1
|
Li F, Li N, Wang A, Liu X. Correlation Analysis and Prognostic Impacts of Biological Characteristics in Elderly Patients with Acute Myeloid Leukemia. Clin Interv Aging 2022; 17:1187-1197. [PMID: 35967966 PMCID: PMC9369099 DOI: 10.2147/cia.s375000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Background The significant heterogeneity of elderly AML patients’ biological features has caused stratification difficulties and adverse prognosis. This paper did a correlation study between their genetic mutations, clinical features, and prognosis to further stratify them. Methods 90 newly diagnosed elderly acute myeloid leukemia (AML) patients (aged ≥60 years) who detected genetic mutations by next-generation sequencing (NGS) were enrolled between April 2015 and March 2021 in our medical center. Results A total of 29 genetic mutations were identified in 82 patients among 90 cases with a frequency of 91.1%. DNMT3A, BCOR, U2AF1, and BCORL1 mutations were unevenly distributed among different FAB classifications (p < 0.05). DNMT3A, IDH2, NPM1, FLT3-ITD, ASXL1, IDH1, SRSF2, BCOR, NRAS, RUNX1, U2AF1, MPO, and WT1 mutations were distributed differently when an immunophenotype was expressed or not expressed (p<0.05). NPM1 and FLT3-ITD had higher mutation frequencies in patients with normal chromosome karyotypes than abnormal chromosome karyotypes (p<0.001, p=0.005). DNMT3A and NRAS mutations predicted lower CR rates. DNMT3A, TP53, and U2AF1 mutations were related to unfavorable OS. TET2 mutation with CD123+, CD11b+ or CD34- predicted lower CR rate. IDH2+/CD34- predicted lower CR rate. ASXL1+/CD38+ and SRSF2+/CD123- predicted shorter OS. Conclusion The study showed specific correlations between elderly AML patients’ genetic mutations and clinical features, some of which may impact prognosis.
Collapse
Affiliation(s)
- Fengli Li
- Department of Hematology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, People’s Republic of China
| | - Na Li
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Anyou Wang
- Department of Hematology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, People’s Republic of China
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
- Anyou Wang, Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Lujiang Road No. 17, Hefei, 230001, People’s Republic of China, Tel/Fax +86-551-62283863, Email
| | - Xin Liu
- Department of Hematology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, People’s Republic of China
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
- Correspondence: Xin Liu, Department of Hematology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Lujiang Road No. 17, Hefei, 230001, People’s Republic of China, Tel/Fax +86-551-62283863, Email
| |
Collapse
|
2
|
Zhu YQ, Wu LY. [Effect of U2AF1 Mutation to Inflammatory Cytokine Expression in SKM-1 Cells through FOXO3a-Bim Signaling Pathway]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2021; 29:1858-1863. [PMID: 34893123 DOI: 10.19746/j.cnki.issn.1009-2137.2021.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To investigate the effect of U2AF1 gene mutation to inflammatory cytokine in SKM-1 cell of human myelodysplastic syndromes (MDS), and whether the above effects were mediated by FOXO3a-Bim signaling pathway. METHODS Wide-type U2AF1 and mutant U2AF1 (the serine residue 34 was replaced by phenylalanine, and named as S34F) recombinant expression plasmids were constructed. Lentiviruses were packaged and transfected into SKM-1 cells. The expression of FOXO3a was up-regulated by lentiviruses, and its transfection rate was investigated. The cell proliferation was detected by CCK-8 method. Flow cytometry was used to detect the apoptosis and cycle of the cells. The expression pro-inflammatory cytokine IL-1β, IL-6, TNF-α and anti-inflammatory cytokine IL-4 were detected by qRT-PCR. FOXO3a, Bim, Bcl-2 and Bax protein expression levels were detected by Western blot. RESULTS Compared with the control group, the cell apoptosis rate, pro-inflammatory cytokine IL-1β and TNF-α transcription levels were significantly increased in the S34F group (P<0.05); cell cycle was blocked at the G2 phase; cell proliferation and the anti-inflammatory cytokine IL-4 transcription level were significantly decreased; the expression levels of FOXO3a, Bim and Bax protein were significantly increased (P<0.05); while the expression level of Bcl-2 protein was significantly decreased (P<0.05). The up-regulation of FOXO3a could significantly inhibited the proliferation and increased cell apoptosis of SKM-1 cells with U2AF1 S34F mutation; cell cycle was blocked at the S and G2 phases; the pro-inflammatory cytokine IL-1β and TNF-α transcription levels were significantly decreased (P<0.05), and the transcription level of anti-inflammatory cytokine IL-4 showed no statistically significant as compared with control group (P>0.05). CONCLUSION U2AF1 S34F mutation can regulate inflammatory phenotype in SKM-1 cells, which may be mediated through FOXO3a-Bim signaling pathway.
Collapse
Affiliation(s)
- Yu-Qian Zhu
- Department of Hematology, The Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, China
| | - Ling-Yun Wu
- Department of Hematology, The Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, China,E-mail:
| |
Collapse
|
3
|
Horiuchi K, Perez-Cerezales S, Papasaikas P, Ramos-Ibeas P, López-Cardona AP, Laguna-Barraza R, Fonseca Balvís N, Pericuesta E, Fernández-González R, Planells B, Viera A, Suja JA, Ross PJ, Alén F, Orio L, Rodriguez de Fonseca F, Pintado B, Valcárcel J, Gutiérrez-Adán A. Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12 Intron Splicing-Defective Zrsr1 Mutant Mice. Cell Rep 2019; 23:143-155. [PMID: 29617656 DOI: 10.1016/j.celrep.2018.03.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/28/2017] [Accepted: 03/08/2018] [Indexed: 11/18/2022] Open
Abstract
The U2AF35-like ZRSR1 has been implicated in the recognition of 3' splice site during spliceosome assembly, but ZRSR1 knockout mice do not show abnormal phenotypes. To analyze ZRSR1 function and its precise role in RNA splicing, we generated ZRSR1 mutant mice containing truncating mutations within its RNA-recognition motif. Homozygous mutant mice exhibited severe defects in erythrocytes, muscle stretch, and spermatogenesis, along with germ cell sloughing and apoptosis, ultimately leading to azoospermia and male sterility. Testis RNA sequencing (RNA-seq) analyses revealed increased intron retention of both U2- and U12-type introns, including U12-type intron events in genes with key functions in spermatogenesis and spermatid development. Affected U2 introns were commonly found flanking U12 introns, suggesting functional cross-talk between the two spliceosomes. The splicing and tissue defects observed in mutant mice attributed to ZRSR1 loss of function suggest a physiological role for this factor in U12 intron splicing.
Collapse
Affiliation(s)
- Keiko Horiuchi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology (RCAST), University of Tokyo, Tokyo 153-8904, Japan
| | - Serafín Perez-Cerezales
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Panagiotis Papasaikas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Priscila Ramos-Ibeas
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | | | - Ricardo Laguna-Barraza
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Noelia Fonseca Balvís
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Eva Pericuesta
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Raul Fernández-González
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Benjamín Planells
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Alberto Viera
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose Angel Suja
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Juan Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Francisco Alén
- Dpto. Psicobiología, Facultad de Psicología, UCM, Campus de Somosaguas, Madrid, Spain
| | - Laura Orio
- Dpto. Psicobiología, Facultad de Psicología, UCM, Campus de Somosaguas, Madrid, Spain
| | - Fernando Rodriguez de Fonseca
- Dpto. Psicobiología, Facultad de Psicología, UCM, Campus de Somosaguas, Madrid, Spain; UGC Salud Mental, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga-Hospital Universitario Regional de Málaga, Avda. Carlos Haya 82, Pabellón de Gobierno, 29010 Málaga, Spain
| | - Belén Pintado
- Servicio de Transgénicos, CNB-CSIC, UAM, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alfonso Gutiérrez-Adán
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain.
| |
Collapse
|
4
|
Torres M, Pacheco C, Valverde A, Rebollo AC, Moral A, Vallejo JA, Mateo A. CA 549 and SP2 in postoperative breast cancer patients. Comparison with CA 15.3, CEA and TPA. Int J Biol Markers 2018; 10:94-9. [PMID: 7561245 DOI: 10.1177/172460089501000205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The levels of CA 549 and SP2 were measured in 430 subjects: 100 healthy blood donors, 130 patients with benign diseases and 200 postoperative breast cancer patients. In the latter group, the serum levels of CA 15.3, CEA and TPA were also measured. The Kolmogorov-Smirnov, Mann Whitney and McNemar tests were used for statistical analysis. The upper normal limits were established on the basis of the values obtained in the healthy blood donors group, the benign diseases group and R.O.C. analysis of the breast cancer group. They were: CA 549 = 13 U/ml, SP2 = 14 U/ml, CA 15.3 = 35 U/ml, CEA = 5 ng/ml and TPA = 110 U/ml. The sensitivity, specificity and accuracy in the breast cancer group were, respectively: CA 549 = 78.1%, 97.1% and 88%; SP2 = 21.9%, 90.4% and 57.5%; CEA = 66.7%, 95.2% and 81.5%; CA 15.3 = 80.2%, 98.1% and 89.5%, and TPA = 73.9%, 78.8% and 76.5%. Statistical analysis showed significant differences only between CA 15.3, the marker which gave the best results, and SP2 (p<0.001). There were no significant differences with the association of two or three tumor markers.
Collapse
Affiliation(s)
- M Torres
- Nuclear Medicine Service, Hospital Reina Sofía, Córdoba, Spain
| | | | | | | | | | | | | |
Collapse
|
5
|
Wei Y, Liu Q, Dong H, Zhou Z, Hao Y, Chen X, Xu L. Selection of Reference Genes for Real-Time Quantitative PCR in Pinus massoniana Post Nematode Inoculation. PLoS One 2016; 11:e0147224. [PMID: 26800152 PMCID: PMC4723224 DOI: 10.1371/journal.pone.0147224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/30/2015] [Indexed: 11/19/2022] Open
Abstract
Pinus massoniaia Lamb has gained more and more attention as the most important tree species for timber and forestation in South China. Gene expression studies are of great importance to identify new and elite cultivars. Real-time quantitative PCR, a highly sensitive and specific method, is commonly used in the analysis of gene expression. The appropriate reference genes must be employed to normalize the calculation program for ascertaining repeatable and significant results. Herein, eleven housekeeping genes were evaluated during different stages of P. massoniana post nematode inoculation in this study. Three statistical approaches such as geNorm, NormFinder and BestKeeper were selected to analyze the stability of candidate genes. The results indicated that U2af and β-TUB were the most stable reference genes. These two genes could be used for the normalization in most of the experiments of P. massoniana, while Histone and AK were the least stable ones. In addition, EF expressed at the lowest average Ct value was the most abundant candidate gene. As an important gene associated with defense mechanisms, ABC transporter was analyzed by qRT-PCR, and the results were used to confirm the reliability of two genes. The selected reference genes in the present study will be conducive to future gene expression normalized by qRT-PCR in P. massoniana.
Collapse
Affiliation(s)
- Yongcheng Wei
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Fuyang, Zhejiang, 311400, China
| | - Qinghua Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
- State Forestry Administration Engineering Research Center of Masson Pine, Fuyang, Zhejiang 311400, China
| | - Hongyu Dong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Yanping Hao
- Anhui Academy of Forestry, Hefei, Anhui 230000, China
| | - Xuelian Chen
- Anhui Academy of Forestry, Hefei, Anhui 230000, China
| | - Liuyi Xu
- Anhui Academy of Forestry, Hefei, Anhui 230000, China
| |
Collapse
|
6
|
Whisenant TC, Peralta ER, Aarreberg LD, Gao NJ, Head SR, Ordoukhanian P, Williamson JR, Salomon DR. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells. PLoS One 2015; 10:e0144409. [PMID: 26641092 PMCID: PMC4671683 DOI: 10.1371/journal.pone.0144409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/16/2015] [Indexed: 12/22/2022] Open
Abstract
Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as "central" interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, "peripheral" interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA splicing interactomes that is important for understanding T cell activation.
Collapse
Affiliation(s)
- Thomas C. Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eigen R. Peralta
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lauren D. Aarreberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Nina J. Gao
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Phillip Ordoukhanian
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jamie R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
7
|
Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res 2015; 43:10492-505. [PMID: 26400176 PMCID: PMC4666398 DOI: 10.1093/nar/gkv956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 11/14/2022] Open
Abstract
The 3' untranslated regions (3' UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3' UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3' UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3' UTRs.
Collapse
Affiliation(s)
- Mojca Tajnik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Alessandra Vigilante
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Simon Braun
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Nicholas M Luscombe
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Kathi Zarnack
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Julian König
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| |
Collapse
|
8
|
Shirai CL, Ley JN, White BS, Kim S, Tibbitts J, Shao J, Ndonwi M, Wadugu B, Duncavage EJ, Okeyo-Owuor T, Liu T, Griffith M, McGrath S, Magrini V, Fulton RS, Fronick C, O'Laughlin M, Graubert TA, Walter MJ. Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. Cancer Cell 2015; 27:631-43. [PMID: 25965570 PMCID: PMC4430854 DOI: 10.1016/j.ccell.2015.04.008] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/16/2015] [Accepted: 04/13/2015] [Indexed: 01/12/2023]
Abstract
Heterozygous somatic mutations in the spliceosome gene U2AF1 occur in ∼ 11% of patients with myelodysplastic syndromes (MDS), the most common adult myeloid malignancy. It is unclear how these mutations contribute to disease. We examined in vivo hematopoietic consequences of the most common U2AF1 mutation using a doxycycline-inducible transgenic mouse model. Mice expressing mutant U2AF1(S34F) display altered hematopoiesis and changes in pre-mRNA splicing in hematopoietic progenitor cells by whole transcriptome analysis (RNA-seq). Integration with human RNA-seq datasets determined that common mutant U2AF1-induced splicing alterations are enriched in RNA processing genes, ribosomal genes, and recurrently mutated MDS and acute myeloid leukemia-associated genes. These findings support the hypothesis that mutant U2AF1 alters downstream gene isoform expression, thereby contributing to abnormal hematopoiesis in patients with MDS.
Collapse
Affiliation(s)
- Cara Lunn Shirai
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - James N Ley
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Brian S White
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Sanghyun Kim
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Justin Tibbitts
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Jin Shao
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Matthew Ndonwi
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Brian Wadugu
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Theresa Okeyo-Owuor
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tuoen Liu
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Malachi Griffith
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Sean McGrath
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Vincent Magrini
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Robert S Fulton
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Catrina Fronick
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | | | - Timothy A Graubert
- Massachusetts General Hospital/Harvard Medical School, Boston, MA 02114, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA.
| |
Collapse
|
9
|
Hong JY, Seo JY, Kim SH, Jung HA, Park S, Kim K, Jung CW, Kim JS, Park JS, Kim HJ, Jang JH. Mutations in the Spliceosomal Machinery Genes SRSF2, U2AF1, and ZRSR2 and Response to Decitabine in Myelodysplastic Syndrome. Anticancer Res 2015; 35:3081-3089. [PMID: 25964599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Hypomethylating agents, such as azacitidine and decitabine, now constitute one of the mainstays of myelodysplastic syndrome (MDS) treatment. In recent years, novel recurrent mutations in multiple genes encoding RNA spliceosomal machinery (SRSF2, U2AF1, ZRSR2, SF3B1) were revealed. However, the clinical impact of these mutations on the outcomes of treatment of MDS patients with hypomethylating agents has not been described. PATIENTS AND METHODS A total of 58 de novo MDS patients were included in the study who had received first-line decitabine treatment. Polymerase chain reaction (PCR) followed by direct sequencing analyses was performed for the spliceosomal machinery genes including SRSF2, U2AF1 and ZRSR2. RESULTS In the present analysis of 58 Korean MDS patients, mutations in the splicing machinery genes SRSF2, U2AF1 and ZRSR2 were detected in 5 (8.6%), 10 (17.2%) and 6 (10.3%) patients, respectively, and the incidence of SRSF2 mutation was lower than those of previous series. The overall response rates (ORRs) including complete remission (CR), partial response (PR), and marrow CR (mCR) were 42.9% in the spliceosome wild-type (WT) group and 46.7% in the spliceosome-mutated group (p>0.999). The median OS was 22.0 months in the spliceosome-WT group and 15.9 months in the spliceosome-mutated group (p=0.267) CONCLUSION: This study firstly reports the impact of mutations of the spliceosomal machinery genes on the outcomes of decitabine treatment in MDS. The mutational status of the SRSF2, U2AF1 and ZRSR2 did not affect the response rate or survival in MDS patients who had received first-line decitabine treatment. Further studies are needed to confirm the prognostic relevance of spliceosome mutations to the clinical outcomes of treatment with hypomethylating agents.
Collapse
Affiliation(s)
- Jung Yong Hong
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Ja-Young Seo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea Department of Laboratory Medicine, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyun Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Silvia Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kihyun Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chul Won Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Seok Kim
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Joon Seong Park
- Department of Oncology-Hematology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jun Ho Jang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| |
Collapse
|
10
|
Engle EK, Fisher DAC, Miller CA, McLellan MD, Fulton RS, Moore DM, Wilson RK, Ley TJ, Oh ST. Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia. Leukemia 2015; 29:869-76. [PMID: 25252869 PMCID: PMC4374044 DOI: 10.1038/leu.2014.289] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/15/2014] [Accepted: 09/18/2014] [Indexed: 12/16/2022]
Abstract
Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single-nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML.
Collapse
Affiliation(s)
- E K Engle
- Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - D A C Fisher
- Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - C A Miller
- The Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - M D McLellan
- The Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - R S Fulton
- The Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - D M Moore
- Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - R K Wilson
- The Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - T J Ley
- The Genome Institute, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - S T Oh
- Division of Hematology, Washington University School of Medicine, St Louis, MO, USA
| |
Collapse
|
11
|
Becerra S, Montes M, Hernández-Munain C, Suñé C. Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo. RNA 2015; 21:438-57. [PMID: 25605964 PMCID: PMC4338339 DOI: 10.1261/rna.047258.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The first stable complex formed during the assembly of spliceosomes onto pre-mRNA substrates in mammals includes U1 snRNP, which recognizes the 5' splice site, and the splicing factors SF1 and U2AF, which bind the branch point sequence, polypyrimidine tract, and 3' splice site. The 5' and 3' splice site complexes are thought to be joined together by protein-protein interactions mediated by factors that ensure the fidelity of the initial splice site recognition. In this study, we identified and characterized PRPF40B, a putative mammalian ortholog of the U1 snRNP-associated yeast splicing factor Prp40. PRPF40B is highly enriched in speckles with a behavior similar to splicing factors. We demonstrated that PRPF40B interacts directly with SF1 and associates with U2AF(65). Accordingly, PRPF40B colocalizes with these splicing factors in the cell nucleus. Splicing assays with reporter minigenes revealed that PRPF40B modulates alternative splice site selection. In the case of Fas regulation of alternative splicing, weak 5' and 3' splice sites and exonic sequences are required for PRPF40B function. Placing our data in a functional context, we also show that PRPF40B depletion increased Fas/CD95 receptor number and cell apoptosis, which suggests the ability of PRPF40B to alter the alternative splicing of key apoptotic genes to regulate cell survival.
Collapse
Affiliation(s)
| | | | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | | |
Collapse
|
12
|
Marechal D, Pereira PL, Duchon A, Herault Y. Dosage of the Abcg1-U2af1 region modifies locomotor and cognitive deficits observed in the Tc1 mouse model of Down syndrome. PLoS One 2015; 10:e0115302. [PMID: 25706610 PMCID: PMC4338106 DOI: 10.1371/journal.pone.0115302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/24/2014] [Indexed: 11/22/2022] Open
Abstract
Down syndrome (DS) results from one extra copy of human chromosome 21 and leads to several alterations including intellectual disabilities and locomotor defects. The transchromosomic Tc1 mouse model carrying an extra freely-segregating copy of human chromosome 21 was developed to better characterize the relation between genotype and phenotype in DS. The Tc1 mouse exhibits several locomotor and cognitive deficits related to DS. In this report we analyzed the contribution of the genetic dosage of 13 conserved mouse genes located between Abcg1 and U2af1, in the telomeric part of Hsa21. We used the Ms2Yah model carrying a deletion of the corresponding interval in the mouse genome to rescue gene dosage in the Tc1/Ms2Yah compound mice to determine how the different behavioral phenotypes are affected. We detected subtle changes with the Tc1/Ms2Yah mice performing better than the Tc1 individuals in the reversal paradigm of the Morris water maze. We also found that Tc1/Ms2Yah compound mutants performed better in the rotarod than the Tc1 mice. This data support the impact of genes from the Abcg1-U2af1 region as modifiers of Tc1-dependent memory and locomotor phenotypes. Our results emphasize the complex interactions between triplicated genes inducing DS features.
Collapse
Affiliation(s)
- Damien Marechal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Patricia Lopes Pereira
- Transgenese et Archivage Animaux Modèles, TAAM, CNRS, UPS44, 3B rue de la Férollerie 45071 Orléans, France
| | - Arnaud Duchon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 1 rue Laurent Fries, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Institut Clinique de la Souris, ICS, 1 rue Laurent Fries, 67404 Illkirch, France
- * E-mail:
| |
Collapse
|
13
|
Ilagan JO, Ramakrishnan A, Hayes B, Murphy ME, Zebari AS, Bradley P, Bradley RK. U2AF1 mutations alter splice site recognition in hematological malignancies. Genome Res 2015; 25:14-26. [PMID: 25267526 PMCID: PMC4317169 DOI: 10.1101/gr.181016.114] [Citation(s) in RCA: 208] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 09/25/2014] [Indexed: 01/30/2023]
Abstract
Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. U2AF1 mutations cause differential splicing of hundreds of genes, affecting biological pathways such as DNA methylation (DNMT3B), X chromosome inactivation (H2AFY), the DNA damage response (ATR, FANCA), and apoptosis (CASP8). We show that U2AF1 mutations alter the preferred 3' splice site motif in patients, in cell culture, and in vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1's zinc finger domains.
Collapse
Affiliation(s)
- Janine O Ilagan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Aravind Ramakrishnan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Division of Medical Oncology, School of Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Brian Hayes
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Michele E Murphy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Ahmad S Zebari
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Philip Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
| |
Collapse
|
14
|
Marzese DM, Liu M, Huynh JL, Hirose H, Donovan NC, Huynh KT, Kiyohara E, Chong K, Cheng D, Tanaka R, Morton DL, Barkhoudarian G, Kelly DF, Hoon DS. Brain metastasis is predetermined in early stages of cutaneous melanoma by CD44v6 expression through epigenetic regulation of the spliceosome. Pigment Cell Melanoma Res 2015; 28:82-93. [PMID: 25169209 PMCID: PMC4309554 DOI: 10.1111/pcmr.12307] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/12/2014] [Accepted: 08/12/2014] [Indexed: 12/20/2022]
Abstract
Melanoma brain metastasis (MBM) is frequent and has a very poor prognosis with no current predictive factors or therapeutic molecular targets. Our study unravels the molecular alterations of cell-surface glycoprotein CD44 variants during melanoma progression to MBM. High expression of CD44 splicing variant 6 (CD44v6) in primary melanoma (PRM) and regional lymph node metastases from AJCC Stage IIIC patients significantly predicts MBM development. The expression of CD44v6 also enhances the migration of MBM cells by hyaluronic acid and hepatocyte growth factor exposure. Additionally, CD44v6-positive MBM migration is reduced by blocking with a CD44v6-specific monoclonal antibody or knocking down CD44v6 by siRNA. ESRP1 and ESRP2 splicing factors correlate with CD44v6 expression in PRM, and ESRP1 knockdown significantly decreases CD44v6 expression. However, an epigenetic silencing of ESRP1 is observed in metastatic melanoma, specifically in MBM. In advanced melanomas, CD44v6 expression correlates with PTBP1 and U2AF2 splicing factors, and PTBP1 knockdown significantly decreases CD44v6 expression. Overall, these findings open a new avenue for understanding the high affinity of melanoma to progress to MBM, suggesting CD44v6 as a potential MBM-specific factor with theranostic utility for stratifying patients.
Collapse
Affiliation(s)
- Diego M. Marzese
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Michelle Liu
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Jamie L. Huynh
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Hajime Hirose
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Nicholas C. Donovan
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Kelly T. Huynh
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Eiji Kiyohara
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Kelly Chong
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - David Cheng
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Ryo Tanaka
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Donald L. Morton
- Division of Surgical Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Garni Barkhoudarian
- Brain Tumor Center & Pituitary Disorders Program, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Daniel F. Kelly
- Brain Tumor Center & Pituitary Disorders Program, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Dave S.B. Hoon
- Dept of Molecular Oncology, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404, USA
| |
Collapse
|
15
|
Abstract
Atypical chronic myeloid leukemia (aCML) and chronic neutrophilic leukemia (CNL) are rare myeloid neoplasms defined largely by morphologic criteria. The discovery of CSF3R mutations in aCML and CNL have prompted a more comprehensive genetic profiling of these disorders. These studies have revealed aCML to be a genetically more heterogeneous disease than CNL, however, several groups have reported that SETBP1 and ASXL1 mutations occur at a high frequency and carry prognostic value in both diseases. We also report a novel finding-our study reveals a high frequency of U2AF1 mutations at codon Q157 associated with CSF3R mutant myeloid neoplasms. Collectively, these findings will refine the WHO diagnostic criteria of aCML and CNL and help us understand the genetic lesions and dysregulated signaling pathways contributing to disease development. Novel therapies that emerge from these genetic findings will need to be investigated in the setting of a clinical trial to determine the safety and efficacy of targeting various oncogenic drivers, such as JAK1/2 inhibition in CSF3R-T618I-positive aCML and CNL. In summary, recent advances in the genetic characterization of CNL and aCML are instrumental toward the development of new lines of therapy for these rare leukemias that lack an established standard of care and are historically associated with a poor prognosis.
Collapse
MESH Headings
- Carrier Proteins/genetics
- Codon
- Hematology/methods
- Hematology/standards
- Humans
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/diagnosis
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Neutrophilic, Chronic/diagnosis
- Leukemia, Neutrophilic, Chronic/genetics
- Medical Oncology/methods
- Medical Oncology/standards
- Mutation
- Nuclear Proteins/genetics
- Prognosis
- Receptors, Colony-Stimulating Factor/genetics
- Repressor Proteins/genetics
- Ribonucleoproteins/genetics
- Signal Transduction
- Splicing Factor U2AF
Collapse
Affiliation(s)
- Kim-Hien T Dao
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR; and
| | - Jeffrey W Tyner
- Knight Cancer Institute, Department of Cell, Development and Cancer Biology, Oregon Health & Science University, Portland, OR
| |
Collapse
|
16
|
Ohta S, Yamamoto T. [Alternative splicing regulation during somatic cell reprogramming]. Seikagaku 2014; 86:807-811. [PMID: 25675823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
|
17
|
Shao C, Yang B, Wu T, Huang J, Tang P, Zhou Y, Zhou J, Qiu J, Jiang L, Li H, Chen G, Sun H, Zhang Y, Denise A, Zhang DE, Fu XD. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nat Struct Mol Biol 2014. [PMID: 25326705 DOI: 10.1038/nsmb2906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The U2AF heterodimer has been well studied for its role in defining functional 3' splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3' splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3' splice site associated either with the alternative exon, to cause exon skipping, or with the competing constitutive exon, to induce exon inclusion. We further demonstrate partial functional impairment with leukemia-associated mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states.
Collapse
Affiliation(s)
- Changwei Shao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Laboratoire de Recherche en Informatique, Institut de Génétique et Microbiologie I, Université Paris-Sud and Centre National de la Recherche Scientifique, Orsay, France
| | - Tongbin Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Jie Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Li Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Geng Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Alain Denise
- Laboratoire de Recherche en Informatique, Institut de Génétique et Microbiologie I, Université Paris-Sud and Centre National de la Recherche Scientifique, Orsay, France
| | - Dong-Er Zhang
- UC San Diego Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Xiang-Dong Fu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
18
|
Shen W, Clemente MJ, Hosono N, Yoshida K, Przychodzen B, Yoshizato T, Shiraishi Y, Miyano S, Ogawa S, Maciejewski JP, Makishima H. Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest 2014; 124:4529-38. [PMID: 25244093 DOI: 10.1172/jci74747] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/10/2014] [Indexed: 12/13/2022] Open
Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is a nonmalignant clonal disease of hematopoietic stem cells that is associated with hemolysis, marrow failure, and thrombophilia. PNH has been considered a monogenic disease that results from somatic mutations in the gene encoding PIGA, which is required for biosynthesis of glycosylphosphatidylinisotol-anchored (GPI-anchored) proteins. The loss of certain GPI-anchored proteins is hypothesized to provide the mutant clone with an extrinsic growth advantage, but some features of PNH argue that there are intrinsic drivers of clonal expansion. Here, we performed whole-exome sequencing of paired PNH+ and PNH- fractions on samples taken from 12 patients as well as targeted deep sequencing of an additional 36 PNH patients. We identified additional somatic mutations that resulted in a complex hierarchical clonal architecture, similar to that observed in myeloid neoplasms. In addition to mutations in PIGA, mutations were found in genes known to be involved in myeloid neoplasm pathogenesis, including TET2, SUZ12, U2AF1, and JAK2. Clonal analysis indicated that these additional mutations arose either as a subclone within the PIGA-mutant population, or prior to PIGA mutation. Together, our data indicate that in addition to PIGA mutations, accessory genetic events are frequent in PNH, suggesting a stepwise clonal evolution derived from a singular stem cell clone.
Collapse
|
19
|
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. New Phytol 2014; 203:424-436. [PMID: 24749484 DOI: 10.1111/nph.12821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
20
|
Tian J, Zhu B, Tian Y, Zhong R, Miao X, Wang L. [Association between pancreatic cancer risk and the interaction of U2AF65 gene polymorphisms and smoking]. Zhonghua Liu Xing Bing Xue Za Zhi 2014; 35:710-713. [PMID: 25174478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To determine the association between U2 small nuclear ribonucleoprotein auxiliary factor 35/65 (U2AF35 and U2AF65) and pancreatic cancer (PC). METHODS A two-stage analysis case-control study was conducted. Four candidate tag single nucleotide polymorphisms (tagSNPs) were genotyped by Taqman Openarray assay in a screening population living in Central China (298 PC cases and 525 controls). Thereafter, rs310445 in U2AF65 was genotyped by TaqMan real-time polymerase chain reaction (RT-PCR) in a validation Chinese Han population from Beijing (413 cases and 557 controls). RESULTS rs310445 in U2AF65 gene was significantly associated with PC in both screened population and combined population. Subjects with C allele had a higher risk of PC compared to those with the TT genotype, with OR of 1.31 (95%CI:1.07-1.60, P = 0.010) for the combined population. A synergic effect of smoking and C allele of rs310445 was also observed in the combined population, with Synergic Index of 2.08 (95% CI:1.37-2.78) in the combined population. CONCLUSION Our findings suggested the interaction between smoking and U2AF65 might play a role in PC. These findings should be confirmed by further independently large-scale population studies.
Collapse
Affiliation(s)
- Jing Tian
- Department of Epidemiology and Biostatistics,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College,Beijing 100005, China
| | - Beibei Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology
| | - Yao Tian
- Department of Epidemiology and Biostatistics,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College,Beijing 100005, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology
| | | | - Li Wang
- Department of Epidemiology and Biostatistics,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College,Beijing 100005, China.
| |
Collapse
|
21
|
Jang YH, Park HY, Lee KC, Thu MP, Kim SK, Suh MC, Kang H, Kim JK. A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana. Plant J 2014; 78:591-603. [PMID: 24580679 DOI: 10.1111/tpj.12491] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 05/20/2023]
Abstract
During initial spliceosome assembly, SF1 binds to intron branch points and interacts with U2 snRNP auxiliary factor 65 (U2AF65). Here, we present evidence indicating that AtSF1, the Arabidopsis SF1 homolog, interacts with AtU2AF65a and AtU2AF65b, the Arabidopsis U2AF65 homologs. A mutant allele of AtSF1 (At5g51300) that contains a T-DNA insertion conferred pleiotropic developmental defects, including early flowering and abnormal sensitivity to abscisic acid. An AtSF1 promoter-driven GUS reporter assay showed that AtSF1 promoter activity was temporally and spatially altered, and that full AtSF1 promoter activity required a significant proportion of the coding region. DNA chip analyses showed that only a small proportion of the transcriptome was altered by more than twofold in either direction in the AtSF1 mutant. Expression of the mRNAs of many heat shock proteins was more than fourfold higher in the mutant strain; these mRNAs were among those whose expression was increased most in the mutant strain. An RT-PCR assay revealed an altered alternative splicing pattern for heat shock transcription factor HsfA2 (At2g26150) in the mutant; this altered splicing is probably responsible for the increased expression of the target genes induced by HsfA2. Altered alternative splicing patterns were also detected for the transcripts of other genes in the mutant strain. These results suggest that AtSF1 has functional similarities to its yeast and metazoan counterparts.
Collapse
Affiliation(s)
- Yun Hee Jang
- Plant Signaling Network Research Center, School of Life Sciences and Biotechnology, Korea University, Seoul, 136-701, Korea
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One 2014; 9:e87361. [PMID: 24498085 PMCID: PMC3909098 DOI: 10.1371/journal.pone.0087361] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 12/20/2013] [Indexed: 01/23/2023] Open
Abstract
Although recurrent somatic mutations in the splicing factor U2AF1 (also known as U2AF35) have been identified in multiple cancer types, the effects of these mutations on the cancer transcriptome have yet to be fully elucidated. Here, we identified splicing alterations associated with U2AF1 mutations across distinct cancers using DNA and RNA sequencing data from The Cancer Genome Atlas (TCGA). Using RNA-Seq data from 182 lung adenocarcinomas and 167 acute myeloid leukemias (AML), in which U2AF1 is somatically mutated in 3-4% of cases, we identified 131 and 369 splicing alterations, respectively, that were significantly associated with U2AF1 mutation. Of these, 30 splicing alterations were statistically significant in both lung adenocarcinoma and AML, including three genes in the Cancer Gene Census, CTNNB1, CHCHD7, and PICALM. Cell line experiments expressing U2AF1 S34F in HeLa cells and in 293T cells provide further support that these altered splicing events are caused by U2AF1 mutation. Consistent with the function of U2AF1 in 3' splice site recognition, we found that S34F/Y mutations cause preferences for CAG over UAG 3' splice site sequences. This report demonstrates consistent effects of U2AF1 mutation on splicing in distinct cancer cell types.
Collapse
Affiliation(s)
- Angela N. Brooks
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Peter S. Choi
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Luc de Waal
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Tanaz Sharifnia
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marcin Imielinski
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Gordon Saksena
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Chandra Sekhar Pedamallu
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Andrey Sivachenko
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mara Rosenberg
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Juliann Chmielecki
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Michael S. Lawrence
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David S. DeLuca
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Gad Getz
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
23
|
Litvinova LS, Mazunin IO, Gutsol AA, Sokhonevich NA, Khaziakhmatova OG, Kofanova KA. [Dose-response effect of steroid hormones on the Gfi1 and U2afil4 gene expression in T lymphocytes at different stages of differentiation]. Mol Biol (Mosk) 2014; 47:656-66. [PMID: 24466755 DOI: 10.7868/s0026898413040095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Alternative splicing of Ptprc gene is a key event in memory T cell differentiation. This gene encodes transmembrane tyrosine phosphatase CD45. One of potential mechanisms of alternative splicing regulation is based on antagonistic effects of auxiliary splicing factor U2AF26 and transcription factor Gfi1. These two proteins regulate antigen-dependent T cell activation. We have shown that steroid hormones have different effects on U2af1l4 and Gfi1 transcription regulation in dissimilar differentiation stage cell culture, subjected to antigen-independent stimulation. Low concentrations of glucocorticoid (Dex) and female sex hormone (Est) can activate expression of U2af1l4 in re-stimulated cells that probably induce terminal receptor CD45 isoforms formation mechanism, whereas high doses of hormones inhibit the process. In the same conditions Dex in a wide range of concentrations (10(-5)-10(-7) M) and Est (10(-6) and 10(-7) M) activate U2af1l4 gene expression that probably leads to "surrogate memory T cells" formation. Dose dependent testosterone (Test) effect is opposite to Est and Dex effect on priming (CD45RO+) and naive (CD45RA+) lymphocytes. The role of steroid hormones in memory T cell differentiation in antigen-independent stimulation conditions is of great interest for the understanding of chronic hormonal and immune disbalance mechanisms.
Collapse
|
24
|
Patnaik MM, Padron E, LaBorde RR, Lasho TL, Finke CM, Hanson CA, Hodnefield JM, Knudson RA, Ketterling RP, Al-kali A, Pardanani A, Ali NA, Komrokji RS, Tefferi A. Mayo prognostic model for WHO-defined chronic myelomonocytic leukemia: ASXL1 and spliceosome component mutations and outcomes. Leukemia 2013; 27:1504-10. [PMID: 23531518 DOI: 10.1038/leu.2013.88] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
We evaluated the prognostic relevance of several clinical and laboratory parameters in 226 Mayo Clinic patients with chronic myelomonocytic leukemia (CMML): 152 (67%) males and median age 71 years. At a median follow-up of 15 months, 166 (73%) deaths and 33 (14.5%) leukemic transformations were documented. In univariate analysis, significant risk factors for survival included anemia, thrombocytopenia, increased levels of white blood cells, absolute neutrophils, absolute monocyte count (AMC), absolute lymphocytes, peripheral blood and bone marrow blasts, and presence of circulating immature myeloid cells (IMCs). Spliceosome component (P=0.4) and ASXL1 mutations (P=0.37) had no impact survival. On multivariable analysis, increased AMC (>10 × 10(9)/l, relative risk (RR) 2.5, 95% confidence interval (CI) 1.7-3.8), presence of circulating IMC (RR 2.0, 95% CI 1.4-2.7), decreased hemoglobin (<10 g/dl, RR 1.6, 99% CI 1.2-2.2) and decreased platelet count (<100 × 10(9)/l, RR 1.4, 99% CI 1.0-1.9) remained significant. Using these four risk factors, a new prognostic model for overall (high risk, RR 4.4, 95% CI 2.9-6.7; intermediate risk, RR 2.0, 95% CI 1.4-2.9) and leukemia-free survival (high risk, RR 4.9, 95% CI 1.9-12.8; intermediate risk, RR 2.6, 95% CI 1.1-5.9) performed better than other conventional risk models and was validated in an independent cohort of 268 CMML patients.
Collapse
Affiliation(s)
- M M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Patnaik MM, Lasho TL, Finke CM, Hanson CA, Hodnefield JM, Knudson RA, Ketterling RP, Pardanani A, Tefferi A. Spliceosome mutations involving SRSF2, SF3B1, and U2AF35 in chronic myelomonocytic leukemia: prevalence, clinical correlates, and prognostic relevance. Am J Hematol 2013; 88:201-6. [PMID: 23335386 DOI: 10.1002/ajh.23373] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/22/2012] [Accepted: 11/26/2012] [Indexed: 01/19/2023]
Abstract
SRSF2, SF3B1, and U2AF35 (U2AF1) are the three most frequent genes involved with spliceosome mutations in myeloid malignancies. SF3B1 mutations are most frequent (~80%) in myelodysplastic syndromes (MDS) with ring sideroblasts (RS) but lack prognostic relevance. SRSF2 mutations are associated with shortened overall (OS) and leukemia-free survival (LFS) in both MDS and myelofibrosis. In this study of 226 patients with chronic myelomonocytic leukemia (CMML), mutational frequencies were 40% for SRSF2 (all affecting P95), 6% for SF3B1 (primarily K700E) and 9% for U2AF35 (mostly S34F and Q157P/R). These mutations were mutually exclusive and 54% of the patients displayed at least one mutation. The three mutation groups were phenotypically similar, with the exception of higher RS% (P < 0.0001) in patients with SF3B1 mutations. At a median follow-up of 15 months, 176 (78%) deaths and 32 (14%) leukemic transformations were documented. OS (median survivals of 17, 16, 17, and 20 months; P = 0.48) and LFS (leukemic transformation rates of 17, 13, 15, and 5%; P = 0.63) were similar among patients with none of the three mutations, SRSF2, SF3B1, or U2AF35 mutations, respectively. We conclude that SRSF2 is the most frequently mutated spliceosome gene in CMML but neither it nor SF3B1 or U2AF35 mutations are prognostically relevant.
Collapse
Affiliation(s)
- Mrinal M Patnaik
- Division of Hematology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe N, Ule J. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 2013; 152:453-66. [PMID: 23374342 PMCID: PMC3629564 DOI: 10.1016/j.cell.2012.12.023] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 09/22/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
Abstract
There are ~650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion. Here, we present a mechanism for protecting the human transcriptome from the aberrant exonization of transposable elements. Quantitative iCLIP data show that the RNA-binding protein hnRNP C competes with the splicing factor U2AF65 at many genuine and cryptic splice sites. Loss of hnRNP C leads to formation of previously suppressed Alu exons, which severely disrupt transcript function. Minigene experiments explain disease-associated mutations in Alu elements that hamper hnRNP C binding. Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease.
Collapse
Affiliation(s)
- Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Mojca Tajnik
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1104 Ljubljana, Slovenia
| | - Iñigo Martincorena
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Isabelle Stévant
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alejandro Reyes
- EMBL, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Anders
- EMBL, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nicholas M. Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, Gower Street, London WC1E 6BT, UK
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- Okinawa Institute for Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| |
Collapse
|
27
|
Wang W, Maucuer A, Gupta A, Manceau V, Thickman KR, Bauer WJ, Kennedy SD, Wedekind JE, Green MR, Kielkopf CL. Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure 2012; 21:197-208. [PMID: 23273425 DOI: 10.1016/j.str.2012.10.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/26/2012] [Accepted: 10/26/2012] [Indexed: 11/15/2022]
Abstract
The essential splicing factors U2AF⁶⁵ and SF1 cooperatively bind consensus sequences at the 3' end of introns. Phosphorylation of SF1 on a highly conserved "SPSP" motif enhances its interaction with U2AF⁶⁵ and the pre-mRNA. Here, we reveal that phosphorylation induces essential conformational changes in SF1 and in the SF1/U2AF⁶⁵/3' splice site complex. Crystal structures of the phosphorylated (P)SF1 domain bound to the C-terminal domain of U2AF⁶⁵ at 2.29 Å resolution and of the unphosphorylated SF1 domain at 2.48 Å resolution demonstrate that phosphorylation induces a disorder-to-order transition within a previously unknown SF1/U2AF⁶⁵ interface. We find by small-angle X-ray scattering that the local folding of the SPSP motif transduces into global conformational changes in the nearly full-length (P)SF1/U2AF⁶⁵/3' splice site assembly. We further determine that SPSP phosphorylation and the SF1/U2AF⁶⁵ interface are essential in vivo. These results offer a structural prototype for phosphorylation-dependent control of pre-mRNA splicing factors.
Collapse
Affiliation(s)
- Wenhua Wang
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Qiu ZR, Chico L, Chang J, Shuman S, Schwer B. Genetic interactions of hypomorphic mutations in the m7G cap-binding pocket of yeast nuclear cap binding complex: an essential role for Cbc2 in meiosis via splicing of MER3 pre-mRNA. RNA 2012; 18:1996-2011. [PMID: 23002122 PMCID: PMC3479390 DOI: 10.1261/rna.033746.112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 08/03/2012] [Indexed: 05/17/2023]
Abstract
Nuclear cap binding protein complex (CBC) is a heterodimer of a small subunit (Cbc2 in yeast) that binds the m(7)G cap and a large subunit (Sto1 in yeast) that interacts with karyopherins. In order to probe the role of cap recognition in yeast CBC function, we introduced alanine mutations (Y24A, F91A, D120A, D122A, R129A, and R133A) and N-terminal deletions (NΔ21 and NΔ42) in the cap-binding pocket of Cbc2. These lesions had no effect on vegetative growth, but they ameliorated the cold-sensitivity of tgs1Δ cells that lack trimethylguanosine caps (a phenotype attributed to ectopic association of CBC with the m(7)G cap of the normally TMG-capped U1 snRNA), thereby attesting to their impact on cap binding in vivo. Further studies of the Cbc2-Y24A variant revealed synthetic lethality or sickness with null mutations of proteins involved in early steps of spliceosome assembly (Nam8, Mud1, Swt21, Mud2, Ist3, and Brr1) and with otherwise benign mutations of Msl5, the essential branchpoint binding protein. Whereas the effects of weakening CBC-cap interactions are buffered by other actors in the splicing pathway during mitotic growth, the NΔ42 allele causes a severe impediment to yeast sporulation and meiosis. RNA analysis revealed a selective defect in the splicing of MER3 and SAE3 transcripts in cbc2-NΔ42 diploids during attempted sporulation. An intronless MER3 cDNA fully restored sporulation and spore viability in the cbc2-NΔ42 strain, signifying that MER3 splicing is a limiting transaction. These studies reveal a new level of splicing control during meiosis that is governed by nuclear CBC.
Collapse
Affiliation(s)
- Zhicheng R. Qiu
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Lidia Chico
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Jonathan Chang
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| |
Collapse
|
29
|
Qian J, Yao DM, Lin J, Qian W, Wang CZ, Chai HY, Yang J, Li Y, Deng ZQ, Ma JC, Chen XX. U2AF1 mutations in Chinese patients with acute myeloid leukemia and myelodysplastic syndrome. PLoS One 2012; 7:e45760. [PMID: 23029227 PMCID: PMC3446943 DOI: 10.1371/journal.pone.0045760] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 08/24/2012] [Indexed: 12/22/2022] Open
Abstract
Somatic mutations of U2AF1 gene have recently been identified in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). In this study, we analyzed the frequency and clinical impact of U2AF1 mutations in a cohort of 452 Chinese patients with myeloid neoplasms. Mutations in U2AF1 were found in 2.5% (7/275) of AML and 6.3% (6/96) of MDS patients, but in none of 81 CML. All mutations were heterozygous missense mutations affecting codon S34 or Q157. There was no significant association of U2AF1 mutation with blood parameters, FAB subtypes, karyotypes and other gene mutations in AML. The overall survival (OS) of AML patients with U2AF1 mutation (median 3 months) was shorter than those without mutation (median 7 months) (P = 0.035). No difference in the OS was observed between MDS patients with and without U2AF1 mutations. Our data show that U2AF1 mutation is a recurrent event at a low frequency in AML and MDS.
Collapse
Affiliation(s)
- Jun Qian
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Dong-ming Yao
- Department of Laboratory Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jiang Lin
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
- * E-mail: (JL); (WQ)
| | - Wei Qian
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
- * E-mail: (JL); (WQ)
| | - Cui-zhu Wang
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Hai-yan Chai
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jing Yang
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Yun Li
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Zhao-qun Deng
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Ji-chun Ma
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Xing-xing Chen
- Department of Haematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| |
Collapse
|
30
|
Day IS, Golovkin M, Palusa SG, Link A, Ali GS, Thomas J, Richardson DN, Reddy ASN. Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing. Plant J 2012; 71:936-47. [PMID: 22563826 DOI: 10.1111/j.1365-313x.2012.05042.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
SR45 is a serine/arginine-rich (SR)-like protein with two arginine/serine-rich (RS) domains. We have previously shown that SR45 regulates alternative splicing (AS) by differential selection of 5' and 3' splice sites. However, it is unknown how SR45 regulates AS. To gain mechanistic insights into the roles of SR45 in splicing, we screened a yeast two-hybrid library with SR45. This screening resulted in the isolation of two spliceosomal proteins, U1-70K and U2AF(35) b that are known to function in 5' and 3' splice site selection, respectively. This screen not only confirmed our prior observation that U1-70K and SR45 interact, but also helped to identify an additional interacting partner (U2AF(35) ). In vitro and in vivo analyses revealed an interaction of SR45 with both paralogs of U2AF(35) . Furthermore, we show that the RS1 and RS2 domains of SR45, and not the RNA recognition motif (RRM) domain, associate independently with both U2AF(35) proteins. Interaction studies among U2AF(35) paralogs and between U2AF(35) and U1-70K revealed that U2AF(35) can form homo- or heterodimers and that U2AF(35) proteins can associate with U1-70K. Using RNA probes from SR30 intron 10, whose splicing is altered in the sr45 mutant, we show that SR45 and U2AF(35) b bind to different parts of the intron, with a binding site for SR45 in the 5' region and two binding regions, each ending with a known 3' splice site, for U2AF(35) b. These results suggest that SR45 recruits U1snRNP and U2AF to 5' and 3' splice sites, respectively, by interacting with pre-mRNA, U1-70K and U2AF(35) and modulates AS.
Collapse
Affiliation(s)
- Irene S Day
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Ortuño-Pineda C, Galindo-Rosales JM, Calderón-Salinas JV, Villegas-Sepúlveda N, Saucedo-Cárdenas O, De Nova-Ocampo M, Valdés J. Binding of hnRNP H and U2AF65 to respective G-codes and a poly-uridine tract collaborate in the N50-5'ss selection of the REST N exon in H69 cells. PLoS One 2012; 7:e40315. [PMID: 22792276 PMCID: PMC3390395 DOI: 10.1371/journal.pone.0040315] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 06/04/2012] [Indexed: 11/19/2022] Open
Abstract
The splicing of the N exon in the pre-mRNA coding for the RE1-silencing transcription factor (REST) results in a truncated protein that modifies the expression pattern of some of its target genes. A weak 3'ss, three alternative 5'ss (N4-, N50-, and N62-5'ss) and a variety of putative target sites for splicing regulatory proteins are found around the N exon; two GGGG codes (G2-G3) and a poly-Uridine tract (N-PU) are found in front of the N50-5'ss. In this work we analyzed some of the regulatory factors and elements involved in the preferred selection of the N50-5'ss (N50 activation) in the small cell lung cancer cell line H69. Wild type and mutant N exon/β-globin minigenes recapitulated N50 exon splicing in H69 cells, and showed that the N-PU and the G2-G3 elements are required for N50 exon splicing. Biochemical and knockdown experiments identified these elements as U2AF65 and hnRNP H targets, respectively, and that they are also required for N50 exon activation. Compared to normal MRC5 cells, and in keeping with N50 exon activation, U2AF65, hnRNP H and other splicing factors were highly expressed in H69 cells. CLIP experiments revealed that hnRNP H RNA-binding occurs first and is a prerequisite for U2AF65 RNA binding, and EMSA and CLIP experiments suggest that U2AF65-RNA recognition displaces hnRNP H and helps to recruit other splicing factors (at least U1 70K) to the N50-5'ss. Our results evidenced novel hnRNP H and U2AF65 functions: respectively, U2AF65-recruiting to a 5'ss in humans and the hnRNP H-displacing function from two juxtaposed GGGG codes.
Collapse
Affiliation(s)
- Carlos Ortuño-Pineda
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del I.P.N., México D.F., México
| | | | | | - Nicolás Villegas-Sepúlveda
- D1epartamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., México D.F., México
| | - Odila Saucedo-Cárdenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo Léon, Monterrey N.L. México
- División de Genética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey N.L., México
| | - Mónica De Nova-Ocampo
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía-IPN, México D.F., México
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del I.P.N., México D.F., México
- * E-mail:
| |
Collapse
|
32
|
Ogawa S. [Deregulated splicing machinery in myelodysplastic syndromes]. Rinsho Ketsueki 2012; 53:493-496. [PMID: 22728550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
|
33
|
Wang C, Wilson-Berry L, Schedl T, Hansen D. TEG-1 CD2BP2 regulates stem cell proliferation and sex determination in the C. elegans germ line and physically interacts with the UAF-1 U2AF65 splicing factor. Dev Dyn 2012; 241:505-21. [PMID: 22275078 PMCID: PMC3466600 DOI: 10.1002/dvdy.23735] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2012] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND For a stem cell population to exist over an extended period, a balance must be maintained between self-renewing (proliferating) and differentiating daughter cells. Within the Caenorhabditis elegans germ line, this balance is controlled by a genetic regulatory pathway, which includes the canonical Notch signaling pathway. RESULTS Genetic screens identified the gene teg-1 as being involved in regulating the proliferation versus differentiation decision in the C. elegans germ line. Cloning of TEG-1 revealed that it is a homolog of mammalian CD2BP2, which has been implicated in a number of cellular processes, including in U4/U6.U5 tri-snRNP formation in the pre-mRNA splicing reaction. The position of teg-1 in the genetic pathway regulating the proliferation versus differentiation decision, its single mutant phenotype, and its enrichment in nuclei, all suggest TEG-1 also functions as a splicing factor. TEG-1, as well as its human homolog, CD2BP2, directly bind to UAF-1 U2AF65, a component of the U2 auxiliary factor. CONCLUSIONS TEG-1 functions as a splicing factor and acts to regulate the proliferation versus meiosis decision. The interaction of TEG-1 CD2BP2 with UAF-1 U2AF65, combined with its previously described function in U4/U6.U5 tri-snRNP, suggests that TEG-1 CD2BP2 functions in two distinct locations in the splicing cascade.
Collapse
Affiliation(s)
- Chris Wang
- University of Calgary, Department of Biological Sciences, Alberta, Calgary, Canada
| | | | | | | |
Collapse
|
34
|
Corrionero A, Raker VA, Izquierdo JM, Valcárcel J. Strict 3' splice site sequence requirements for U2 snRNP recruitment after U2AF binding underlie a genetic defect leading to autoimmune disease. RNA 2011; 17:401-411. [PMID: 21233219 PMCID: PMC3039140 DOI: 10.1261/rna.2444811] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 11/10/2010] [Indexed: 05/30/2023]
Abstract
We report that the 3' splice site associated with the alternatively spliced exon 6 of the Fas receptor CD95 displays strict sequence requirements and that a mutation that disrupts this particular sequence arrangement leads to constitutive exon 6 skipping in a patient suffering from autoimmune lymphoproliferative syndrome (ALPS). Specifically, we find an absolute requirement for RCAG/G at the 3' splice site (where R represents purine, and / indicates the intron/exon boundary) and the balance between exon inclusion and skipping is exquisitely sensitive to single nucleotide variations in the uridine content of the upstream polypyrimidine (Py)-tract. Biochemical experiments revealed that the ALPS patient mutation reduces U2 snRNP recruitment to the 3' splice site region and that this effect cannot be explained by decreased interaction with the U2 snRNP Auxiliary Factor U2AF, whose 65- and 35-kDa subunits recognize the Py-tract and 3' splice site AG, respectively. The effect of the mutation, which generates a tandem of two consecutive AG dinucleotides at the 3' splice site, can be suppressed by increasing the distance between the AGs, mutating the natural 3' splice site AG or increasing the uridine content of the Py-tract at a position distal from the 3' splice site. The suppressive effects of these additional mutations correlate with increased recruitment of U2 snRNP but not with U2AF binding, again suggesting that the strict architecture of Fas intron 5 3' splice site region is tuned to regulate alternative exon inclusion through modulation of U2 snRNP assembly after U2AF binding.
Collapse
|
35
|
Gupta A, Jenkins JL, Kielkopf CL. RNA induces conformational changes in the SF1/U2AF65 splicing factor complex. J Mol Biol 2011; 405:1128-38. [PMID: 21146534 PMCID: PMC3037027 DOI: 10.1016/j.jmb.2010.11.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/02/2010] [Accepted: 11/27/2010] [Indexed: 10/18/2022]
Abstract
Spliceosomes assemble on pre-mRNA splice sites through a series of dynamic ribonucleoprotein complexes, yet the nature of the conformational changes remains unclear. Splicing factor 1 (SF1) and U2 auxiliary factor (U2AF(65)) cooperatively recognize the 3' splice site during the initial stages of pre-mRNA splicing. Here, we used small-angle X-ray scattering to compare the molecular dimensions and ab initio shape restorations of SF1 and U2AF(65) splicing factors, as well as the SF1/U2AF(65) complex in the absence and presence of AdML (adenovirus major late) splice site RNAs. The molecular dimensions of the SF1/U2AF(65)/RNA complex substantially contracted by 15 Å in the maximum dimension, relative to the SF1/U2AF(65) complex in the absence of RNA ligand. In contrast, no detectable changes were observed for the isolated SF1 and U2AF(65) splicing factors or their individual complexes with RNA, although slight differences in the shapes of their molecular envelopes were apparent. We propose that the conformational changes that are induced by assembly of the SF1/U2AF(65)/RNA complex serve to position the pre-mRNA splice site optimally for subsequent stages of splicing.
Collapse
Affiliation(s)
- Ankit Gupta
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | | | | |
Collapse
|
36
|
Abstract
Yeast and human Tgs1 are orthologous RNA cap (guanine-N2) methyltransferases that convert m(7)G caps into the 2,2,7-trimethylguanosine (TMG) caps characteristic of spliceosomal snRNAs. TMG caps are dispensable for vegetative yeast growth, but are essential in the absence of Mud2, the putative yeast homolog of human splicing factor U2AF. Here we exploited the synthetic lethal interactions of tgs1Delta and mud2Delta mutations to identify essential structural features of the Tgs1 and Mud2 proteins. Thirty-two new mutations were introduced into human Tgs1 and surveyed for their effects on function in vivo in yeast and on the two sequential guanine-N2 methylation reactions in vitro. The structure-function data highlight a strictly essential pi-cation interaction between Trp766 and the m(7)G base and a network of important enzymic contacts to the cap triphosphate via Lys646, Tyr771, Arg807, and Lys836. Mud2 is a 527-amino acid polypeptide composed of a hydrophilic N-terminal domain and a C-terminal RRM domain. We found that the RRM domain is necessary but not sufficient for Mud2 function in complementing growth of tgs1Delta mud2Delta and mud1Delta mud2Delta strains. Other changes in Mud2 elicited distinct phenotypes in tgs1Delta versus mud1Delta backgrounds. mud2Delta also caused a severe growth defect in cells lacking the Tgs1-binding protein encoded by the nonessential gene YNR004w (now renamed SWM2, synthetic with mud2Delta). Mud2 mutational effects in the swm2Delta background paralleled those for mud1Delta. The requirements for Mud2 function are apparently more stringent when yeast cells lack TMG caps than when they lack Mud1 or Swm2.
Collapse
Affiliation(s)
- Jonathan Chang
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | | | | |
Collapse
|
37
|
de Chiara C, Menon RP, Strom M, Gibson TJ, Pastore A. Phosphorylation of S776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors. PLoS One 2009; 4:e8372. [PMID: 20037628 PMCID: PMC2791216 DOI: 10.1371/journal.pone.0008372] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 11/16/2009] [Indexed: 12/02/2022] Open
Abstract
Ataxin-1 (Atx1), a member of the polyglutamine (polyQ) expanded protein family, is responsible for spinocerebellar ataxia type 1. Requirements for developing the disease are polyQ expansion, nuclear localization and phosphorylation of S776. Using a combination of bioinformatics, cell and structural biology approaches, we have identified a UHM ligand motif (ULM), present in proteins associated with splicing, in the C-terminus of Atx1 and shown that Atx1 interacts with and influences the function of the splicing factor U2AF65 via this motif. ULM comprises S776 of Atx1 and overlaps with a nuclear localization signal and a 14-3-3 binding motif. We demonstrate that phosphorylation of S776 provides the molecular switch which discriminates between 14-3-3 and components of the spliceosome. We also show that an S776D Atx1 mutant previously designed to mimic phosphorylation is unsuitable for this aim because of the different chemical properties of the two groups. Our results indicate that Atx1 is part of a complex network of interactions with splicing factors and suggest that development of the pathology is the consequence of a competition of aggregation with native interactions. Studies of the interactions formed by non-expanded Atx1 thus provide valuable hints for understanding both the function of the non-pathologic protein and the causes of the disease.
Collapse
Affiliation(s)
- Cesira de Chiara
- National Institute for Medical Research, Medical Research Council, London, United Kingdom
| | - Rajesh P. Menon
- National Institute for Medical Research, Medical Research Council, London, United Kingdom
| | - Molly Strom
- National Institute for Medical Research, Medical Research Council, London, United Kingdom
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Annalisa Pastore
- National Institute for Medical Research, Medical Research Council, London, United Kingdom
- * E-mail:
| |
Collapse
|
38
|
Haraguchi N, Tani T. [Analysis of the regulatory mechanism for the constitutive splicing using molecular genetics in fission yeast]. Tanpakushitsu Kakusan Koso 2009; 54:2038-2043. [PMID: 21089614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
|
39
|
Ohno M. [Control of RNA distribution between the nucleus and cytoplasm]. Tanpakushitsu Kakusan Koso 2009; 54:2114-2120. [PMID: 21089627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
|
40
|
Ma L, Horvitz HR. Mutations in the Caenorhabditis elegans U2AF large subunit UAF-1 alter the choice of a 3' splice site in vivo. PLoS Genet 2009; 5:e1000708. [PMID: 19893607 PMCID: PMC2762039 DOI: 10.1371/journal.pgen.1000708] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
The removal of introns from eukaryotic RNA transcripts requires the activities of five multi-component ribonucleoprotein complexes and numerous associated proteins. The lack of mutations affecting splicing factors essential for animal survival has limited the study of the in vivo regulation of splicing. From a screen for suppressors of the Caenorhabditis elegans unc-93(e1500) rubberband Unc phenotype, we identified mutations in genes that encode the C. elegans orthologs of two splicing factors, the U2AF large subunit (UAF-1) and SF1/BBP (SFA-1). The uaf-1(n4588) mutation resulted in temperature-sensitive lethality and caused the unc-93 RNA transcript to be spliced using a cryptic 3′ splice site generated by the unc-93(e1500) missense mutation. The sfa-1(n4562) mutation did not cause the utilization of this cryptic 3′ splice site. We isolated four uaf-1(n4588) intragenic suppressors that restored the viability of uaf-1 mutants at 25°C. These suppressors differentially affected the recognition of the cryptic 3′ splice site and implicated a small region of UAF-1 between the U2AF small subunit-interaction domain and the first RNA recognition motif in affecting the choice of 3′ splice site. We constructed a reporter for unc-93 splicing and using site-directed mutagenesis found that the position of the cryptic splice site affects its recognition. We also identified nucleotides of the endogenous 3′ splice site important for recognition by wild-type UAF-1. Our genetic and molecular analyses suggested that the phenotypic suppression of the unc-93(e1500) Unc phenotype by uaf-1(n4588) and sfa-1(n4562) was likely caused by altered splicing of an unknown gene. Our observations provide in vivo evidence that UAF-1 can act in regulating 3′ splice-site choice and establish a system that can be used to investigate the in vivo regulation of RNA splicing in C. elegans. Eukaryotic genes contain intervening intronic sequences that must be removed from pre-mRNA transcripts by RNA splicing to generate functional messenger RNAs. While studying genes that encode and control a presumptive muscle potassium channel complex in the nematode Caenorhabditis elegans, we found that mutations in two splicing factors, the U2AF large subunit and SF1/BBP suppress the rubberband Unc phenotype caused by a rare missense mutation in the gene unc-93. Mutations affecting the U2AF large subunit caused the recognition of a cryptic 3′ splice site generated by the unc-93 mutation, providing in vivo evidence that the U2AF large subunit can affect splice-site selection. By contrast, an SF1/BBP mutation that suppressed the rubberband Unc phenotype did not cause splicing using this cryptic 3′ splice site. Our genetic studies identified a region of the U2AF large subunit important for its effect on 3′ splice-site choice. Our mutagenesis analysis of in vivo transgene splicing identified a positional effect on weak 3′ splice site selection and nucleotides of the endogenous 3′ splice site important for recognition. The system we have defined should facilitate future in vivo analyses of pre–mRNA splicing.
Collapse
Affiliation(s)
- Long Ma
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - H. Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
41
|
Tanabe N, Kimura A, Yoshimura K, Shigeoka S. Plant-specific SR-related protein atSR45a interacts with spliceosomal proteins in plant nucleus. Plant Mol Biol 2009; 70:241-52. [PMID: 19238562 DOI: 10.1007/s11103-009-9469-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/08/2009] [Indexed: 05/08/2023]
Abstract
Serine/arginine-rich (SR) protein and its homologues (SR-related proteins) are important regulators of constitutive and/or alternative splicing and other aspects of mRNA metabolism. To clarify the contribution of a plant-specific and stress-responsive SR-related protein, atSR45a, to splicing events, here we analyzed the interaction of atSR45a with the other splicing factors by conducting a yeast two-hybrid assay and a bimolecular fluorescence complementation analysis. The atSR45a-1a and -2 proteins, the presumed mature forms produced by alternative splicing of atSR45a, interacted with U1-70K and U2AF(35)b, splicing factors for the initial definition of 5' and 3' splice sites, respectively, in the early stage of spliceosome assembly. Both proteins also interacted with themselves, other SR proteins (atSR45 and atSCL28), and PRP38-like protein, a homologue of the splicing factor essential for cleavage of the 5' splice site. The mapping of deletion mutants of atSR45a proteins revealed that the C-terminal arginine/serine-rich (RS) domain of atSR45a proteins are required for the interaction with U1-70K, U2AF(35)b, atSR45, atSCL28, PRP38-like protein, and themselves, and the N-terminal RS domain enhances the interaction efficiency. Interestingly, the distinctive N-terminal extension in atSR45a-1a protein, but not atSR45a-2 protein, inhibited the interaction with these splicing factors. These findings suggest that the atSR45a proteins help to form the bridge between 5' and 3' splice sites in the spliceosome assembly and the efficiency of spliceosome formation is affected by the expression ratio of atSR45a-1a and atSR45a-2.
Collapse
Affiliation(s)
- Noriaki Tanabe
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara, Japan
| | | | | | | |
Collapse
|
42
|
Martins de Araújo M, Bonnal S, Hastings ML, Krainer AR, Valcárcel J. Differential 3' splice site recognition of SMN1 and SMN2 transcripts by U2AF and U2 snRNP. RNA 2009; 15:515-23. [PMID: 19244360 PMCID: PMC2661831 DOI: 10.1261/rna.1273209] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 01/14/2009] [Indexed: 05/20/2023]
Abstract
Spinal Muscular atrophy is a prevalent genetic disease caused by mutation of the SMN1 gene, which encodes the SMN protein involved in assembly of small nuclear ribonucleoprotein (snRNP) complexes. A paralog of the gene, SMN2, cannot provide adequate levels of functional SMN because exon 7 is skipped in a significant fraction of the mature transcripts. A C to T transition located at position 6 of exon 7 is critical for the difference in exon skipping between SMN1 and SMN2. Here we report that this nucleotide difference results in increased ultraviolet light-mediated crosslinking of the splicing factor U2AF(65) with the 3' splice site of SMN1 intron 6 in HeLa nuclear extract. U2 snRNP association, analyzed by native gel electrophoresis, is also more efficient on SMN1 than on SMN2, particularly under conditions of competition, suggesting more effective use of limiting factors. Two trans-acting factors implicated in SMN regulation, SF2/ASF and hnRNP A1, promote and repress, respectively, U2 snRNP recruitment to both RNAs. Interestingly, depending on the transcript and the regulatory factor, the effects on U2 binding not always correlate with changes in U2AF(65) crosslinking. Furthermore, blocking recognition of a Tra2-beta1-dependent splicing enhancer located in exon 7 inhibits U2 snRNP recruitment without affecting U2AF(65) crosslinking. Collectively, the results suggest that both U2AF binding and other steps of U2 snRNP recruitment can be control points in SMN splicing regulation.
Collapse
|
43
|
Corsini L, Sattler M. Backbone assignment of the UHM domain of Puf60 free and bound to five ligands. Biomol NMR Assign 2008; 2:211-214. [PMID: 19636907 DOI: 10.1007/s12104-008-9123-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 09/17/2008] [Indexed: 05/28/2023]
Abstract
U2AF homology motifs (UHM) are protein domains that bind peptidic UHM ligand motifs (ULM) and thus form an intricate network of interactions involved in splicing regulation. Here, we report the backbone assignment of the UHM domain of the splicing factor Puf60 as well as (1)H, (15)N chemical shifts upon binding of the ULM peptides U2AF(65) (85-112), SF1 (1-25), SF3b155 (194-229), SF3b155 (317-357), and Prp16 (201-238).
Collapse
Affiliation(s)
- Lorenzo Corsini
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, D-69117, Germany
| | | |
Collapse
|
44
|
Luo Y, Wang Y. [Alternative splicing of SmU2AF65 in Solanum melongena L]. Yi Chuan 2008; 30:1499-1505. [PMID: 19073560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
U2AF (U2 snRNP auxiliary factor), an essential auxiliary factor for pre-mRNA splicing, is highly conserved across species. Here we report the cloning and expression analysis of the homologous gene (SmU2AF65) encoding the large subunit of U2AF65 in Solanum melongena. Gene specific primers for Rapid Amplification of cDNA Ends (RACE) are designed according to the genomic sequence of eggplant BAC 77N19 and the full length cDNA of tobacco NpU2AF65 a and b. The full length cDNA of SmU2AF65 (GenBank accession No. EU543263) contains a complete open reading fragment encoding a 554 amino acid protein, and the deduced protein contains three conserved RNA recognition domains (RRM). RT-PCR assays indicate that SmU2AF65 is constitutively expressed in leaf, flower, and root, with a different transcript found in root originated from alternative splicing.
Collapse
Affiliation(s)
- Yan Luo
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | | |
Collapse
|
45
|
Abstract
Alternative splicing of transcripts in a signal-dependent manner has emerged as an important concept to ensure appropriate expression of splice variants under different conditions. Binding of the general splicing factor U2AF to splice sites preceding alternatively spliced exons has been suggested to be an important step for splice site recognition. For splicing to proceed, U2AF has to be replaced by other factors. We show here that U2AF interacts with the signal-dependent splice regulator Sam68 and that forced expression of Sam68 results in enhanced binding of the U2AF65 subunit to an alternatively spliced pre-mRNA sequence in vivo. Conversely, the rapid signal-induced and phosphorylation-dependent interference with Sam68 binding to RNA was accompanied by reduced pre-mRNA occupancy of U2AF in vivo. Our data suggest that Sam68 can affect splice site occupancy by U2AF in signal-dependent splicing. We propose that the induced release of U2AF from pre-mRNA provides a regulatory step to control alternative splicing.
Collapse
Affiliation(s)
- Anne Tisserant
- Forschungszentrum Karlsruhe GmbH, Institut für Toxikologie und Genetik, Karlsruhe, Germany
| | - Harald König
- Forschungszentrum Karlsruhe GmbH, Institut für Toxikologie und Genetik, Karlsruhe, Germany
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
46
|
Kent OA, Macmillan AM. Proteins specifically modified with a chemical nuclease as probes of RNA-protein interaction. Methods Mol Biol 2008; 488:191-200. [PMID: 18982292 DOI: 10.1007/978-1-60327-475-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Oliver A Kent
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | | |
Collapse
|
47
|
Abstract
Recognition of polypyrimidine (Py) tracts typically present between the branch point and the 3' splice site by the large subunit of the essential splicing factor U2AF is a key early step in pre-mRNA splicing. Diverse intronic sequence arrangements exist, however, including 3' splice sites lacking recognizable Py tracts, which raises the question of how general the requirement for U2AF is for various intron architectures. Our analysis of fission yeast introns in vivo has unexpectedly revealed that whereas introns lacking Py tracts altogether remain dependent on both subunits of U2AF, introns with long Py tracts, unconventionally positioned upstream of branch points, are unaffected by U2AF inactivation. Nevertheless, mutation of these Py tracts causes strong dependence on the large subunit U2AF59. We also find that Py tract diversity influences the requirement for the conserved C-terminal domain of U2AF59 (RNA recognition motif 3), which has been implicated in protein-protein interactions with other splicing factors. Together, these results suggest that in addition to Py tract binding by U2AF, supplementary mechanisms of U2AF recruitment and 3' splice site identification exist to accommodate diverse intron architectures, which have gone unappreciated in biochemical studies of model pre-mRNAs.
Collapse
Affiliation(s)
- Vinod Sridharan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | | |
Collapse
|
48
|
Matlin AJ, Southby J, Gooding C, Smith CWJ. Repression of alpha-actinin SM exon splicing by assisted binding of PTB to the polypyrimidine tract. RNA 2007; 13:1214-23. [PMID: 17592047 PMCID: PMC1924891 DOI: 10.1261/rna.219607] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 05/17/2007] [Indexed: 05/08/2023]
Abstract
Polypyrimidine tract binding protein (PTB) acts as a regulatory repressor of a large number of alternatively spliced exons, often requiring multiple binding sites in order to repress splicing. In one case, cooperative binding of PTB has been shown to accompany repression. The SM exon of the alpha-actinin pre-mRNA is also repressed by PTB, leading to inclusion of the alternative upstream NM exon. The SM exon has a distant branch point located 386 nt upstream of the exon with an adjacent 26 nucleotide pyrimidine tract. Here we have analyzed PTB binding to the NM and SM exon region of the alpha-actinin pre-mRNA. We find that three regions of the intron bind PTB, including the 3' end of the polypyrimidine tract (PPT) and two additional regions between the PPT and the SM exon. The downstream PTB binding sites are essential for full repression and promote binding of PTB to the PPT with a consequent reduction in U2AF(65) binding. Our results are consistent with a repressive mechanism in which cooperative binding of PTB to the PPT competes with binding of U2AF(65), thereby specifically blocking splicing of the SM exon.
Collapse
|
49
|
Corsini L, Bonnal S, Bonna S, Basquin J, Hothorn M, Scheffzek K, Valcárcel J, Sattler M. U2AF-homology motif interactions are required for alternative splicing regulation by SPF45. Nat Struct Mol Biol 2007; 14:620-9. [PMID: 17589525 DOI: 10.1038/nsmb1260] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Accepted: 05/03/2007] [Indexed: 11/09/2022]
Abstract
The U2AF-homology motif (UHM) mediates protein-protein interactions between factors involved in constitutive RNA splicing. Here we report that the splicing factor SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also called CD95). The SPF45 UHM is necessary for this activity and binds UHM-ligand motifs (ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. We describe a 2.1-A crystal structure of SPF45-UHM in complex with a ULM peptide from SF3b155. Features distinct from those of previously described UHM-ULM structures allowed the design of mutations in the SPF45 UHM that selectively impair binding to individual ULMs. Splicing assays using the ULM-selective SPF45 variants demonstrate that individual UHM-ULM interactions are required for FAS splicing regulation by SPF45 in vivo. Our data suggest that networks of UHM-ULM interactions are involved in regulating alternative splicing.
Collapse
Affiliation(s)
- Lorenzo Corsini
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, D-69117 Heidelberg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Hastings ML, Allemand E, Duelli DM, Myers MP, Krainer AR. Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF(65). PLoS One 2007; 2:e538. [PMID: 17579712 PMCID: PMC1888729 DOI: 10.1371/journal.pone.0000538] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 05/22/2007] [Indexed: 11/19/2022] Open
Abstract
Pre-mRNA splicing is a crucial step in gene expression, and accurate recognition of splice sites is an essential part of this process. Splice sites with weak matches to the consensus sequences are common, though it is not clear how such sites are efficiently utilized. Using an in vitro splicing-complementation approach, we identified PUF60 as a factor that promotes splicing of an intron with a weak 3′ splice-site. PUF60 has homology to U2AF65, a general splicing factor that facilitates 3′ splice-site recognition at the early stages of spliceosome assembly. We demonstrate that PUF60 can functionally substitute for U2AF65in vitro, but splicing is strongly stimulated by the presence of both proteins. Reduction of either PUF60 or U2AF65 in cells alters the splicing pattern of endogenous transcripts, consistent with the idea that regulation of PUF60 and U2AF65 levels can dictate alternative splicing patterns. Our results indicate that recognition of 3′ splice sites involves different U2AF-like molecules, and that modulation of these general splicing factors can have profound effects on splicing.
Collapse
Affiliation(s)
- Michelle L. Hastings
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Eric Allemand
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dominik M. Duelli
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Michael P. Myers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Adrian R. Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|