1
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Zhang Z, Huang R, Lai Y. Expression signature of ten small nuclear RNAs serves as novel biomarker for prognosis prediction of acute myeloid leukemia. Sci Rep 2023; 13:18489. [PMID: 37898705 PMCID: PMC10613265 DOI: 10.1038/s41598-023-45626-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023] Open
Abstract
This study aimed to screen for small nuclear RNAs (snRNAs) associated with the prognosis of acute myeloid leukemia (AML) by using The Cancer Genome Atlas (TCGA) whole-transcriptome sequencing dataset. A total of 130 AML patients from TCGA cohort with complete prognostic information and transcriptome data were enrolled in the current study. Comprehensive survival and functional enrichment analyses were performed to explore the prognostic value and potential biological functions of prognostic snRNAs in AML patients. In the current study, we screened 72 snRNAs that were notably associated with the clinical outcome of AML and developed an expression signature consist of ten snRNAs, that can be accurately applied to assess the overall survival of AML patients. Functional mechanism analysis revealed that this expression signature may be strongly linked to some classical tumor-associated pathways, such as Notch and Wnt pathways, as well as being closely related to B and T cell receptor pathways. Furthermore, we screened six compounds (chicago sky blue 6 B, 5230742, clorsulon, nefopam, nicardipine, and streptomycin) that may serve as targeted therapeutic drugs for AML using connectivity maps. Tumor immunoassays indicated significant differences in the immune microenvironment of the bone marrow tissue between high-risk and low-risk AML patients. Immune infiltration analysis also revealed significant differences in the abundance of multiple immune cells in the bone marrow of the two groups of AML patients groups. In conclusion, our results revealed a novel prognostic expression signature of AML consisting of ten snRNAs, and we conducted a preliminary exploration of its potential biological functions and tumor immunity.
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Affiliation(s)
- Zhongming Zhang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning, 530021, Guangxi, People's Republic of China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning, 530021, Guangxi, People's Republic of China
| | - Yongrong Lai
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning, 530021, Guangxi, People's Republic of China.
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2
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Insco ML, Abraham BJ, Dubbury SJ, Kaltheuner IH, Dust S, Wu C, Chen KY, Liu D, Bellaousov S, Cox AM, Martin BJ, Zhang T, Ludwig CG, Fabo T, Modhurima R, Esgdaille DE, Henriques T, Brown KM, Chanock SJ, Geyer M, Adelman K, Sharp PA, Young RA, Boutz PL, Zon LI. Oncogenic CDK13 mutations impede nuclear RNA surveillance. Science 2023; 380:eabn7625. [PMID: 37079685 PMCID: PMC10184553 DOI: 10.1126/science.abn7625] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We found that disrupted nuclear RNA surveillance is oncogenic. Cyclin-dependent kinase 13 (CDK13) is mutated in melanoma, and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We found recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.
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Affiliation(s)
- Megan L. Insco
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Sara J. Dubbury
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ines H. Kaltheuner
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Sofia Dust
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Constance Wu
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Kevin Y. Chen
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Stanislav Bellaousov
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Anna M. Cox
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Benjamin J.E. Martin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Calvin G. Ludwig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Tania Fabo
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Rodsy Modhurima
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Dakarai E. Esgdaille
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Phillip A. Sharp
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Richard A. Young
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Paul L. Boutz
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, 14642, USA
- Center for Biomedical Informatics, University of Rochester, Rochester, NY, 14642, USA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
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3
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Liang Z, Su D, Liu K, Jiang H. Comprehensive analysis of molecular mechanism and a novel prognostic signature based on small nuclear RNA biomarkers in gastric cancer patients. Open Med (Wars) 2022; 17:991-1006. [PMID: 35733621 PMCID: PMC9164292 DOI: 10.1515/med-2022-0493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 11/24/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are rarely reported in cancer. This study is based on The Cancer Genome Atlas genome-wide data set to explore the prognostic value and molecular mechanism of snRNAs in gastric cancer (GC). Gene ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis were used to explore the molecular mechanism of snRNAs. A total of 351 patients were included in the survival analysis, and 14 prognostic snRNAs were identified using multivariate survival analysis. We constructed a prognostic signature containing nine snRNAs, which can signally classify patients into high- and low-risk phenotypes (adjusted P < 0.0001, hazard ratio = 2.671, 95% confidence interval = 1.850–3.858). Combining the molecular mechanisms obtained by the three functional enrichment approaches, we concluded that this prognostic signature snRNAs participated in classical tumor-related signaling pathways, including Notch, PI3K, toll-like receptor, etc.; cell adhesion; cell cycle; cell proliferation; and other biological processes that affect the biological phenotype of cancer cells. We also found significant downregulation of the abundance of immune cell infiltrates and immune microenvironment scores for high-risk phenotypes of GC patients. In conclusion, this study has identified 14 prognostic snRNAs signally associated with GC overall survival and also constructed a novel prognostic signature containing nine prognostic snRNAs.
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Affiliation(s)
- Ziyu Liang
- Department of Gastroenterology, The Third Affiliated Hospital of Guangxi Medical University , Nanning , 530000, Guangxi Zhuang Autonomous Region , People’s Republic of China
| | - Dongxing Su
- Department of Gastroenterology, The Third Affiliated Hospital of Guangxi Medical University , Nanning , 530000, Guangxi Zhuang Autonomous Region , People’s Republic of China
| | - Kang Liu
- Department of Radiation Oncology , The First Affiliated Hospital of Guangxi Medical University , Nanning , 530021, Guangxi Zhuang Autonomous Region , People’s Republic of China
| | - Haixing Jiang
- Department of Gastroenterology , The First Affiliated Hospital of Guangxi Medical University , Shuang Yong Road 6 , Nanning , 530021, Guangxi Zhuang Autonomous Region , People’s Republic of China
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4
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Dharmalingam P, Mahalingam R, Yalamanchili HK, Weng T, Karmouty-Quintana H, Guha A, A Thandavarayan R. Emerging roles of alternative cleavage and polyadenylation (APA) in human disease. J Cell Physiol 2021; 237:149-160. [PMID: 34378793 DOI: 10.1002/jcp.30549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022]
Abstract
In the messenger RNA (mRNA) maturation process, the 3'-end of pre-mRNA is cleaved and a poly(A) sequence is added, this is an important determinant of mRNA stability and its cellular functions. More than 60%-70% of human genes have three or more polyadenylation (APA) sites and can be cleaved at different sites, generating mRNA transcripts of varying lengths. This phenomenon is termed as alternative cleavage and polyadenylation (APA) and it plays role in key biological processes like gene regulation, cell proliferation, senescence, and also in various human diseases. Loss of regulatory microRNA binding sites and interactions with RNA-binding proteins leading to APA are largely investigated in human diseases. However, the functions of the core APA machinery and related factors during disease conditions remain largely unknown. In this review, we discuss the roles of polyadenylation machinery in relation to brain disease, cardiac failure, pulmonary fibrosis, cancer, infectious conditions, and other human diseases. Collectively, we believe this review will be a useful avenue for understanding the emerging role of APA in the pathobiology of various human diseases.
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Affiliation(s)
- Prakash Dharmalingam
- Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai, India
| | - Rajasekaran Mahalingam
- Laboratory of Neuroimmunology, Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics - Neurology, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - Tingting Weng
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ashrith Guha
- Department of Cardiology, Houston Methodist DeBakey Heart & Vascular Center, Houston, Texas, USA
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5
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Alternative Polyadenylation: a new frontier in post transcriptional regulation. Biomark Res 2020; 8:67. [PMID: 33292571 PMCID: PMC7690165 DOI: 10.1186/s40364-020-00249-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Polyadenylation of pre-messenger RNA (pre-mRNA) specific sites and termination of their downstream transcriptions are signaled by unique sequence motif structures such as AAUAAA and its auxiliary elements. Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that processes RNA products depending on its 3'-untranslated region (3'-UTR) specific sequence signal. APA processing can generate several mRNA isoforms from a single gene, which may have different biological functions on their target gene. As a result, cellular genomic stability, proliferation capability, and transformation feasibility could all be affected. Furthermore, APA modulation regulates disease initiation and progression. APA status could potentially act as a biomarker for disease diagnosis, severity stratification, and prognosis forecast. While the advance of modern throughout technologies, such as next generation-sequencing (NGS) and single-cell sequencing techniques, have enriched our knowledge about APA, much of APA biological process is unknown and pending for further investigation. Herein, we review the current knowledge on APA and how its regulatory complex factors (CFI/IIm, CPSF, CSTF, and RBPs) work together to determine RNA splicing location, cell cycle velocity, microRNA processing, and oncogenesis regulation. We also discuss various APA experiment strategies and the future direction of APA research.
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6
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Coutinho MF, Matos L, Santos JI, Alves S. RNA Therapeutics: How Far Have We Gone? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:133-177. [PMID: 31342441 DOI: 10.1007/978-3-030-19966-1_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.
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Affiliation(s)
- Maria Francisca Coutinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Liliana Matos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Juliana Inês Santos
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal
| | - Sandra Alves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Porto, Portugal.
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7
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Shi J, Deng Y, Huang S, Huang C, Wang J, Xiang AP, Yao C. Suboptimal RNA-RNA interaction limits U1 snRNP inhibition of canonical mRNA 3' processing. RNA Biol 2019; 16:1448-1460. [PMID: 31242075 DOI: 10.1080/15476286.2019.1636596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is increasingly appreciated that U1 snRNP transcriptomically suppresses the usage of intronic polyadenylation site (PAS) of mRNAs, an outstanding question is why frequently used PASs are not suppressed. Here we found that U1 snRNP could be transiently associated with sequences upstream of actionable PASs in human cells, and RNA-RNA interaction might contribute to the association. By focusing on individual PAS, we showed that the stable assembly of U1 snRNP near PAS might be generally required for U1 inhibition of mRNA 3' processing. Therefore, actionable PASs that often lack optimal U1 snRNP docking site nearby is free from U1 inhibitory effect. Consistently, natural 5' splicing site (5'-SS) is moderately enriched ~250 nt upstream of intronic PASs whose usage is sensitive to functional knockdown of U1 snRNA. Collectively, our results provided an insight into how U1 snRNP selectively inhibits the usage of PASs in a cellular context, and supported a prevailing model that U1 snRNP scans pre-mRNA through RNA-RNA interaction to find a stable interaction site to exercise its function in pre-mRNA processing, including repressing the usage of cryptic PASs.
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Affiliation(s)
- Junjie Shi
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Shanshan Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chunliu Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Jinkai Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou , China.,Center for Precision Medicine, Sun Yat-sen University , Guangzhou , China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou , China
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8
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Xu X, Ji H, Jin X, Cheng Z, Yao X, Liu Y, Zhao Q, Zhang T, Ruan J, Bu W, Chen Z, Gao S. Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5' and 3' End Small RNAs. Front Genet 2019; 10:105. [PMID: 30838030 PMCID: PMC6382676 DOI: 10.3389/fgene.2019.00105] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/30/2019] [Indexed: 12/03/2022] Open
Abstract
In this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of both 5′ and 3′ end small RNAs (5′ and 3′ sRNAs). 5′ and 3′ sRNAs alone can be used to annotate nuclear non-coding and mitochondrial genes at 1-bp resolution and identify new steady RNAs, which are usually transcribed from functional genes. Then, we provided a simple and cost effective way for the annotation of nuclear non-coding and mitochondrial genes and the identification of new steady RNAs, particularly long non-coding RNAs (lncRNAs). Using 5′ and 3′ sRNAs, the annotation of human mitochondrial was corrected and a novel ncRNA named non-coding mitochondrial RNA 1 (ncMT1) was reported for the first time in this study. We also found that most of human tRNA genes have downstream lncRNA genes as lncTRS-TGA1-1 and corrected the misunderstanding of them in previous studies. Using 5′, 3′, and intronic sRNAs, we reported for the first time that enzymatic double-stranded RNA (dsRNA) cleavage and RNA interference (RNAi) might be involved in the RNA degradation and gene expression regulation of U1 snRNA in human. We provided a different perspective on the regulation of gene expression in U1 snRNA. We also provided a novel view on cancer and virus-induced diseases, leading to find diagnostics or therapy targets from the ribonuclease III (RNase III) family and its related pathways. Our findings pave the way toward a rediscovery of dsRNA cleavage and RNAi, challenging classical theories.
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Affiliation(s)
- Xiaofeng Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haishuo Ji
- College of Life Sciences, Nankai University, Tianjin, China.,Institute of Statistics, Nankai University, Tianjin, China
| | - Xiufeng Jin
- College of Life Sciences, Nankai University, Tianjin, China
| | - Zhi Cheng
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xue Yao
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yanqiang Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Zhao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Tao Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, China.,Institute of Statistics, Nankai University, Tianjin, China
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9
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Park JE, Cartegni L. In Vitro Modulation of Endogenous Alternative Splicing Using Splice-Switching Antisense Oligonucleotides. Methods Mol Biol 2018; 1648:39-52. [PMID: 28766288 DOI: 10.1007/978-1-4939-7204-3_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regulation of alternative splicing can be harnessed by antisense-based compounds to control gene expression. Antisense-mediated splicing interference has become a valuable molecular tool to modulate endogenous alternative splicing patterns, to correct cryptic or aberrant splicing, to reduce gene expression by triggering nonsense-mediated mRNA decay, and to activate intronic polyadenylation, both in vitro and in vivo. Here, we describe methods to induce and analyze the modulation of RNA processing, using modified splice-switching antisense oligonucleotides, such as phosphorodiamidate morpholino (PMO).
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Affiliation(s)
- Jeong Eun Park
- Susan Lehman Cullman Laboratory for Cancer Research, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Luca Cartegni
- Susan Lehman Cullman Laboratory for Cancer Research, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
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10
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Cheng Z, Sun Y, Niu X, Shang Y, Ruan J, Chen Z, Gao S, Zhang T. Gene expression profiling reveals U1 snRNA regulates cancer gene expression. Oncotarget 2017; 8:112867-112874. [PMID: 29348872 PMCID: PMC5762557 DOI: 10.18632/oncotarget.22842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/10/2017] [Indexed: 11/25/2022] Open
Abstract
U1 small nuclear RNA (U1 snRNA), as one of the most abundant ncRNAs in human cells, plays an important role in splicing of pre-mRNAs. Compared to previous studies which have focused on the primary function of U1 snRNA and the neurodegenerative diseases caused by abnormalities of U1 snRNA, this study is to investigate how U1 snRNA over-expression affects the expression of mammal genes on a genome-wide scale. By comparing the gene expression profiles of U1 snRNA over-expressed cells with those of their controls using microarray experiments, 916 genes or loci were identified significantly Differentially Expressed (DE). These 595 up-regulated DE genes and 321 down-regulated DE genes were analyzed using annotations from GO categories and pathways from the KEGG database. As a result, three of 12 enriched pathways were well-known cancer pathways, while the other nine pathways were associated to cancers in previous studies. The further analysis of 73 genes involved in 12 pathways suggested that U1 snRNA could regulate cancer gene expression. The microarray data under the GEO Series accession number GSE84304 is available in the NCBI GEO database.
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Affiliation(s)
- Zhi Cheng
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, P.R. China
| | - Yu Sun
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- Institute of Statistics, Nankai University, Tianjin 300071, P.R. China
| | - Xiaoran Niu
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
| | - Yingchun Shang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, P.R. China
| | - Shan Gao
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- Institute of Statistics, Nankai University, Tianjin 300071, P.R. China
| | - Tao Zhang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
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11
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Lee NC, Lee YM, Chen PW, Byrne BJ, Hwu WL. Mutation-adapted U1 snRNA corrects a splicing error of the dopa decarboxylase gene. Hum Mol Genet 2017; 25:5142-5147. [PMID: 27658936 DOI: 10.1093/hmg/ddw323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/16/2016] [Indexed: 12/29/2022] Open
Abstract
Aromatic l-amino acid decarboxylase (AADC) deficiency is an inborn error of monoamine neurotransmitter synthesis, which results in dopamine, serotonin, epinephrine and norepinephrine deficiencies. The DDC gene founder mutation IVS6 + 4A > T is highly prevalent in Chinese patients with AADC deficiency. In this study, we designed several U1 snRNA vectors to adapt U1 snRNA binding sequences of the mutated DDC gene. We found that only the modified U1 snRNA (IVS-AAA) that completely matched both the intronic and exonic U1 binding sequences of the mutated DDC gene could correct splicing errors of either the mutated human DDC minigene or the mouse artificial splicing construct in vitro. We further injected an adeno-associated viral (AAV) vector to express IVS-AAA in the brain of a knock-in mouse model. This treatment was well tolerated and improved both the survival and brain dopamine and serotonin levels of mice with AADC deficiency. Therefore, mutation-adapted U1 snRNA gene therapy can be a promising method to treat genetic diseases caused by splicing errors, but the efficiency of such a treatment still needs improvements.
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Affiliation(s)
- Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-May Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pin-Wen Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Barry J Byrne
- Powell Gene Therapy Center, University of Florida, Gainesville, FL, USA
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
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Ly PT, Tang SJ, Roca X. Alternative polyadenylation expands the mRNA isoform repertoire of human CD46. Gene 2017; 625:21-30. [PMID: 28476687 DOI: 10.1016/j.gene.2017.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 11/28/2022]
Abstract
Alternative polyadenylation is a prevalent mechanism regulating mammalian gene expression. While tandem 3'-Untranslated-Region (3'UTR) polyadenylation changes expression levels, Intronic PolyAdenylation generates shorter transcripts encoding truncated proteins. Intronic PolyAdenylation regulates 20% of genes and is especially common in receptor tyrosine-kinase transcripts, generating soluble repressors. Here we report that human CD46, encoding a TransMembrane repressor of complement and T-cell co-stimulator, expresses multiple isoforms by alternative polyadenylation. We provide evidence for polyadenylation at several introns by RT-PCR of 5' intronic fragments, and by increase in such isoforms via functional U1 knockdown. We mapped various Intronic PolyAdenylation Sites by 3' Rapid Amplification of cDNA Ends (3'RACE), which could generate soluble or membrane-bound but tail-less CD46. Intronic PolyAdenylation could add to the source of soluble CD46 isoforms in fluids and tissues, which increase in cancers and autoimmune syndromes. Furthermore, 3'RACE identified three PolyAdenylation Sites within the last intron and exon, whose transcripts with shortened 3'UTRs could support higher CD46 expression. Finally, 3'RACE revealed that the CD46 Pseudogene only expresses short transcripts by early polyadenylation in intron 2. Overall, we report a wide variety of CD46 mRNA isoforms which could generate new protein isoforms, adding to the diverse physiological and pathological roles of CD46.
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Affiliation(s)
- Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; The Neuroscience and Behavioral Disorders Programme, Duke-NUS Graduate Medical School, Singapore
| | - Sze Jing Tang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
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13
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Abstract
More than 15% of all disease-causing mutations result in mRNA splicing defects. U1 snRNA binds to the 5' splice site (5'ss) through base pairing. Mutation-adapted U1 snRNA (with compensatory U1 snRNA changes) and exon-specific U1 snRNA (complementary to intronic sequences) have been shown to suppress 5'ss mutations in cellular and animal models. Areas covered: The history, mechanism of action, and efficacy of U1 snRNA-mediated gene therapy are covered. The clinical utility of this technology and its limitations will be discussed. Expert commentary: Recently, gene therapies with mutation-adapted U1 snRNAs have been conducted on animal models, including aromatic l-amino acid decarboxylase deficiency and spinal muscular atrophy. However, although U1-mediated therapy has the advantage of maintaining the regulated expression of defective genes, its accuracy and efficacy needs to be improved before clinical application of this technique is possible.
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Affiliation(s)
- Wuh-Liang Hwu
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
| | - Yu-May Lee
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
| | - Ni-Chung Lee
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
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14
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Oliveira LN, Casaletti L, Báo SN, Borges CL, de Sousa Lima P, de Almeida Soares CM. Characterizing the nuclear proteome of Paracoccidioides spp. Fungal Biol 2016; 120:1209-24. [PMID: 27647238 DOI: 10.1016/j.funbio.2016.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Paracoccidioidomycosis is an endemic disease in Latin America, caused by thermo dimorphic fungi of the genus Paracoccidioides. Although previous proteome analyses of Paracoccidioides spp. have been carried out, the nuclear subproteome of this pathogen has not been described. In this way, we aimed to characterize the nuclear proteome of Paracoccidioides species, in the yeast form. For that, yeast cells were disrupted and submitted to cell fractionation. The purity of the nuclear fraction was confirmed by fluorescence and electron microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allowed the identification of 867 proteins. In order to support our enrichment method for nuclear proteins, bioinformatics analysis were applied that allowed the identification of 281 proteins with nuclear localization. The analysis revealed proteins related to DNA maintenance, gene expression, synthesis and processing of messenger and ribosomal RNAs, likewise proteins of nuclear-cytoplasmic traffic. It was also possible to detect some proteins that are poorly expressed, like transcription factors involved in important roles such as resistance to abiotic stress, sporulation, cellular growth and DNA and chromatin maintenance. This is the first descriptive nuclear proteome of Paracoccidioides spp. that can be useful as an important platform base for fungi-specific nuclear processes.
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Affiliation(s)
- Lucas Nojosa Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Luciana Casaletti
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil; Escola de Engenharia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, 74605-010, Brazil
| | - Sônia Nair Báo
- Laboratório de Microscopia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil.
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15
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Erson-Bensan AE. Alternative polyadenylation and RNA-binding proteins. J Mol Endocrinol 2016; 57:F29-34. [PMID: 27208003 DOI: 10.1530/jme-16-0070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 12/22/2022]
Abstract
Our understanding of the extent of microRNA-based gene regulation has expanded in an impressive pace over the past decade. Now, we are beginning to better appreciate the role of 3'-UTR (untranslated region) cis-elements which harbor not only microRNA but also RNA-binding protein (RBP) binding sites that have significant effect on the stability and translational rate of mRNAs. To add further complexity, alternative polyadenylation (APA) emerges as a widespread mechanism to regulate gene expression by producing shorter or longer mRNA isoforms that differ in the length of their 3'-UTRs or even coding sequences. Resulting shorter mRNA isoforms generally lack cis-elements where trans-acting factors bind, and hence are differentially regulated compared with the longer isoforms. This review focuses on the RBPs involved in APA regulation and their action mechanisms on APA-generated isoforms. A better understanding of the complex interactions between APA and RBPs is promising for mechanistic and clinical implications including biomarker discovery and new therapeutic approaches.
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Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological SciencesOrta Dogu Teknik Universitesi (ODTU) (METU), Universiteler Mahallesi, Cankaya, Ankara, Turkey
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16
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Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov 2016; 2:16013. [PMID: 27462460 PMCID: PMC4906801 DOI: 10.1038/celldisc.2016.13] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.
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17
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Erson-Bensan AE, Can T. Alternative Polyadenylation: Another Foe in Cancer. Mol Cancer Res 2016; 14:507-17. [PMID: 27075335 DOI: 10.1158/1541-7786.mcr-15-0489] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/30/2016] [Indexed: 11/16/2022]
Abstract
Advancements in sequencing and transcriptome analysis methods have led to seminal discoveries that have begun to unravel the complexity of cancer. These studies are paving the way toward the development of improved diagnostics, prognostic predictions, and targeted treatment options. However, it is clear that pieces of the cancer puzzle are still missing. In an effort to have a more comprehensive understanding of the development and progression of cancer, we have come to appreciate the value of the noncoding regions of our genomes, partly due to the discovery of miRNAs and their significance in gene regulation. Interestingly, the miRNA-mRNA interactions are not solely dependent on variations in miRNA levels. Instead, the majority of genes harbor multiple polyadenylation signals on their 3' UTRs (untranslated regions) that can be differentially selected on the basis of the physiologic state of cells, resulting in alternative 3' UTR isoforms. Deregulation of alternative polyadenylation (APA) has increasing interest in cancer research, because APA generates mRNA 3' UTR isoforms with potentially different stabilities, subcellular localizations, translation efficiencies, and functions. This review focuses on the link between APA and cancer and discusses the mechanisms as well as the tools available for investigating APA events in cancer. Overall, detection of deregulated APA-generated isoforms in cancer may implicate some proto-oncogene activation cases of unknown causes and may help the discovery of novel cases; thus, contributing to a better understanding of molecular mechanisms of cancer. Mol Cancer Res; 14(6); 507-17. ©2016 AACR.
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Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU) (ODTU), Ankara, Turkey.
| | - Tolga Can
- Department of Computer Engineering, Middle East Technical University (METU) (ODTU), Ankara, Turkey
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18
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Therapeutic activity of modified U1 core spliceosomal particles. Nat Commun 2016; 7:11168. [PMID: 27041075 PMCID: PMC4822034 DOI: 10.1038/ncomms11168] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/25/2016] [Indexed: 12/15/2022] Open
Abstract
Modified U1 snRNAs bound to intronic sequences downstream of the 5′ splice site correct exon skipping caused by different types of mutations. Here we evaluate the therapeutic activity and structural requirements of these exon-specific U1 snRNA (ExSpeU1) particles. In a severe spinal muscular atrophy, mouse model, ExSpeU1, introduced by germline transgenesis, increases SMN2 exon 7 inclusion, SMN protein production and extends life span. In vitro, RNA mutant analysis and silencing experiments show that while U1A protein is dispensable, the 70K and stem loop IV elements mediate most of the splicing rescue activity through improvement of exon and intron definition. Our findings indicate that precise engineering of the U1 core spliceosomal RNA particle has therapeutic potential in pathologies associated with exon-skipping mutations. Modification of the spliceosome is being tested as a potential therapy for exon-skipping diseases, such as spinal muscular atrophy (SMA). Here the authors show that 70K and stem loop IV structural elements of a modified U1 particle are essential for splicing enhancement and effective treatment of SMA mice.
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19
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Kondo Y, Oubridge C, van Roon AMM, Nagai K. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. eLife 2015; 4. [PMID: 25555158 PMCID: PMC4383343 DOI: 10.7554/elife.04986] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 12/12/2022] Open
Abstract
U1 snRNP binds to the 5′ exon-intron junction of pre-mRNA and thus plays a
crucial role at an early stage of pre-mRNA splicing. We present two crystal
structures of engineered U1 sub-structures, which together reveal at atomic
resolution an almost complete network of protein–protein and RNA-protein
interactions within U1 snRNP, and show how the 5′ splice site of pre-mRNA is
recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between
pre-mRNA and the 5′-end of U1 snRNA. The binding of the RNA duplex is
stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA
backbone around the splice junction but U1-C makes no base-specific contacts with
pre-mRNA. The structure, together with RNA binding assays, shows that the selection
of 5′-splice site nucleotides by U1 snRNP is achieved predominantly through
basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched
5′-splice sites. DOI:http://dx.doi.org/10.7554/eLife.04986.001 Genes are made up of long stretches of DNA. The regions of a gene that code for
proteins (known as exons) are interrupted by stretches of non-coding DNA called
introns. To produce proteins from a gene, the DNA is ‘transcribed’ to
form pre-mRNA molecules, from which the introns must be removed in a process called
splicing. The remaining exons are then joined together to form a mature mRNA molecule
that contains the instructions to build a protein. Errors in the splicing process can
lead to numerous diseases, such as cancer. A molecular machine known as a spliceosome is responsible for splicing the pre-mRNA
molecules. This consists of five different complexes called small nuclear
ribonucleoprotein particles (snRNPs), which are in turn made up from numerous
proteins and RNA molecules. The spliceosome assembles anew every time it splices, and
an early step in this assembly process involves the interaction of an snRNP called U1
with the start of an intron in the pre-mRNA. This interaction then stimulates the
assembly of the rest of the spliceosome. In 2009, researchers reported the structure
of the U1 snRNP, but the structure did not contain enough detail to reveal how the
snRNP recognizes the start of an intron. Kondo, Oubridge et al., including some of the researchers involved in the 2009 work,
now present the crystal structure of the human version of the U1 snRNP in more
detail. High-quality crystal structures of the complete U1 snRNP molecule could not
be obtained because the arrangement of the RNA molecules in the snRNP prevented a
regular crystal from forming. Kondo, Oubridge et al. instead engineered two
subcomponents of U1 snRNP that each crystallized well, and determined their
structures. This revealed that the interactions between the various parts of the U1
snRNP form a complex network. A protein present in the U1 snRNP, known as U1-C, had previously been reported to be
able to recognize introns on its own—without requiring the complete U1 snRNP.
Kondo, Oubridge et al. reveal that this is not the case and that U1-C does not read
the intron RNA sequence directly. Instead, U1 snRNP is able to find the start of the
intron because the U1 RNA can stably bind to this site. The U1-C protein can however
adjust the strength of this binding to ensure that the spliceosome can operate with a
variety of intron start sequences (or signals). DOI:http://dx.doi.org/10.7554/eLife.04986.002
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Affiliation(s)
- Yasushi Kondo
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chris Oubridge
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anne-Marie M van Roon
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Kiyoshi Nagai
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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Abstract
The spliceosomal factor TRAP150 is essential for pre-mRNA splicing in vivo and, when overexpressed, it enhances splicing efficiency. In this study, we found that TRAP150 interacted with the cleavage and polyadenylation specificity factor (CPSF) and co-fractionated with CPSF and RNA polymerase II. Moreover, TRAP150 preferentially associated with the U1 small ribonucleoprotein (snRNP). However, our data do not support a role for TRAP150 in alternative 5′ splice site or exon selection or in alternative polyadenylation. Because U1 snRNP participates in premature cleavage and polyadenylation (PCPA), we tested whether TRAP150 is a cofactor in the control of PCPA. Although TRAP150 depletion had no significant effect on PCPA, overexpression of TRAP150 forced activation of a cryptic 3′ splice site, yielding spliced PCPA transcripts. Mechanistic studies showed that TRAP150-activated splicing occurred in composite but not authentic terminal exons, and such an activity was enhanced by debilitation of U1 snRNP or interference with transcription elongation or termination. Together, these results indicate that TRAP150 provides an additional layer of PCPA regulation, through which it may increase the diversity of abortive RNA transcripts under conditions of compromised gene expression.
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Affiliation(s)
- Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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21
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Guiro J, O'Reilly D. Insights into the U1 small nuclear ribonucleoprotein complex superfamily. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:79-92. [DOI: 10.1002/wrna.1257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/17/2014] [Accepted: 07/14/2014] [Indexed: 12/12/2022]
Affiliation(s)
- J Guiro
- Institute of Biosciences; University of Sao Paulo; Sao Paulo Brazil
| | - D O'Reilly
- Sir William Dunn School of Pathology; Oxford United Kingdom
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22
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Barton M, Santucci-Pereira J, Russo J. Molecular pathways involved in pregnancy-induced prevention against breast cancer. Front Endocrinol (Lausanne) 2014; 5:213. [PMID: 25540638 PMCID: PMC4261797 DOI: 10.3389/fendo.2014.00213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/25/2014] [Indexed: 12/18/2022] Open
Abstract
Pregnancy produces a protective effect against breast cancer in women who had their first full term pregnancy (FTP) in their middle twenties. The later in life the first delivery occurs, the higher the risk of breast cancer development. Also, transiently during the postpartum period, the risk of developing breast cancer increases. This transient increased risk is taken over by a long-lasting protective period. The genomic profile of parous women has shown pregnancy induces a long-lasting "genomic signature" that explains the preventive effect on breast cancer. This signature reveals that chromatin remodeling is the driver of the differentiation process conferred by FTP. The chromatin remodeling process may be the ultimate step mediating the protection of the breast against developing breast cancer in post-menopausal years.
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Affiliation(s)
- Maria Barton
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, USA
| | - Julia Santucci-Pereira
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, USA
| | - Jose Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, USA
- *Correspondence: Jose Russo, The Irma H Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, 333 Cottman Avenue, Room P2037, Philadelphia, PA 19111, USA e-mail:
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