the repertoires of factors that control neuronal microexons. These results have illuminated molecular mechanisms that activate the splicing of microexons, including those that control gene expression programs critical for neurogenesis, as well as synaptic protein translation and neuronal activity. Remarkably, individual disruption of specific microexons in these pathways results in autism-like phenotypes and cognitive impairment in mice. This review discusses these findings and their implications for delivering new therapeutic strategies for neurological disorders.
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15
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Yamazaki T, Liu L, Manley JL. TCF3 mutually exclusive alternative splicing is controlled by long-range cooperative actions between hnRNPH1 and PTBP1. RNA (NEW YORK, N.Y.) 2019; 25:1497-1508. [PMID: 31391218 PMCID: PMC6795145 DOI: 10.1261/rna.072298.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/31/2019] [Indexed: 05/22/2023]
Abstract
TCF3, also known as E2A, is a well-studied transcription factor that plays an important role in stem cell maintenance and hematopoietic development. The TCF3 gene encodes two related proteins, E12 and E47, which arise from mutually exclusive alternative splicing (MEAS). Since these two proteins have different DNA binding and dimerization domains, this AS event must be strictly regulated to ensure proper isoform ratios. Previously, we found that heterogeneous nuclear ribonucleoprotein (hnRNP) H1/F regulates TCF3 AS by binding to exonic splicing silencers (ESSs) in exon 18b. Here, we identify conserved intronic splicing silencers (ISSs) located between, and far from, the two mutually exclusive exons, and show that they are essential for MEAS. Further, we demonstrate that the hnRNP PTBP1 binds the ISS and is a regulator of TCF3 AS. We also demonstrate that hnRNP H1 and PTBP1 regulate TCF3 AS reciprocally, and that position-dependent interactions between these factors are essential for proper TCF3 MEAS. Our study provides a new model in which MEAS is regulated by cooperative actions of distinct hnRNPs bound to ISSs and ESSs.
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Affiliation(s)
- Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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16
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SRSF1 and PTBP1 Are trans-Acting Factors That Suppress the Formation of a CD33 Splicing Isoform Linked to Alzheimer's Disease Risk. Mol Cell Biol 2019; 39:MCB.00568-18. [PMID: 31208978 PMCID: PMC6712934 DOI: 10.1128/mcb.00568-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 06/08/2019] [Indexed: 12/19/2022] Open
Abstract
A single nucleotide polymorphism (SNP) in exon 2 of the CD33 gene is associated with reduced susceptibility to late-onset Alzheimer’s disease (AD) and causal for elevated mRNA lacking exon 2. In contrast to full-length CD33, transcripts lacking exon 2 result in CD33 protein unable to suppress activation responses in myeloid cells, including microglia. Currently, little is known about the regulation of CD33 exon 2 splicing. A single nucleotide polymorphism (SNP) in exon 2 of the CD33 gene is associated with reduced susceptibility to late-onset Alzheimer’s disease (AD) and causal for elevated mRNA lacking exon 2. In contrast to full-length CD33, transcripts lacking exon 2 result in CD33 protein unable to suppress activation responses in myeloid cells, including microglia. Currently, little is known about the regulation of CD33 exon 2 splicing. Using functional genomics and proteomic approaches, we found that SRSF1 and PTBP1 act as splicing enhancers to increase CD33 exon 2 inclusion in mRNA. Binding of PTBP1 to RNA sequences proximal to the intron 1-exon 2 splice junction is altered by the SNP and represents a potential mechanism behind the SNP-genotype dependent alternative splicing. Our studies also reveal that binding of SRSF1 to the CD33 RNA is not altered by the SNP genotype. Instead, a putative SRSF1 binding sequence at the 3′ end of exon 2 directs CD33 exon 2 inclusion into the mRNA, indicating that PTBP1 and SRSF1 promote full-length isoform expression through different mechanisms. Our findings shed light on molecular interactions that regulate CD33 exon 2 splicing, ultimately impacting receptor expression on the cell surface. These data aid in the understanding of CD33’s regulation of microglial signaling underpinning the AD genetic associations.
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17
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Kuehner JN, Bruggeman EC, Wen Z, Yao B. Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet 2019; 10:268. [PMID: 31019524 PMCID: PMC6458251 DOI: 10.3389/fgene.2019.00268] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
Precise genetic and epigenetic spatiotemporal regulation of gene expression is critical for proper brain development, function and circuitry formation in the mammalian central nervous system. Neuronal differentiation processes are tightly regulated by epigenetic mechanisms including DNA methylation, histone modifications, chromatin remodelers and non-coding RNAs. Dysregulation of any of these pathways is detrimental to normal neuronal development and functions, which can result in devastating neuropsychiatric disorders, such as depression, schizophrenia and autism spectrum disorders. In this review, we focus on the current understanding of epigenetic regulations in brain development and functions, as well as their implications in neuropsychiatric disorders.
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Affiliation(s)
- Janise N Kuehner
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Emily C Bruggeman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States.,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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18
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Zhang M, Ergin V, Lin L, Stork C, Chen L, Zheng S. Axonogenesis Is Coordinated by Neuron-Specific Alternative Splicing Programming and Splicing Regulator PTBP2. Neuron 2019; 101:690-706.e10. [PMID: 30733148 DOI: 10.1016/j.neuron.2019.01.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 11/08/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022]
Abstract
How a neuron acquires an axon is a fundamental question. Piecemeal identification of many axonogenesis-related genes has been done, but coordinated regulation is unknown. Through unbiased transcriptome profiling of immature primary cortical neurons during early axon formation, we discovered an association between axonogenesis and neuron-specific alternative splicing. Known axonogenesis genes exhibit little expression alternation but widespread splicing changes. Axonogenesis-associated splicing is governed by RNA binding protein PTBP2, which is enriched in neurons and peaks around axonogenesis in the brain. Cortical depletion of PTBP2 prematurely induces axonogenesis-associated splicing, causes imbalanced expression of axonogenesis-associated isoforms, and specifically affects axon formation in vitro and in vivo. PTBP2-controlled axonogenesis-associated Shtn1 splicing determines SHTN1's capacity to regulate actin interaction, polymerization, and axon growth. Precocious Shtn1 isoform switch contributes to disorganized axon formation of Ptbp2-/- neurons. We conclude that PTBP2-orchestrated alternative splicing programming is required for robust generation of a single axon in mammals.
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Affiliation(s)
- Min Zhang
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Volkan Ergin
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Lin Lin
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Cheryl Stork
- Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Liang Chen
- Department of Biological Sciences, Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
| | - Sika Zheng
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA; Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, Riverside, CA 92521, USA.
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19
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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20
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Vuokila N, Lukasiuk K, Bot AM, van Vliet EA, Aronica E, Pitkänen A, Puhakka N. miR-124-3p is a chronic regulator of gene expression after brain injury. Cell Mol Life Sci 2018; 75:4557-4581. [PMID: 30155647 PMCID: PMC11105702 DOI: 10.1007/s00018-018-2911-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023]
Abstract
Traumatic brain injury (TBI) initiates molecular and cellular pathologies that underlie post-injury morbidities, including hippocampus-related memory decline and epileptogenesis. Non-coding small RNAs are master regulators of gene expression with the potential to affect multiple molecular pathways. To evaluate whether hippocampal gene expression networks are chronically regulated by microRNAs after TBI, we sampled the dentate gyrus of rats with severe TBI induced by lateral fluid-percussion injury 3 months earlier. Ingenuity pathway analysis revealed 30 upregulated miR-124-3p targets, suggesting that miR-124-3p is downregulated post-TBI (z-score = - 5.146, p < 0.05). Droplet digital polymerase chain reaction (ddPCR) and in situ hybridization confirmed the chronic downregulation of miR-124-3p (p < 0.05). Quantitative PCR analysis of two targets, Plp2 and Stat3, indicated that their upregulation correlated with the miR-124-3p downregulation (r = - 0.647, p < 0.05; r = - 0.629, p < 0.05, respectively). Immunohistochemical staining of STAT3 confirmed the increased protein expression. STRING analysis showed that 9 of the 30 miR-124-3p targets belonged to a STAT3 network. Reactome analysis and data mining connected the targets especially to inflammation and signal transduction. L1000CDS2 software revealed drugs (e.g., importazole, trichostatin A, and IKK-16) that could reverse the observed molecular changes. The translational value of our data was emphasized by in situ hybridization showing chronic post-traumatic downregulation of miR-124-3p in the dentate gyrus of TBI patients. Analysis of another brain injury model, status epilepticus, highlighted the fact that chronic downregulation of miR-124 is a common phenomenon after brain injury. Together, our findings indicate that miR-124-3p is a chronic modulator of molecular networks relevant to post-injury hippocampal pathologies in experimental models and in humans.
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Affiliation(s)
- Niina Vuokila
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland
| | - Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Anna Maria Bot
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Erwin A van Vliet
- Department of (Neuro)pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Amsterdam, The Netherlands
| | - Asla Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland.
| | - Noora Puhakka
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland.
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21
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Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell 2018; 72:510-524.e12. [DOI: 10.1016/j.molcel.2018.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/27/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022]
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22
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Rawcliffe DFR, Österman L, Nordin A, Holmberg M. PTBP1 acts as a dominant repressor of the aberrant tissue-specific splicing of ISCU in hereditary myopathy with lactic acidosis. Mol Genet Genomic Med 2018; 6:887-897. [PMID: 30209894 PMCID: PMC6305642 DOI: 10.1002/mgg3.413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/23/2018] [Accepted: 04/17/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hereditary myopathy with lactic acidosis (HML) is an autosomal recessive disease caused by an intron mutation in the iron-sulfur cluster assembly (ISCU) gene. The mutation results in aberrant splicing, where part of the intron is retained in the final mRNA transcript, giving rise to a truncated nonfunctional ISCU protein. Using an ISCU mini-gene system, we have previously shown that PTBP1 can act as a repressor of the mis-splicing of ISCU, where overexpression of PTBP1 resulted in a decrease of the incorrect splicing. In this study, we wanted to, in more detail, analyze the role of PTBP1 in the regulation of endogenous ISCU mis-splicing. METHODS Overexpression and knockdown of PTBP1 was performed in myoblasts from two HML patients and a healthy control. Quantification of ISCU mis-splicing was done by qRTPCR. Biotinylated ISCU RNA, representing wildtype and mutant intron sequence, was used in a pull-down assay with nuclear extracts from myoblasts. Levels of PTBP1 in human cell lines and mice tissues were analyzed by qRTPCR and western blot. RESULTS PTBP1 overexpression in HML patient myoblasts resulted in a substantial decrease of ISCU mis-splicing while knockdown of PTBP1 resulted in a drastic increase. The effect could be observed in both patient and control myoblasts. We could also show that PTBP1 interacts with both the mutant and wild-type ISCU intron sequence, but with a higher affinity to the mutant sequence. Furthermore, low levels of PTBP1 among examined mouse tissues correlated with high levels of incorrect splicing of ISCU. CONCLUSION Our results show that PTBP1 acts as a dominant repressor of ISCU mis-splicing. We also show an inverse correlation between the levels of PTBP1 and ISCU mis-splicing, suggesting that the high level of mis-splicing in the skeletal muscle is primarily due to the low levels of PTBP1.
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Affiliation(s)
- Denise F. R. Rawcliffe
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
| | - Lennart Österman
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
| | - Angelica Nordin
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
| | - Monica Holmberg
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
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23
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Hu J, Qian H, Xue Y, Fu XD. PTB/nPTB: master regulators of neuronal fate in mammals. BIOPHYSICS REPORTS 2018; 4:204-214. [PMID: 30310857 PMCID: PMC6153489 DOI: 10.1007/s41048-018-0066-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 07/21/2018] [Indexed: 01/15/2023] Open
Abstract
PTB was initially discovered as a polypyrimidine tract-binding protein (hence the name), which corresponds to a specific RNA-binding protein associated with heterogeneous ribonucleoprotein particle (hnRNP I). The PTB family consists of three members in mammalian genomes, with PTBP1 (PTB) expressed in most cell types, PTBP2 (also known as nPTB or brPTB) exclusively found in the nervous system, and PTBP3 (also known as ROD1) predominately detected in immune cells. During neural development, PTB is down-regulated, which induces nPTB, and the expression of both PTB and nPTB becomes diminished when neurons mature. This programed switch, which largely takes place at the splicing level, is critical for the development of the nervous system, with PTB playing a central role in neuronal induction and nPTB guarding neuronal maturation. Remarkably, sequential knockdown of PTB and nPTB has been found to be necessary and sufficient to convert non-neuronal cells to the neuronal lineage. These findings, coupled with exquisite understanding of the molecular circuits regulated by these RNA-binding proteins, establish a critical foundation for their future applications in regenerative medicine.
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Affiliation(s)
- Jing Hu
- 1Department of Cellular and Molecular Medicine, University of California, La Jolla, San Diego, CA 92093-0651 USA
| | - Hao Qian
- 1Department of Cellular and Molecular Medicine, University of California, La Jolla, San Diego, CA 92093-0651 USA
| | - Yuanchao Xue
- 2Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiang-Dong Fu
- 1Department of Cellular and Molecular Medicine, University of California, La Jolla, San Diego, CA 92093-0651 USA.,2Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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24
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Dvinge H. Regulation of alternative
mRNA
splicing: old players and new perspectives. FEBS Lett 2018; 592:2987-3006. [DOI: 10.1002/1873-3468.13119] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Heidi Dvinge
- Department of Biomolecular Chemistry School of Medicine and Public Health University of Wisconsin‐Madison WI USA
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25
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hnRNP A1/A2 and Sam68 collaborate with SRSF10 to control the alternative splicing response to oxaliplatin-mediated DNA damage. Sci Rep 2018; 8:2206. [PMID: 29396485 PMCID: PMC5797138 DOI: 10.1038/s41598-018-20360-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 01/17/2018] [Indexed: 12/02/2022] Open
Abstract
Little is known about how RNA binding proteins cooperate to control splicing, and how stress pathways reconfigure these assemblies to alter splice site selection. We have shown previously that SRSF10 plays an important role in the Bcl-x splicing response to DNA damage elicited by oxaliplatin in 293 cells. Here, RNA affinity assays using a portion of the Bcl-x transcript required for this response led to the recovery of the SRSF10-interacting protein 14-3-3ε and the Sam68-interacting protein hnRNP A1. Although SRSF10, 14-3-3ε, hnRNP A1/A2 and Sam68 do not make major contributions to the regulation of Bcl-x splicing under normal growth conditions, upon DNA damage they become important to activate the 5′ splice site of pro-apoptotic Bcl-xS. Our results indicate that DNA damage reconfigures the binding and activity of several regulatory RNA binding proteins on the Bcl-x pre-mRNA. Moreover, SRSF10, hnRNP A1/A2 and Sam68 collaborate to drive the DNA damage-induced splicing response of several transcripts that produce components implicated in apoptosis, cell-cycle control and DNA repair. Our study reveals how the circuitry of splicing factors is rewired to produce partnerships that coordinate alternative splicing across processes crucial for cell fate.
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26
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Chen L, Weinmeister R, Kralovicova J, Eperon LP, Vorechovsky I, Hudson AJ, Eperon IC. Stoichiometries of U2AF35, U2AF65 and U2 snRNP reveal new early spliceosome assembly pathways. Nucleic Acids Res 2017; 45:2051-2067. [PMID: 27683217 PMCID: PMC5389562 DOI: 10.1093/nar/gkw860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/16/2016] [Indexed: 12/24/2022] Open
Abstract
The selection of 3΄ splice sites (3΄ss) is an essential early step in mammalian RNA splicing reactions, but the processes involved are unknown. We have used single molecule methods to test whether the major components implicated in selection, the proteins U2AF35 and U2AF65 and the U2 snRNP, are able to recognize alternative candidate sites or are restricted to one pre-specified site. In the presence of adenosine triphosphate (ATP), all three components bind in a 1:1 stoichiometry with a 3΄ss. Pre-mRNA molecules with two alternative 3΄ss can be bound concurrently by two molecules of U2AF or two U2 snRNPs, so none of the components are restricted. However, concurrent occupancy inhibits splicing. Stoichiometric binding requires conditions consistent with coalescence of the 5΄ and 3΄ sites in a complex (I, initial), but if this cannot form the components show unrestricted and stochastic association. In the absence of ATP, when complex E forms, U2 snRNP association is unrestricted. However, if protein dephosphorylation is prevented, an I-like complex forms with stoichiometric association of U2 snRNPs and the U2 snRNA is base-paired to the pre-mRNA. Complex I differs from complex A in that the formation of complex A is associated with the loss of U2AF65 and 35.
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Affiliation(s)
- Li Chen
- University of Leicester, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, Leicester LE1 9HN, UK
| | - Robert Weinmeister
- University of Leicester, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, Leicester LE1 9HN, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Lucy P Eperon
- University of Leicester, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, Leicester LE1 9HN, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Andrew J Hudson
- University of Leicester, Leicester Institute for Structural and Chemical Biology and Department of Chemistry, Leicester LE1 7RH, UK
| | - Ian C Eperon
- University of Leicester, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, Leicester LE1 9HN, UK
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27
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Ying Y, Wang XJ, Vuong CK, Lin CH, Damianov A, Black DL. Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. Cell 2017; 170:312-323.e10. [PMID: 28708999 DOI: 10.1016/j.cell.2017.06.022] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/31/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022]
Abstract
Proteins of the Rbfox family act with a complex of proteins called the Large Assembly of Splicing Regulators (LASR). We find that Rbfox interacts with LASR via its C-terminal domain (CTD), and this domain is essential for its splicing activity. In addition to LASR recruitment, a low-complexity (LC) sequence within the CTD contains repeated tyrosines that mediate higher-order assembly of Rbfox/LASR and are required for splicing activation by Rbfox. This sequence spontaneously aggregates in solution to form fibrous structures and hydrogels, suggesting an assembly similar to the insoluble cellular inclusions formed by FUS and other proteins in neurologic disease. Unlike the pathological aggregates, we find that assembly of the Rbfox CTD plays an essential role in its normal splicing function. Rather than simple recruitment of individual regulators to a target exon, alternative splicing choices also depend on the higher-order assembly of these regulators within the nucleus.
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Affiliation(s)
- Yi Ying
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiao-Jun Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Celine K Vuong
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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28
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Hannigan MM, Zagore LL, Licatalosi DD. Ptbp2 Controls an Alternative Splicing Network Required for Cell Communication during Spermatogenesis. Cell Rep 2017; 19:2598-2612. [PMID: 28636946 PMCID: PMC5543815 DOI: 10.1016/j.celrep.2017.05.089] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 01/12/2023] Open
Abstract
Alternative splicing has essential roles in development. Remarkably, spermatogenic cells express more alternatively spliced RNAs compared to most whole tissues; however, regulation of these RNAs remains unclear. Here, we characterize the alternative splicing landscape during spermatogenesis and reveal an essential function for the RNA-binding protein Ptbp2 in this highly regulated developmental program. We found that Ptbp2 controls a network of genes involved in cell adhesion, migration, and polarity, suggesting that splicing regulation by Ptbp2 is critical for germ cell communication with Sertoli cells (multifunctional somatic cells necessary for spermatogenesis). Indeed, Ptbp2 ablation in germ cells resulted in disorganization of the filamentous actin (F-actin) cytoskeleton in Sertoli cells, indicating that alternative splicing regulation is necessary for cellular crosstalk during germ cell development. Collectively, the data delineate an alternative splicing regulatory network essential for spermatogenesis, the splicing factor that controls it, and its biological importance in germ-Sertoli communication.
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Affiliation(s)
- Molly M Hannigan
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Donny D Licatalosi
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.
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29
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Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. eLife 2016; 5. [PMID: 27882870 PMCID: PMC5122456 DOI: 10.7554/elife.19743] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022] Open
Abstract
Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest. DOI:http://dx.doi.org/10.7554/eLife.19743.001
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, Phoenix, United States
| | - Darryl Chui
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
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30
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Keppetipola NM, Yeom KH, Hernandez AL, Bui T, Sharma S, Black DL. Multiple determinants of splicing repression activity in the polypyrimidine tract binding proteins, PTBP1 and PTBP2. RNA (NEW YORK, N.Y.) 2016; 22:1172-1180. [PMID: 27288314 PMCID: PMC4931110 DOI: 10.1261/rna.057505.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 05/16/2016] [Indexed: 06/06/2023]
Abstract
Most human genes generate multiple protein isoforms through alternative pre-mRNA splicing, but the mechanisms controlling alternative splicing choices by RNA binding proteins are not well understood. These proteins can have multiple paralogs expressed in different cell types and exhibiting different splicing activities on target exons. We examined the paralogous polypyrimidine tract binding proteins PTBP1 and PTBP2 to understand how PTBP1 can exhibit greater splicing repression activity on certain exons. Using both an in vivo coexpression assay and an in vitro splicing assay, we show that PTBP1 is more repressive than PTBP2 per unit protein on a target exon. Constructing chimeras of PTBP1 and 2 to determine amino acid features that contribute to their differential activity, we find that multiple segments of PTBP1 increase the repressive activity of PTBP2. Notably, when either RRM1 of PTBP2 or the linker peptide separating RRM2 and RRM3 are replaced with the equivalent PTBP1 sequences, the resulting chimeras are highly active for splicing repression. These segments are distinct from the known region of interaction for the PTBP1 cofactors Raver1 and Matrin3 in RRM2. We find that RRM2 of PTBP1 also increases the repression activity of an otherwise PTBP2 sequence, and that this is potentially explained by stronger binding by Raver1. These results indicate that multiple features over the length of the two proteins affect their ability to repress an exon.
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Affiliation(s)
- Niroshika M Keppetipola
- California State University Fullerton, Department of Chemistry and Biochemistry, Fullerton, California 92831, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Adrian L Hernandez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Tessa Bui
- California State University Fullerton, Department of Chemistry and Biochemistry, Fullerton, California 92831, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
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31
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Geuens T, Bouhy D, Timmerman V. The hnRNP family: insights into their role in health and disease. Hum Genet 2016; 135:851-67. [PMID: 27215579 PMCID: PMC4947485 DOI: 10.1007/s00439-016-1683-5] [Citation(s) in RCA: 721] [Impact Index Per Article: 80.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that contribute to multiple aspects of nucleic acid metabolism including alternative splicing, mRNA stabilization, and transcriptional and translational regulation. Many hnRNPs share general features, but differ in domain composition and functional properties. This review will discuss the current knowledge about the different hnRNP family members, focusing on their structural and functional divergence. Additionally, we will highlight their involvement in neurodegenerative diseases and cancer, and the potential to develop RNA-based therapies.
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Affiliation(s)
- Thomas Geuens
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Delphine Bouhy
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium.
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32
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Tang SJ, Luo S, Ho JXJ, Ly PT, Goh E, Roca X. Characterization of the Regulation of CD46 RNA Alternative Splicing. J Biol Chem 2016; 291:14311-14323. [PMID: 27226545 DOI: 10.1074/jbc.m115.710350] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Indexed: 11/06/2022] Open
Abstract
Here we present a detailed analysis of the alternative splicing regulation of human CD46, which generates different isoforms with distinct functions. CD46 is a ubiquitous membrane protein that protects host cells from complement and plays other roles in immunity, autophagy, and cell adhesion. CD46 deficiency causes an autoimmune disorder, and this protein is also involved in pathogen infection and cancer. Before this study, the mechanisms of CD46 alternative splicing remained unexplored even though dysregulation of this process has been associated with autoimmune diseases. We proved that the 5' splice sites of CD46 cassette exons 7 and 8 encoding extracellular domains are defined by noncanonical mechanisms of base pairing to U1 small nuclear RNA. Next we characterized the regulation of CD46 cassette exon 13, whose inclusion or skipping generates different cytoplasmic tails with distinct functions. Using splicing minigenes, we identified multiple exonic and intronic splicing enhancers and silencers that regulate exon 13 inclusion via trans-acting splicing factors like PTBP1 and TIAL1. Interestingly, a common splicing activator such as SRSF1 appears to repress CD46 exon 13 inclusion. We also report that expression of CD46 mRNA isoforms is further regulated by non-sense-mediated mRNA decay and transcription speed. Finally, we successfully manipulated CD46 exon 13 inclusion using antisense oligonucleotides, opening up opportunities for functional studies of the isoforms as well as for therapeutics for autoimmune diseases. This study provides insight into CD46 alternative splicing regulation with implications for its function in the immune system and for genetic disease.
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Affiliation(s)
- Sze Jing Tang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shufang Luo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jia Xin Jessie Ho
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Eling Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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33
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Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins. Gene 2016; 587:107-19. [PMID: 27154819 DOI: 10.1016/j.gene.2016.04.057] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 04/30/2016] [Indexed: 01/04/2023]
Abstract
Alternative pre-mRNA splicing provides a source of vast protein diversity by removing non-coding sequences (introns) and accurately linking different exonic regions in the correct reading frame. The regulation of alternative splicing is essential for various cellular functions in both pathological and physiological conditions. In eukaryotic cells, this process is commonly used to increase proteomic diversity and to control gene expression either co- or post-transcriptionally. Alternative splicing occurs within a megadalton-sized, multi-component machine consisting of RNA and proteins; during the splicing process, this complex undergoes dynamic changes via RNA-RNA, protein-protein and RNA-protein interactions. Co-transcriptional splicing functionally integrates the transcriptional machinery, thereby enabling the two processes to influence one another, whereas post-transcriptional splicing facilitates the coupling of RNA splicing with post-splicing events. This review addresses the structural aspects of spliceosomes and the mechanistic implications of their stepwise assembly on the regulation of pre-mRNA splicing. Moreover, the role of phosphorylation-based, signal-induced changes in the regulation of the splicing process is demonstrated.
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34
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Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol 2016; 72:497-511. [PMID: 27050129 PMCID: PMC4822562 DOI: 10.1107/s2059798316001248] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.
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Affiliation(s)
- Galina A. Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Eigen Peralta
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Carol L. Farr
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott A. Lesley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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35
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Abstract
The U2AF heterodimer is generally accepted to play a vital role in defining functional 3' splice sites in pre-mRNA splicing. Given prevalent mutations in U2AF, particularly in the U2AF1 gene (which encodes for the U2AF35 subunit) in blood disorders and other human cancers, there are renewed interests in these classic splicing factors to further understand their regulatory functions in RNA metabolism in both physiological and disease settings. We recently reported that U2AF has a maximal capacity to directly bind ˜88% of functional 3' splice sites in the human genome and that numerous U2AF binding events also occur in various exonic and intronic locations, thus providing additional mechanisms for the regulation of alternative splicing besides their traditional role in titrating weak splice sites in the cell. These findings, coupled with the existence of multiple related proteins to both U2AF65 and U2AF35, beg a series of questions on the universal role of U2AF in functional 3' splice site definition, their binding specificities in vivo, potential mechanisms to bypass their requirement for certain intron removal events, contribution of splicing-independent functions of U2AF to important cellular functions, and the mechanism for U2AF mutations to invoke specific diseases in humans.
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Affiliation(s)
- Tongbin Wu
- a Department of Medicine ; University of California, San Diego ; La Jolla , CA USA
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36
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Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. eLife 2015; 4:e09268. [PMID: 26705333 PMCID: PMC4755740 DOI: 10.7554/elife.09268] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022] Open
Abstract
The RNA-binding proteins PTBP1 and PTBP2 control programs of alternative splicing during neuronal development. PTBP2 was found to maintain embryonic splicing patterns of many synaptic and cytoskeletal proteins during differentiation of neuronal progenitor cells (NPCs) into early neurons. However, the role of the earlier PTBP1 program in embryonic stem cells (ESCs) and NPCs was not clear. We show that PTBP1 controls a program of neuronal gene expression that includes the transcription factor Pbx1. We identify exons specifically regulated by PTBP1 and not PTBP2 as mouse ESCs differentiate into NPCs. We find that PTBP1 represses Pbx1 exon 7 and the expression of the neuronal Pbx1a isoform in ESCs. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of neuronal genes. Thus, PTBP1 controls the activity of Pbx1 to suppress its neuronal transcriptional program prior to induction of NPC development. DOI:http://dx.doi.org/10.7554/eLife.09268.001 The neurons that transmit information around the nervous system develop in several stages. Embryonic stem cells specialize to form neuronal progenitor cells, which then develop into neurons. These cell types have different characteristics, in part because they make different proteins or different versions of the same proteins. To make a protein, the DNA sequence of a gene is used to build a molecule of ribonucleic acid (RNA) that acts as a template for the protein. However, not all of this sequence codes for the protein. The non-coding regions must be removed from the RNA, and the remaining “exons” joined together to form the final “mRNA” template. Not all of the exons are necessarily included in the final mRNA molecule. By joining together different combinations of exons, several different versions of a protein can be produced from a single gene. This process is known as alternative splicing. One way that alternative splicing is controlled is through proteins that bind to RNA and determine which exons are included or excluded from the final mRNA molecule. PTBP1 is an RNA-binding protein that controls alternative splicing in embryonic stem cells and neuronal progenitor cells. Embryonic stem cells have the ability to develop into all the cells of the body. In contrast, neuronal progenitor cells are restricted in their development and only give rise to specialized cells of the nervous system. The role of PTBP1 in these properties was not clear. Linares et al. have now used a range of techniques to study the RNA molecules produced in these two cell types and how these RNAs change when PTBP1 is removed. This identified many RNAs whose splicing is regulated by PTBP1, including mRNAs of the gene that produces a protein called Pbx1, which is an important regulator of neuronal development. Further investigation revealed that PTBP1 prevents a particular exon being included in the mRNA template for Pbx1. This creates an embryonic stem cell form of Pbx1 that does not affect neuronal genes. Removal of PTBP1 allows splicing of the Pbx1 exon and produces a version of Pbx1 that is found in neuronal progenitor cells and which turns on neuronal genes. Thus, through its action on Pbx1, one role of PTBP1 is to enable stem cells to maintain their non-neuronal properties and prevent their premature development into neuronal progenitor cells. The gene for Pbx1 is only one of many genes controlled by PTBP1 at the level of splicing. One challenge for the future will be to understand how these genes work together in a common program that determines the properties of stem cells. Another question regards how the different Pbx1 proteins in stem cells and in neuronal progenitors can exert different effects in the cells where they are made. DOI:http://dx.doi.org/10.7554/eLife.09268.002
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Affiliation(s)
- Anthony J Linares
- Molecular Biology Institute Graduate Program, University of California, Los Angeles, Los Angeles, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Andrey Damianov
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Katrina L Adams
- Molecular Biology Institute Graduate Program, University of California, Los Angeles, Los Angeles, United States.,Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Bennett G Novitch
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
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37
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Sohail M, Xie J. Diverse regulation of 3' splice site usage. Cell Mol Life Sci 2015; 72:4771-93. [PMID: 26370726 PMCID: PMC11113787 DOI: 10.1007/s00018-015-2037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/12/2015] [Accepted: 09/03/2015] [Indexed: 01/13/2023]
Abstract
The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.
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Affiliation(s)
- Muhammad Sohail
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
- Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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Boesler C, Rigo N, Agafonov DE, Kastner B, Urlaub H, Will CL, Lührmann R. Stable tri-snRNP integration is accompanied by a major structural rearrangement of the spliceosome that is dependent on Prp8 interaction with the 5' splice site. RNA (NEW YORK, N.Y.) 2015; 21:1993-2005. [PMID: 26385511 PMCID: PMC4604437 DOI: 10.1261/rna.053991.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/21/2015] [Indexed: 05/22/2023]
Abstract
Exon definition is the predominant initial spliceosome assembly pathway in higher eukaryotes, but it remains much less well-characterized compared to the intron-defined assembly pathway. Addition in trans of an excess of 5'ss containing RNA to a splicing reaction converts a 37S exon-defined complex, formed on a single exon RNA substrate, into a 45S B-like spliceosomal complex with stably integrated U4/U6.U5 tri-snRNP. This 45S complex is compositonally and structurally highly similar to an intron-defined spliceosomal B complex. Stable tri-snRNP integration during B-like complex formation is accompanied by a major structural change as visualized by electron microscopy. The changes in structure and stability during transition from a 37S to 45S complex can be induced in affinity-purified cross-exon complexes by adding solely the 5'ss RNA oligonucleotide. This conformational change does not require the B-specific proteins, which are recruited during this stabilization process, or site-specific phosphorylation of hPrp31. Instead it is triggered by the interaction of U4/U6.U5 tri-snRNP components with the 5'ss sequence, most importantly between Prp8 and nucleotides at the exon-intron junction. These studies provide novel insights into the conversion of a cross-exon to cross-intron organized spliceosome and also shed light on the requirements for stable tri-snRNP integration during B complex formation.
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Affiliation(s)
- Carsten Boesler
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Norbert Rigo
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Dmitry E Agafonov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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39
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Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB. Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Res 2015; 25:858-71. [PMID: 25883322 PMCID: PMC4448682 DOI: 10.1101/gr.184390.114] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 04/02/2015] [Indexed: 01/01/2023]
Abstract
RNA binding proteins of the conserved CUGBP1, Elav-like factor (CELF) family contribute to heart and skeletal muscle development and are implicated in myotonic dystrophy (DM). To understand their genome-wide functions, we analyzed the transcriptome dynamics following induction of CELF1 or CELF2 in adult mouse heart and of CELF1 in muscle by RNA-seq, complemented by crosslinking/immunoprecipitation-sequencing (CLIP-seq) analysis of mouse cells and tissues to distinguish direct from indirect regulatory targets. We identified hundreds of mRNAs bound in their 3′ UTRs by both CELF1 and the developmentally induced MBNL1 protein, a threefold greater overlap in target messages than expected, including messages involved in development and cell differentiation. The extent of 3′ UTR binding by CELF1 and MBNL1 predicted the degree of mRNA repression or stabilization, respectively, following CELF1 induction. However, CELF1's RNA binding specificity in vitro was not detectably altered by coincubation with recombinant MBNL1. These findings support a model in which CELF and MBNL proteins bind independently to mRNAs but functionally compete to specify down-regulation or localization/stabilization, respectively, of hundreds of mRNA targets. Expression of many alternative 3′ UTR isoforms was altered following CELF1 induction, with 3′ UTR binding associated with down-regulation of isoforms and genes. The splicing of hundreds of alternative exons was oppositely regulated by these proteins, confirming an additional layer of regulatory antagonism previously observed in a handful of cases. The regulatory relationships between CELFs and MBNLs in control of both mRNA abundance and splicing appear to have evolved to enhance developmental transitions in major classes of heart and muscle genes.
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Affiliation(s)
- Eric T Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Amanda J Ward
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer M Cherone
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jimena Giudice
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas T Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Daniel J Treacy
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Nicole J Lambert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Peter Freese
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tanvi Saxena
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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40
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Evolutionary emergence of a novel splice variant with an opposite effect on the cell cycle. Mol Cell Biol 2015; 35:2203-14. [PMID: 25870105 DOI: 10.1128/mcb.00190-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/06/2015] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing contributes greatly to the diversification of mammalian proteomes, but the molecular basis for the evolutionary emergence of splice variants remains poorly understood. We have recently found a novel class of splicing regulatory elements between the polypyrimidine tract (Py) and 3' AG (REPA) at intron ends in many human genes, including the multifunctional PRMT5 (for protein arginine methyltransferase 5) gene. The PRMT5 element is comprised of two G tracts that arise in most mammals and accompany significant exon skipping in human transcripts. The G tracts inhibit splicing by recruiting heterogeneous nuclear ribonucleoprotein (hnRNP) H and F (H/F) to reduce U2AF65 binding to the Py, causing exon skipping. The resulting novel shorter variant PRMT5S exhibits a histone H4R3 methylation effect similar to that seen with the original longer PRMT5L isoform but exhibits a distinct localization and preferential control of critical genes for cell cycle arrest at interphase in comparison to PRMT5L. This report thus provides a molecular mechanism for the evolutionary emergence of a novel splice variant with an opposite function in a fundamental cell process. The presence of REPA elements in a large group of genes implies their wider impact on different cellular processes for increased protein diversity in humans.
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41
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Sharma S, Wongpalee SP, Vashisht A, Wohlschlegel JA, Black DL. Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Genes Dev 2015; 28:2518-31. [PMID: 25403181 PMCID: PMC4233244 DOI: 10.1101/gad.248625.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Sharma et al. report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice, and a component of the U2 snRNP complex, which assembles across the intron at the 3′ splice site. U1-SL4 interacts with the SF3A1 protein of the U2 snRNP, and this interaction occurs within prespliceosomal complexes assembled on the pre-mRNA. The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Interactions that bring the two splice sites together during spliceosome assembly must occur with a high degree of specificity and fidelity to allow expression of functional mRNAs and make particular alternative splicing choices. Here, we report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice site, and a component of the U2 small nuclear ribonucleoprotein particle (snRNP) complex, which assembles across the intron at the 3′ splice site. Using a U1 snRNP complementation assay, we found that SL4 is essential for splicing in vivo. The addition of free U1-SL4 to a splicing reaction in vitro inhibits splicing and blocks complex assembly prior to formation of the prespliceosomal A complex, indicating a requirement for a SL4 contact in spliceosome assembly. To characterize the interactions of this RNA structure, we used a combination of stable isotope labeling by amino acids in cell culture (SILAC), biotin/Neutravidin affinity pull-down, and mass spectrometry. We show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP. We found that this interaction between the U1 snRNA and SF3A1 occurs within prespliceosomal complexes assembled on the pre-mRNA. Thus, SL4 of the U1 snRNA is important for splicing, and its interaction with SF3A1 mediates contact between the 5′ and 3′ splice site complexes within the assembling spliceosome.
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Affiliation(s)
- Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA; Department of Microbiology, Immunology, and Molecular Genetics
| | | | | | | | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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42
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Kuroda Y, Saito T, Nagai JI, Ida K, Naruto T, Masuno M, Kurosawa K. Microdeletion of 19p13.3 in a girl with Peutz-Jeghers syndrome, intellectual disability, hypotonia, and distinctive features. Am J Med Genet A 2014; 167A:389-93. [PMID: 25487640 DOI: 10.1002/ajmg.a.36813] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/16/2014] [Indexed: 02/06/2023]
Abstract
Peutz-Jeghers syndrome (PJS) is a rare autosomal dominant disease characterized by gastrointestinal polyposis and mucocutaneous pigmentation. Germline point mutations in the serine/threonine kinase 11 (STK11) have been identified in about 70% of patients with PJS. Only a few large genomic deletions have been identified. We report on a girl with PJS and multiple congenital anomalies. She had intellectual disability, umbilical hernia, bilateral inguinal hernias, scoliosis, and distinct facial appearance including prominent mandible, smooth philtrum, and malformed ears. She developed lip pigmentation at the age of 12 years but had no gastrointestinal polyps. Array comparative genomic hybridization revealed an approximately 610 kb deletion at 19p13.3, encompassing STK11. Together with previous reports, the identification of common clinical features suggests that microdeletion at 19p13.3 encompassing STK11 constitutes a distinctive phenotype.
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Affiliation(s)
- Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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43
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Simpson CG, Lewandowska D, Liney M, Davidson D, Chapman S, Fuller J, McNicol J, Shaw P, Brown JWS. Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially. THE NEW PHYTOLOGIST 2014; 203:424-436. [PMID: 24749484 DOI: 10.1111/nph.12821] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/14/2013] [Indexed: 06/03/2023]
Abstract
This paper examines the function of Arabidopsis thaliana AtPTB1 and AtPTB2 as plant splicing factors. The effect on splicing of overexpression of AtPTB1 and AtPTB2 was analysed in an in vivo protoplast transient expression system with a novel mini-exon splicing reporter. A range of mutations in pyrimidine-rich sequences were compared with and without AtPTB and NpU2AF65 overexpression. Splicing analyses of constructs in protoplasts and RNA from overexpression lines used high-resolution reverse transcription polymerase chain reaction (RT-PCR). AtPTB1 and AtPTB2 reduced inclusion/splicing of the potato invertase mini-exon splicing reporter, indicating that these proteins can repress plant intron splicing. Mutation of the polypyrimidine tract and closely associated Cytosine and Uracil-rich (CU-rich) sequences, upstream of the mini-exon, altered repression by AtPTB1 and AtPTB2. Coexpression of a plant orthologue of U2AF65 alleviated the splicing repression of AtPTB1. Mutation of a second CU-rich upstream of the mini-exon 3' splice site led to a decline in mini-exon splicing, indicating the presence of a splicing enhancer sequence. Finally, RT-PCR of AtPTB overexpression lines with c. 90 known alternative splicing (AS) events showed that AtPTBs significantly altered AS of over half the events. AtPTB1 and AtPTB2 are splicing factors that influence alternative splicing. This occurs in the potato invertase mini-exon via the polypyrimidine tract and associated pyrimidine-rich sequence.
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Affiliation(s)
- Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Michele Liney
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Sean Chapman
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John Fuller
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jim McNicol
- Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD2 5DA, UK
| | - Paul Shaw
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
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44
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Zheng X, Cho S, Moon H, Loh TJ, Oh HK, Green MR, Shen H. Polypyrimidine tract binding protein inhibits IgM pre-mRNA splicing by diverting U2 snRNA base-pairing away from the branch point. RNA (NEW YORK, N.Y.) 2014; 20:440-446. [PMID: 24572809 PMCID: PMC3964906 DOI: 10.1261/rna.043737.113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/27/2014] [Indexed: 06/03/2023]
Abstract
The mouse immunoglobulin (IgM) pre-mRNA contains a splicing inhibitor that bears multiple binding sites for the splicing repressor polypyrimidine tract binding protein (PTB). Here we show that the inhibitor directs assembly of an ATP-dependent complex that contains PTB and U1 and U2 small nuclear RNAs (snRNAs). Unexpectedly, although U2 snRNA is present in the inhibitor complex, it is not base-paired to the branch point. We present evidence that inhibitor-bound PTB contacts U2 snRNA to promote base-pairing to an adjacent branch point-like sequence within the inhibitor, thereby preventing the U2 snRNA-branch point interaction and resulting in splicing repression. Our studies reveal a novel mechanism by which PTB represses splicing.
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Affiliation(s)
- Xuexiu Zheng
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Sunghee Cho
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Heegyum Moon
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Tiing Jen Loh
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Huyn Kyung Oh
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Michael R. Green
- Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Haihong Shen
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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45
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Joshi A, Esteve V, Buckroyd AN, Blatter M, Allain FHT, Curry S. Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB). PeerJ 2014; 2:e305. [PMID: 24688880 PMCID: PMC3961105 DOI: 10.7717/peerj.305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/14/2014] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic polypyrimidine tract binding protein (PTB) serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB) is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs). We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34) which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34). The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposite sides that face away from each other. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.
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Affiliation(s)
- Amar Joshi
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Vicent Esteve
- Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland
| | - Adrian N Buckroyd
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Markus Blatter
- Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland
| | | | - Stephen Curry
- Department of Life Sciences, Imperial College, London, United Kingdom
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46
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Li Q, Zheng S, Han A, Lin CH, Stoilov P, Fu XD, Black DL. The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. eLife 2014; 3:e01201. [PMID: 24448406 PMCID: PMC3896118 DOI: 10.7554/elife.01201] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 12/05/2013] [Indexed: 01/10/2023] Open
Abstract
We show that the splicing regulator PTBP2 controls a genetic program essential for neuronal maturation. Depletion of PTBP2 in developing mouse cortex leads to degeneration of these tissues over the first three postnatal weeks, a time when the normal cortex expands and develops mature circuits. Cultured Ptbp2(-/-) neurons exhibit the same initial viability as wild type, with proper neurite outgrowth and marker expression. However, these mutant cells subsequently fail to mature and die after a week in culture. Transcriptome-wide analyses identify many exons that share a pattern of mis-regulation in the mutant brains, where isoforms normally found in adults are precociously expressed in the developing embryo. These transcripts encode proteins affecting neurite growth, pre- and post-synaptic assembly, and synaptic transmission. Our results define a new genetic regulatory program, where PTBP2 acts to temporarily repress expression of adult protein isoforms until the final maturation of the neuron. DOI: http://dx.doi.org/10.7554/eLife.01201.001.
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Affiliation(s)
- Qin Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Sika Zheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Areum Han
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Science, University of California, Los Angeles, Los Angeles, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, United States
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
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47
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Abstract
Alternative splicing plays a prevalent role in generating functionally diversified proteomes from genomes with a more limited repertoire of protein-coding genes. Alternative splicing is frequently regulated with cell type or developmental specificity and in response to signaling pathways, and its mis-regulation can lead to disease. Co-regulated programs of alternative splicing involve interplay between a host of cis-acting transcript features and trans-acting RNA-binding proteins. Here, we review the current state of understanding of the logic and mechanism of regulated alternative splicing and indicate how this understanding can be exploited to manipulate splicing for therapeutic purposes.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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48
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Abstract
Isolating spliceosomes at a specific assembly stage requires a means to stall or enrich for one of the intermediate splicing complexes. We describe strategies to arrest spliceosomes at different points of complex formation and provide a detailed protocol developed for isolating intact splicing complexes arrested between the first and second chemical steps of splicing. Briefly, spliceosomes are assembled on a radiolabeled in vitro-transcribed splicing substrate from components present in nuclear extract of HeLa cells. Spliceosome progression is arrested after the first step of splicing chemistry by mutating the pre-mRNA substrate at the 3' splice site. The substrate also contains binding sites for the MS2 protein, which serve as an affinity tag. Purification of arrested spliceosomes is carried out in two steps: (1) size exclusion chromatography and (2) affinity selection via a fusion of MS2 and maltose-binding protein (MBP). Complex assembly and purification are analyzed by denaturing polyacrylamide gel electrophoresis.
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Affiliation(s)
- Janine O Ilagan
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
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49
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Zaghlool A, Ameur A, Cavelier L, Feuk L. Splicing in the human brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:95-125. [PMID: 25172473 DOI: 10.1016/b978-0-12-801105-8.00005-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It has become increasingly clear over the past decade that RNA has important functions in human cells beyond its role as an intermediate translator of DNA to protein. It is now known that RNA plays highly specific roles in pathways involved in regulatory, structural, and catalytic functions. The complexity of RNA production and regulation has become evident with the advent of high-throughput methods to study the transcriptome. Deep sequencing has revealed an enormous diversity of RNA types and transcript isoforms in human cells. The transcriptome of the human brain is particularly interesting as it contains more expressed genes than other tissues and also displays an extreme diversity of transcript isoforms, indicating that highly complex regulatory pathways are present in the brain. Several of these regulatory proteins are now identified, including RNA-binding proteins that are neuron specific. RNA-binding proteins also play important roles in regulating the splicing process and the temporal and spatial isoform production. While significant progress has been made in understanding the human transcriptome, many questions still remain regarding the basic mechanisms of splicing and subcellular localization of RNA. A long-standing question is to what extent the splicing of pre-mRNA is cotranscriptional and posttranscriptional, respectively. Recent data, including studies of the human brain, indicate that splicing is primarily cotranscriptional in human cells. This chapter describes the current understanding of splicing and splicing regulation in the human brain and discusses the recent global sequence-based analyses of transcription and splicing.
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Affiliation(s)
- Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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50
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Echeverria GV, Cooper TA. Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron. Nucleic Acids Res 2013; 42:1893-903. [PMID: 24185704 PMCID: PMC3919616 DOI: 10.1093/nar/gkt1020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alternative splicing regulates developmentally and tissue-specific gene expression programs, disruption of which have been implicated in numerous diseases. Muscleblind-like 1 (MBNL1) regulates splicing transitions, which are disrupted on loss of MBNL1 function in myotonic dystrophy type 1 (DM1). One such event is MBNL1-mediated activation of insulin receptor exon 11 inclusion, which requires an intronic enhancer element downstream of exon 11. The mechanism of MBNL1-mediated activation of exon inclusion is unknown. We developed an in vitro splicing assay, which robustly recapitulates MBNL1-mediated splicing activation of insulin receptor exon 11 and found that MBNL1 activates removal of the intron upstream of exon 11 upon binding its functional response element in the downstream intron. MBNL1 enhances early spliceosome assembly as evidenced by enhanced complex A formation and binding of U2 small nuclear ribonucleoprotein auxiliary factor 65 kDa subunit (U2AF65) on the upstream intron. We demonstrated that neither the 5′ splice site nor exon 11 sequences are required for MBNL1-activated U2AF65 binding. Interestingly, the 5′ splice site is required for MBNL1-mediated activation of upstream intron removal, although MBNL1 has no effect on U1 snRNA recruitment. These results suggest that MBNL1 directly activates binding of U2AF65 to enhance upstream intron removal to ultimately activate alternative exon inclusion.
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Affiliation(s)
- Gloria V Echeverria
- Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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