1
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Spitzer H, Berry S, Donoghoe M, Pelkmans L, Theis FJ. Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps. Nat Methods 2023:10.1038/s41592-023-01894-z. [PMID: 37248388 PMCID: PMC10333128 DOI: 10.1038/s41592-023-01894-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/25/2023] [Indexed: 05/31/2023]
Abstract
Highly multiplexed imaging holds enormous promise for understanding how spatial context shapes the activity of the genome and its products at multiple length scales. Here, we introduce a deep learning framework called CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis), which uses a conditional variational autoencoder to learn representations of molecular pixel profiles that are consistent across heterogeneous cell populations and experimental perturbations. Clustering these pixel-level representations identifies consistent subcellular landmarks, which can be quantitatively compared in terms of their size, shape, molecular composition and relative spatial organization. Using high-resolution multiplexed immunofluorescence, this reveals how subcellular organization changes upon perturbation of RNA synthesis, RNA processing or cell size, and uncovers links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates. By capturing interpretable cellular phenotypes, we anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organization to identify the rules by which context shapes physiology and disease.
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Affiliation(s)
- Hannah Spitzer
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Scott Berry
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark Donoghoe
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- School of Computation, Information and Technology CIT, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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2
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Zhang F, Velez-Irizarry D, Ernst CW, Huang W. Mapping splice QTLs reveals distinct transcriptional and post-transcriptional regulatory variation of gene expression and identifies putative alternative splicing variation mediating complex trait variation in pigs. BMC Genomics 2023; 24:240. [PMID: 37142954 PMCID: PMC10161646 DOI: 10.1186/s12864-023-09314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/14/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Alternative splicing is an important step in gene expression, generating multiple isoforms for the same genes and greatly expanding the diversity of proteomes. Genetic variation in alternative splicing contributes to phenotypic diversity in natural populations. However, the genetic basis of variation in alternative splicing in livestock including pigs remains poorly understood. RESULTS In this study, using a Duroc x Pietrain F2 pig population, we performed genome-wide analysis of alternative splicing estimated from stranded RNA-Seq data in skeletal muscle. We characterized the genetic architecture of alternative splicing and compared its basic features with those of overall gene expression. We detected a large number of novel alternative splicing events that were not previously annotated. We found heritability of quantitative alternative splicing scores (percent spliced in or PSI) to be lower than that of overall gene expression. In addition, heritabilities showed little correlation between alternative splicing and overall gene expression. We mapped expression QTLs (eQTLs) and splice QTLs (sQTLs) and found them to be largely non-overlapping. Finally, we integrated sQTL mapping with phenotype QTL (pQTL mapping to identify potential mediator of pQTL effect by alternative splicing. CONCLUSIONS Our results suggest that regulatory variation exists at multiple levels and that their genetic controls are distinct, offering opportunities for genetic improvement.
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Affiliation(s)
- Fei Zhang
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
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3
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Gildea MA, Dwyer ZW, Pleiss JA. Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1 st and 2 nd chemical steps. Mol Cell 2022; 82:2967-2981.e6. [PMID: 35830855 PMCID: PMC9391291 DOI: 10.1016/j.molcel.2022.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/31/2022] [Accepted: 06/12/2022] [Indexed: 10/17/2022]
Abstract
We generate high-precision measurements of the in vivo rates of both chemical steps of pre-mRNA splicing across the genome-wide complement of substrates in yeast by coupling metabolic labeling, multiplexed primer-extension sequencing, and kinetic modeling. We demonstrate that the rates of intron removal vary widely, splice-site sequences are primary determinants of 1st step but have little apparent impact on 2nd step rates, and the 2nd step is generally faster than the 1st step. Ribosomal protein genes (RPGs) are spliced faster than non-RPGs at each step, and RPGs share evolutionarily conserved properties that may contribute to their faster splicing. A genetic variant defective in the 1st step of the pathway reveals a genome-wide defect in the 1st step but an unexpected, transcript-specific change in the 2nd step. Our work demonstrates that extended co-transcriptional association is an important determinant of splicing rate, a conclusion at odds with recent claims of ultra-fast splicing.
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Affiliation(s)
- Michael A Gildea
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Zachary W Dwyer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Jeffrey A Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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4
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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5
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Borao S, Ayté J, Hümmer S. Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing. Int J Mol Sci 2021; 22:ijms222212444. [PMID: 34830325 PMCID: PMC8624252 DOI: 10.3390/ijms222212444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5' and 3' splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.
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Affiliation(s)
- Sonia Borao
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Correspondence: (J.A.); (S.H.)
| | - Stefan Hümmer
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Translational Molecular Pathology, Vall d’Hebron Research Institute (VHIR), CIBERONC, 08035 Barcelona, Spain
- Correspondence: (J.A.); (S.H.)
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6
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Payán-Bravo L, Fontalva S, Peñate X, Cases I, Guerrero-Martínez J, Pareja-Sánchez Y, Odriozola-Gil Y, Lara E, Jimeno-González S, Suñé C, Muñoz-Centeno M, Reyes J, Chávez S. Human prefoldin modulates co-transcriptional pre-mRNA splicing. Nucleic Acids Res 2021; 49:6267-6280. [PMID: 34096575 PMCID: PMC8216451 DOI: 10.1093/nar/gkab446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 11/14/2022] Open
Abstract
Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.
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Affiliation(s)
- Laura Payán-Bravo
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sara Fontalva
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - José Antonio Guerrero-Martínez
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Yerma Pareja-Sánchez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Yosu Odriozola-Gil
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Esther Lara
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Carles Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine “López Neyra” IPBLN-CSIC, PTS, Granada, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - José C Reyes
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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7
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Potapova TA, Romashchenko AG, Yudin NS, Voevoda MI. Ethnicity-specific distribution of <em>TRPM8</em> gene variants in Eurasian populations: signs of selection. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj20.45-o] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- T. A. Potapova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
| | - A. G. Romashchenko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
| | - N. S. Yudin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
| | - M. I. Voevoda
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences;
Federal Research Center of Fundamental and Translational Medicine; Novosibirsk State University
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8
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Brunner AM, Steensma DP. Targeting Aberrant Splicing in Myelodysplastic Syndromes: Biologic Rationale and Clinical Opportunity. Hematol Oncol Clin North Am 2020; 34:379-391. [PMID: 32089217 DOI: 10.1016/j.hoc.2019.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Myelodysplastic syndromes are enriched for somatic mutations in the pre-mRNA splicing apparatus, with recurrent acquired mutations most commonly occurring in SF3B1, SRSF2, U2AF1, and ZRSR2. These mutations appear to be early events in the pathogenesis of disease, and, given their frequency and central role in leukemogenesis, are of interest as potential therapeutic targets. Clinical trials are exploring targets that directly affect the spliceosome (splicing modulators or protein arginine methyltransferase 5 inhibitors) or that exploit possible vulnerabilities created by alternative splicing (inhibiting ATR). Future research is needed to explore novel targets and therapeutic combinations and understand how these mutations lead to clonal dominance.
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Affiliation(s)
- Andrew M Brunner
- Massachusetts General Hospital, Zero Emerson Place, Suite 118, Boston, MA 02114, USA.
| | - David P Steensma
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
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9
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Moreno-Castro C, Prieto-Sánchez S, Sánchez-Hernández N, Hernández-Munain C, Suñé C. Role for the splicing factor TCERG1 in Cajal body integrity and snRNP assembly. J Cell Sci 2019; 132:jcs.232728. [PMID: 31636114 DOI: 10.1242/jcs.232728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/11/2019] [Indexed: 12/29/2022] Open
Abstract
Cajal bodies are nuclear organelles involved in the nuclear phase of small nuclear ribonucleoprotein (snRNP) biogenesis. In this study, we identified the splicing factor TCERG1 as a coilin-associated factor that is essential for Cajal body integrity. Knockdown of TCERG1 disrupts the localization of the components of Cajal bodies, including coilin and NOLC1, with coilin being dispersed in the nucleoplasm into numerous small foci, without affecting speckles, gems or the histone locus body. Furthermore, the depletion of TCERG1 affects the recruitment of Sm proteins to uridine-rich small nuclear RNAs (snRNAs) to form the mature core snRNP. Taken together, the results of this study suggest that TCERG1 plays an important role in Cajal body formation and snRNP biogenesis.
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Affiliation(s)
- Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Noemí Sánchez-Hernández
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
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10
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Balestra D, Branchini A. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Int J Mol Sci 2019; 20:ijms20123036. [PMID: 31234407 PMCID: PMC6627357 DOI: 10.3390/ijms20123036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular strategies tailored to promote/correct the expression and/or processing of defective coagulation factors would represent innovative therapeutic approaches beyond standard substitutive therapy. Here, we focus on the molecular mechanisms and determinants underlying innovative approaches acting at DNA, mRNA and protein levels in inherited coagulation factor deficiencies, and in particular on: (i) gene editing approaches, which have permitted intervention at the DNA level through the specific recognition, cleavage, repair/correction or activation of target sequences, even in mutated gene contexts; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors, as well as the effects on the splicing of missense changes affecting exonic splicing elements; this section includes antisense oligonucleotide- or siRNA-mediated approaches to down-regulate target genes; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions. Overall, these approaches have shown the ability to rescue the expression and/or function of potentially therapeutic levels of coagulation factors in different disease models, thus supporting further studies in the future aimed at evaluating the clinical translatability of these new strategies.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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11
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Song Q, Li M, Fan C, Liu Y, Zheng L, Bao Y, Sun L, Yu C, Song Z, Sun Y, Wang G, Huang Y, Li Y. A novel benzamine lead compound of histone deacetylase inhibitor ZINC24469384 can suppresses HepG2 cells proliferation by upregulating NR1H4. Sci Rep 2019; 9:2350. [PMID: 30787420 PMCID: PMC6382829 DOI: 10.1038/s41598-019-39487-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 01/16/2019] [Indexed: 12/18/2022] Open
Abstract
Histone deacetylases (HDACs) can enzymatically transferred acetyl functional group from protein or lysine residues of histone, so they can regulate the expression of lots of genes. Now HDACs are used as drug targets and many HDAC inhibitors (HDACis) were approved for cancer therapy or in clinical trials. However, the physiological mechanisms and regulatory processes of HDACi anti-cancer effects are largely unexplored and uncompleted. Here we use the virtual screening workflow obtained 25 hit compounds and ZINC24469384 can significantly inhibit HDAC activity while arrest cell cycle at G1/S phase and significantly induced HepG2 cell apoptosis, time-course RNA-seq demonstrate that HepG2 cells transcriptionally respond to ZINC24469384. Pathway analysis of DEGs and DASGs reveal that NR1H4 may play an important role in ZINC24469384-induced anti-proliferation effect and is dramatically alleviated by down-regulating the SOCS2 expression and promoting STAT3 phosphorylation in knockdown NR1H4 HepG2 cells. Analysis based on TCGA database indicated that NR1H4 and SOCS2 were downregulated in liver cancer, this suggest NR1H4 and SOCS2 may play an important role in tumorigenesis. These results indicated that ZINC24469384 is a novel benzamine lead compound of HDACi and provides a novel mechanism for HDACi to inhibit cancer.
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Affiliation(s)
- Qiuhang Song
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Mingyue Li
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Cong Fan
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Yucui Liu
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Lihua Zheng
- Research Center of Agriculture and Medicine gene Engineering of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Luguo Sun
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Chunlei Yu
- Research Center of Agriculture and Medicine gene Engineering of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Zhenbo Song
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Ying Sun
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China
| | - Guannan Wang
- Research Center of Agriculture and Medicine gene Engineering of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yanxin Huang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, 130024, China.
| | - Yuxin Li
- Research Center of Agriculture and Medicine gene Engineering of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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12
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Zhdanov DD, Gladilina YA, Pokrovsky VS, Grishin DV, Grachev VA, Orlova VS, Pokrovskaya MV, Alexandrova SS, Plyasova AA, Sokolov NN. Endonuclease G modulates the alternative splicing of deoxyribonuclease 1 mRNA in human CD4 + T lymphocytes and prevents the progression of apoptosis. Biochimie 2018; 157:158-176. [PMID: 30521874 DOI: 10.1016/j.biochi.2018.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/30/2018] [Indexed: 02/08/2023]
Abstract
Apoptotic endonucleases act cooperatively to fragment DNA and ensure the irreversibility of apoptosis. However, very little is known regarding the potential regulatory links between endonucleases. Deoxyribonuclease 1 (DNase I) inactivation is caused by alternative splicing (AS) of DNase I pre-mRNA skipping exon 4, which occurs in response to EndoG overexpression in cells. The current study aimed to determine the role of EndoG in the regulation of DNase I mRNA AS and the modulation of its enzymatic activity. A strong correlation was identified between the EndoG expression levels and DNase I splice variants in human lymphocytes. EndoG overexpression in CD4+ T cells down-regulated the mRNA levels of the active full-length DNase I variant and up-regulated the levels of the non-active spliced variant, which acts in a dominant-negative fashion. DNase I AS was induced by the translocation of EndoG from mitochondria into nuclei during the development of apoptosis. The DNase I spliced variant was induced by recombinant EndoG or by incubation with EndoG-digested cellular RNA in an in vitro system with isolated cell nuclei. Using antisense DNA oligonucleotides, we identified a 72-base segment that spans the adjacent segments of exon 4 and intron 4 and appears to be responsible for the AS. DNase I-positive CD4+ T cells overexpressing EndoG demonstrated decreased progression towards bleomycin-induced apoptosis. Therefore, EndoG is an endonuclease with the unique ability to inactivate another endonuclease, DNase I, and to modulate the development of apoptosis.
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Affiliation(s)
- Dmitry D Zhdanov
- Institute of Biomedical Chemistry, Pogodinskaya St 10/8, 119121, Moscow, Russia; Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198, Moscow, Russia.
| | - Yulia A Gladilina
- Institute of Biomedical Chemistry, Pogodinskaya St 10/8, 119121, Moscow, Russia
| | - Vadim S Pokrovsky
- Institute of Biomedical Chemistry, Pogodinskaya St 10/8, 119121, Moscow, Russia; Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198, Moscow, Russia; N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478, Moscow, Russia
| | - Dmitry V Grishin
- Institute of Biomedical Chemistry, Pogodinskaya St 10/8, 119121, Moscow, Russia
| | - Vladimir A Grachev
- Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198, Moscow, Russia
| | - Valentina S Orlova
- Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198, Moscow, Russia
| | | | | | - Anna A Plyasova
- Institute of Biomedical Chemistry, Pogodinskaya St 10/8, 119121, Moscow, Russia
| | - Nikolay N Sokolov
- Institute of Biomedical Chemistry, Pogodinskaya St 10/8, 119121, Moscow, Russia
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13
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Zhdanov DD, Gladilina YA, Pokrovsky VS, Grishin DV, Grachev VA, Orlova VS, Pokrovskaya MV, Alexandrova SS, Sokolov NN. Murine regulatory T cells induce death of effector T, B, and NK lymphocytes through a contact-independent mechanism involving telomerase suppression and telomere-associated senescence. Cell Immunol 2018; 331:146-160. [PMID: 29935763 DOI: 10.1016/j.cellimm.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
Regulatory T cells (Tregs) suppress the activity of effector T, B and NK lymphocytes and sustain immunological tolerance, but the proliferative activity of suppressed cells remains unexplored. In the present study, we report that mouse Tregs can induce replicative senescence and the death of responder mouse CD4+CD25- T cells, CD8+ T cells, B cells and NK cells in vitro and in vivo. Contact-independent in vitro co-cultivation with Tregs up-regulated endonuclease G (EndoG) expression and its translocation to the nucleus in responder cells. EndoG localization in the nucleus induced alternative mRNA splicing of the telomerase catalytic subunit Tert and telomerase inhibition. The lack of telomerase activity in proliferating cells led to telomere loss followed by the development of senescence and cell death. Injection of Tregs into mice resulted in EndoG-associated alternative splicing of Tert, telomerase inhibition, telomere loss, senescence development and increased cell death in vivo. The present study describes a novel contact-independent mechanism by which Tregs specify effector cell fate and provides new insights into cellular crosstalk related to immune suppression.
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Affiliation(s)
- Dmitry D Zhdanov
- Institute of Biomedical Chemistry, Pogodinskaya st 10/8, 119121 Moscow, Russia; Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198 Moscow, Russia.
| | - Yulia A Gladilina
- Institute of Biomedical Chemistry, Pogodinskaya st 10/8, 119121 Moscow, Russia
| | - Vadim S Pokrovsky
- Institute of Biomedical Chemistry, Pogodinskaya st 10/8, 119121 Moscow, Russia; Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198 Moscow, Russia; N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia
| | - Dmitry V Grishin
- Institute of Biomedical Chemistry, Pogodinskaya st 10/8, 119121 Moscow, Russia
| | - Vladimir A Grachev
- Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198 Moscow, Russia
| | - Valentina S Orlova
- Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya 6, 117198 Moscow, Russia
| | | | | | - Nikolay N Sokolov
- Institute of Biomedical Chemistry, Pogodinskaya st 10/8, 119121 Moscow, Russia
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14
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Zhdanov DD, Pokrovsky VS, Orlova EV, Orlova VS, Pokrovskaya MV, Aleksandrova SS, Sokolov NN. Intracellular Localization of Apoptotic Endonuclease EndoG and Splice-Variants of Telomerase Catalytic Subunit hTERT. BIOCHEMISTRY (MOSCOW) 2017; 82:894-905. [PMID: 28941457 DOI: 10.1134/s0006297917080041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The activity of telomerase catalytic subunit hTERT (human telomerase reverse transcriptase) can be regulated by alternative splicing of its mRNA. The mechanism of hTERT splicing is not understood in detail. Apoptotic endonuclease EndoG is known to participate in this process. In the present work, the intracellular colocalization and mRNA levels of EndoG and hTERT splice-variants in normal and apoptotic cancer cells were studied. We found that the development of apoptosis increased the expression of EndoG and changed the ratio of hTERT splice-variants, which decreased the telomerase activity in the cells. The development of apoptosis was accompanied by changes in the amount of mRNA and in the localization of EndoG and hTERT splice-variants in the cytoplasm, nuclei, and mitochondria of the cells. The suppression of EndoG expression using RNA interference prevented induction of the α+β- splice-variant of hTERT and inhibition of the telomerase activity. A high degree of the intracellular colocalization of EndoG and hTERT was shown. The changes in the expression and localization of EndoG corresponded with changes in the amount and localization of hTERT splice-variants. These data confirm the participation of EndoG in the alternative splicing of mRNA of the telomerase catalytic subunit and in regulation of the telomerase activity.
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Affiliation(s)
- D D Zhdanov
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121, Russia.
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15
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Huin V, Buée L, Behal H, Labreuche J, Sablonnière B, Dhaenens CM. Alternative promoter usage generates novel shorter MAPT mRNA transcripts in Alzheimer's disease and progressive supranuclear palsy brains. Sci Rep 2017; 7:12589. [PMID: 28974731 PMCID: PMC5626709 DOI: 10.1038/s41598-017-12955-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/12/2017] [Indexed: 11/09/2022] Open
Abstract
Alternative promoter usage is an important mechanism for transcriptome diversity and the regulation of gene expression. Indeed, this alternative usage may influence tissue/subcellular specificity, protein translation and function of the proteins. The existence of an alternative promoter for MAPT gene was considered for a long time to explain differential tissue specificity and differential response to transcription and growth factors between mRNA transcripts. The alternative promoter usage could explain partly the different tau proteins expression patterns observed in tauopathies. Here, we report on our discovery of a functional alternative promoter for MAPT, located upstream of the gene's second exon (exon 1). By analyzing genome databases and brain tissue from control individuals and patients with Alzheimer's disease or progressive supranuclear palsy, we identified novel shorter transcripts derived from this alternative promoter. These transcripts are increased in patients' brain tissue as assessed by 5'RACE-PCR and qPCR. We suggest that these new MAPT isoforms can be translated into normal or amino-terminal-truncated tau proteins. We further suggest that activation of MAPT's alternative promoter under pathological conditions leads to the production of truncated proteins, changes in protein localization and function, and thus neurodegeneration.
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Affiliation(s)
- Vincent Huin
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France.
| | - Luc Buée
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
| | - Hélène Behal
- Univ. Lille, CHU Lille, EA 2694 - Santé publique: épidémiologie et qualité des soins, Unité de Biostatistiques, F-59000, Lille, France
| | - Julien Labreuche
- Univ. Lille, CHU Lille, EA 2694 - Santé publique: épidémiologie et qualité des soins, Unité de Biostatistiques, F-59000, Lille, France
| | - Bernard Sablonnière
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
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16
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Sánchez-Hernández N, Prieto-Sánchez S, Moreno-Castro C, Muñoz-Cobo JP, El Yousfi Y, Boyero-Corral S, Suñé-Pou M, Hernández-Munain C, Suñé C. Targeting proteins to RNA transcription and processing sites within the nucleus. Int J Biochem Cell Biol 2017; 91:194-202. [DOI: 10.1016/j.biocel.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
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17
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Hu J, Wang G, Sun T. Dissecting the roles of the androgen receptor in prostate cancer from molecular perspectives. Tumour Biol 2017; 39:1010428317692259. [PMID: 28475016 DOI: 10.1177/1010428317692259] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Androgen receptor plays a pivotal role in prostate cancer progression, and androgen deprivation therapy to intercept androgen receptor signal pathway is an indispensable treatment for most advanced prostate cancer patients to delay cancer progression. However, the emerging of castration-resistant prostate cancer reminds us the alteration of androgen receptor, which includes androgen receptor mutation, the formation of androgen receptor variants, and androgen receptor distribution in cancer cells. In this review, we introduce the process of androgen receptor and also its variants' formation, translocation, and function alteration by protein modification or interaction with other pathways. We dissect the roles of androgen receptor in prostate cancer from molecular perspective to provide clues for battling prostate cancer, especially castration-resistant prostate cancer.
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Affiliation(s)
- Jieping Hu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Gongxian Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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18
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Alternative Splicing of Toll-Like Receptor 9 Transcript in Teleost Fish Grouper Is Regulated by NF-κB Signaling via Phosphorylation of the C-Terminal Domain of the RPB1 Subunit of RNA Polymerase II. PLoS One 2016; 11:e0163415. [PMID: 27658294 PMCID: PMC5033454 DOI: 10.1371/journal.pone.0163415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/25/2016] [Indexed: 11/19/2022] Open
Abstract
Similar to its mammalian counterparts, teleost Toll-like receptor 9 (TLR9) recognizes unmethylated CpG DNA presented in the genome of bacteria or DNA viruses and initiates signaling pathway(s) for immune responses. We have previously shown that the TLR9 pathway in grouper, an economically important teleost, can be debilitated by an inhibitory gTLR9B isoform, whose production is mediated by RNA alternative splicing. However, how does grouper TLR9 (gTLR9) signaling impinge on the RNA splicing machinery to produce gTlr9B is unknown. Here we show that the gTlr9 alternative splicing is regulated through ligand-induced phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II). We first observed that ligand-activated NF- κB pathway biased the production of the gTlr9B isoform. Because NF- κB is known to recruit p-TEFb kinase, which phosphorylates the Pol II CTD at Ser2 residues, we examined p-TEFb’s role in alternative splicing. We found that promoting p-TEFb kinase activity significantly favored the production of the gTlr9B isoform, whereas inhibiting p-TEFb yielded an opposite result. We further showed that p-TEFb-mediated production of the gTlr9B isoform down-regulates its own immune responses, suggesting a self-limiting mechanism. Taken together, our data indicate a feedback mechanism of the gTLR9 signaling pathway to regulate the alternative splicing machinery, which in turn produces an inhibitor to the pathway.
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19
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Lee H, Goodarzi H, Tavazoie SF, Alarcón CR. TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer. Cancer Res 2016; 76:4994-5005. [PMID: 27328729 DOI: 10.1158/0008-5472.can-15-2322] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 06/14/2016] [Indexed: 12/20/2022]
Abstract
The developmental transcription factor SOX4 contributes to the metastatic spread of multiple solid cancer types, but its direct target genes that mediate cancer progression are not well defined. Using a systematic molecular and genomic approach, we identified the TMEM2 transmembrane protein gene as a direct transcriptional target of SOX4. TMEM2 was transcriptionally activated by SOX4 in breast cancer cells where, like SOX4, TMEM2 was found to mediate proinvasive and promigratory effects. Similarly, TMEM2 was sufficient to promote metastatic colonization of breast cancer cells and its expression in primary breast tumors associated with a higher likelihood of metastatic relapse. Given earlier evidence that genetic inactivation of SOX4 or TMEM2 yield similar defects in cardiac development, our findings lead us to propose that TMEM2 may not only mediate the pathologic effects of SOX4 on cancer progression but also potentially its contributions to embryonic development. Cancer Res; 76(17); 4994-5005. ©2016 AACR.
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Affiliation(s)
- Hyeseung Lee
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York
| | - Hani Goodarzi
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York.
| | - Claudio R Alarcón
- Laboratory of Systems Cancer Biology, Rockefeller University, New York, New York.
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20
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Knott GJ, Bond CS, Fox AH. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res 2016; 44:3989-4004. [PMID: 27084935 PMCID: PMC4872119 DOI: 10.1093/nar/gkw271] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Nuclear proteins are often given a concise title that captures their function, such as 'transcription factor,' 'polymerase' or 'nuclear-receptor.' However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein-protein and protein-nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Archa H Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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21
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Sánchez-Hernández N, Boireau S, Schmidt U, Muñoz-Cobo JP, Hernández-Munain C, Bertrand E, Suñé C. The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing. RNA (NEW YORK, N.Y.) 2016; 22:571-582. [PMID: 26873599 PMCID: PMC4793212 DOI: 10.1261/rna.052795.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/23/2015] [Indexed: 06/05/2023]
Abstract
Coupling between transcription and RNA processing is key for gene regulation. Using live-cell photobleaching techniques, we investigated the factor TCERG1, which coordinates transcriptional elongation with splicing. We demonstrate that TCERG1 is highly mobile in the nucleoplasm and that this mobility is slightly decreased when it is associated with speckles. Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) but not α-amanitin treatment reduced the mobility of TCERG1, which suggests interaction with paused transcription elongation complexes. We found that TCERG1 mobility is rapid at the transcription site (TS) of a reporter that splices post-transcriptionally and that TCERG1 is recruited to the active TS independent of the CTD of RNAPII, thus excluding phosphorylated CTD as a requirement for recruiting this factor to the TS. Importantly, the mobility of TCERG1 is reduced when the reporter splices cotranscriptionally, which suggests that TCERG1 forms new macromolecular complexes when splicing occurs cotranscriptionally. In this condition, spliceostatin A has no effect, indicating that TCERG1 rapidly binds and dissociates from stalled spliceosomal complexes and that the mobility properties of TCERG1 do not depend on events occurring after the initial spliceosome formation. Taken together, these data suggest that TCERG1 binds independently to elongation and splicing complexes, thus performing their coupling by transient interactions rather than by stable association with one or the other complexes. This finding has conceptual implications for understanding the coupling between transcription and RNA processing.
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Affiliation(s)
- Noemí Sánchez-Hernández
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Stéphanie Boireau
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Ute Schmidt
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Juan Pablo Muñoz-Cobo
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
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22
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Shiota M, Fujimoto N, Imada K, Yokomizo A, Itsumi M, Takeuchi A, Kuruma H, Inokuchi J, Tatsugami K, Uchiumi T, Oda Y, Naito S. Potential Role for YB-1 in Castration-Resistant Prostate Cancer and Resistance to Enzalutamide Through the Androgen Receptor V7. J Natl Cancer Inst 2016; 108:djw005. [DOI: 10.1093/jnci/djw005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 01/06/2016] [Indexed: 12/17/2022] Open
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23
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Sheng Z, Sun Y, Zhu R, Jiao N, Tang K, Cao Z, Ma C. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine. PLoS One 2015; 10:e0143742. [PMID: 26606055 PMCID: PMC4659683 DOI: 10.1371/journal.pone.0143742] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 11/09/2015] [Indexed: 01/24/2023] Open
Abstract
Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.
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Affiliation(s)
- Zhen Sheng
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Yi Sun
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Ruixin Zhu
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Na Jiao
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Kailin Tang
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Zhiwei Cao
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
- * E-mail: (ZWC); (CM)
| | - Chao Ma
- School of Life Science and Technology, Tongji University, Shanghai, People’s Republic of China
- Key Lab of Systems Biology, Shanghai Institutes for Biological Science, Chinese Academy of Science, Shanghai, People’s Republic of China
- * E-mail: (ZWC); (CM)
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24
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Ág N, Flipphi M, Karaffa L, Scazzocchio C, Fekete E. Alternatively spliced, spliceosomal twin introns in Helminthosporium solani. Fungal Genet Biol 2015; 85:7-13. [PMID: 26514742 DOI: 10.1016/j.fgb.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 11/24/2022]
Abstract
Spliceosomal twin introns, "stwintrons", have been defined as complex intervening sequences that carry a second intron ("internal intron") interrupting one of the conserved sequence domains necessary for their correct splicing via consecutive excision events. Previously, we have described and experimentally verified stwintrons in species of Sordariomycetes, where an "internal intron" interrupted the donor sequence of an "external intron". Here we describe and experimentally verify two novel stwintrons of the potato pathogen Helminthosporium solani. One instance involves alternative splicing of an internal intron interrupting the donor domain of an external intron and a second one interrupting the acceptor domain of an overlapping external intron, both events leading to identical mature mRNAs. In the second case, an internal intron interrupts the donor domain of the external intron, while an alternatively spliced intron leads to an mRNA carrying a premature chain termination codon. We thus extend the stwintron concept to the acceptor domain and establish a link of the occurrence of stwintrons with that of alternative splicing.
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Affiliation(s)
- Norbert Ág
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Michel Flipphi
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Levente Karaffa
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Dept. of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; Institut de Biologie Intégrative de la Cellule (I2BC), UMR CEA/CNRS/Université Paris-Sud, 91405 Orsay Cedex, France
| | - Erzsébet Fekete
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
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25
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Becerra S, Andrés-León E, Prieto-Sánchez S, Hernández-Munain C, Suñé C. Prp40 and early events in splice site definition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:17-32. [PMID: 26494226 DOI: 10.1002/wrna.1312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/18/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
The alternative splicing (AS) of precursor messenger RNA (pre-mRNA) is a tightly regulated process through which introns are removed to leave the resulting exons in the mRNA appropriately aligned and ligated. The AS of pre-mRNA is a key mechanism for increasing the complexity of proteins encoded in the genome. In humans, more than 90% of genes undergo AS, underscoring the importance of this process in RNA biogenesis. As such, AS misregulation underlies multiple human diseases. The splicing reaction is catalyzed by the spliceosome, a highly dynamic complex that assembles at or near the intron/exon boundaries and undergoes sequential conformational and compositional changes during splicing. The initial recognition of splice sites defines the exons that are going to be removed, which is a critical step in the highly regulated splicing process. Although the available lines of evidence are increasing, the molecular mechanisms governing AS, including the initial interactions occurring at intron/exon boundaries, and the factors that modulate these critical connections by functioning as a scaffold for active-site RNAs or proteins, remain poorly understood. In this review, we summarize the major hallmarks of the initial steps in the splicing process and the role of auxiliary factors that contribute to the assembly of the spliceosomal complex. We also discuss the role of the essential yeast Prp40 protein and its mammalian homologs in the specificity of this pre-mRNA processing event. In addition, we provide the first exhaustive phylogenetic analysis of the molecular evolution of Prp40 family members. WIREs RNA 2016, 7:17-32. doi: 10.1002/wrna.1312 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soraya Becerra
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada 18016, Spain
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26
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Functional Consequences for Apoptosis by Transcription Elongation Regulator 1 (TCERG1)-Mediated Bcl-x and Fas/CD95 Alternative Splicing. PLoS One 2015; 10:e0139812. [PMID: 26462236 PMCID: PMC4604205 DOI: 10.1371/journal.pone.0139812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 09/17/2015] [Indexed: 11/19/2022] Open
Abstract
Here, we present evidence for a specific role of the splicing-related factor TCERG1 in regulating apoptosis in live cells by modulating the alternative splicing of the apoptotic genes Bcl-x and Fas. We show that TCERG1 modulates Bcl-x alternative splicing during apoptosis and its activity in Bcl-x alternative splicing correlates with the induction of apoptosis, as determined by assessing dead cells, sub-G1-phase cells, annexin-V binding, cell viability, and cleavage of caspase-3 and PARP-1. Furthermore, the effect of TCERG1 on apoptosis involved changes in mitochondrial membrane permeabilization. We also found that depletion of TCERG1 reduces the expression of the activated form of the pro-apoptotic mitochondrial membrane protein Bak, which remains inactive by heterodimerizing with Bcl-xL, preventing the initial step of cytochrome c release in Bak-mediated mitochondrial apoptosis. In addition, we provide evidence that TCERG1 also participates in the death receptor-mediated apoptosis pathway. Interestingly, TCERG1 also modulates Fas/CD95 alternative splicing. We propose that TCERG1 sensitizes a cell to apoptotic agents, thus promoting apoptosis by regulating the alternative splicing of both the Bcl-x and Fas/CD95 genes. Our findings may provide a new link between the control of alternative splicing and the molecular events leading to apoptosis.
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Dembowski JA, DeLuca NA. Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes. PLoS Pathog 2015; 11:e1004939. [PMID: 26018390 PMCID: PMC4446364 DOI: 10.1371/journal.ppat.1004939] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/07/2015] [Indexed: 01/01/2023] Open
Abstract
Much of the HSV-1 life cycle is carried out in the cell nucleus, including the expression, replication, repair, and packaging of viral genomes. Viral proteins, as well as cellular factors, play essential roles in these processes. Isolation of proteins on nascent DNA (iPOND) was developed to label and purify cellular replication forks. We adapted aspects of this method to label viral genomes to both image, and purify replicating HSV-1 genomes for the identification of associated proteins. Many viral and cellular factors were enriched on viral genomes, including factors that mediate DNA replication, repair, chromatin remodeling, transcription, and RNA processing. As infection proceeded, packaging and structural components were enriched to a greater extent. Among the more abundant proteins that copurified with genomes were the viral transcription factor ICP4 and the replication protein ICP8. Furthermore, all seven viral replication proteins were enriched on viral genomes, along with cellular PCNA and topoisomerases, while other cellular replication proteins were not detected. The chromatin-remodeling complexes present on viral genomes included the INO80, SWI/SNF, NURD, and FACT complexes, which may prevent chromatinization of the genome. Consistent with this conclusion, histones were not readily recovered with purified viral genomes, and imaging studies revealed an underrepresentation of histones on viral genomes. RNA polymerase II, the mediator complex, TFIID, TFIIH, and several other transcriptional activators and repressors were also affinity purified with viral DNA. The presence of INO80, NURD, SWI/SNF, mediator, TFIID, and TFIIH components is consistent with previous studies in which these complexes copurified with ICP4. Therefore, ICP4 is likely involved in the recruitment of these key cellular chromatin remodeling and transcription factors to viral genomes. Taken together, iPOND is a valuable method for the study of viral genome dynamics during infection and provides a comprehensive view of how HSV-1 selectively utilizes cellular resources.
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Affiliation(s)
- Jill A. Dembowski
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Neal A. DeLuca
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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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 (NEW YORK, N.Y.) 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] [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.
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Affiliation(s)
| | | | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
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Huang Y, Yao X, Wang G. 'Mediator-ing' messenger RNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:257-69. [PMID: 25515410 DOI: 10.1002/wrna.1273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/29/2014] [Accepted: 10/17/2014] [Indexed: 12/27/2022]
Abstract
Pre-messenger RNA (mRNA) processing, generally including capping, mRNA splicing, and cleavage-polyadenylation, is physically and functionally associated with transcription. The reciprocal coupling between transcription and mRNA processing ensures the efficient and regulated gene expression and editing. Multiple transcription factors/cofactors and mRNA processing factors are involved in the coupling process. This review focuses on several classic examples and recent advances that enlarge our understanding of how the transcriptional factors or cofactors, especially the Mediator complex, contribute to the RNA Pol II elongation, mRNA splicing, and polyadenylation.
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Affiliation(s)
- Yan Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Wang Y, Liu J, Huang BO, Xu YM, Li J, Huang LF, Lin J, Zhang J, Min QH, Yang WM, Wang XZ. Mechanism of alternative splicing and its regulation. Biomed Rep 2014; 3:152-158. [PMID: 25798239 DOI: 10.3892/br.2014.407] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing of precursor mRNA is an essential mechanism to increase the complexity of gene expression, and it plays an important role in cellular differentiation and organism development. Regulation of alternative splicing is a complicated process in which numerous interacting components are at work, including cis-acting elements and trans-acting factors, and is further guided by the functional coupling between transcription and splicing. Additional molecular features, such as chromatin structure, RNA structure and alternative transcription initiation or alternative transcription termination, collaborate with these basic components to generate the protein diversity due to alternative splicing. All these factors contributing to this one fundamental biological process add up to a mechanism that is critical to the proper functioning of cells. Any corruption of the process may lead to disruption of normal cellular function and the eventuality of disease. Cancer is one of those diseases, where alternative splicing may be the basis for the identification of novel diagnostic and prognostic biomarkers, as well as new strategies for therapy. Thus, an in-depth understanding of alternative splicing regulation has the potential not only to elucidate fundamental biological principles, but to provide solutions for various diseases.
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Affiliation(s)
- Yan Wang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Liu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - B O Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Yan-Mei Xu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Lin-Feng Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jin Lin
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Zhang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Qing-Hua Min
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Wei-Ming Yang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Xiao-Zhong Wang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
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Xu JF, Yang GH, Pan XH, Zhang SJ, Zhao C, Qiu BS, Gu HF, Hong JF, Cao L, Chen Y, Xia B, Bi Q, Wang YP. Association of GPR126 gene polymorphism with adolescent idiopathic scoliosis in Chinese populations. Genomics 2014; 105:101-7. [PMID: 25479386 DOI: 10.1016/j.ygeno.2014.11.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/19/2014] [Accepted: 11/16/2014] [Indexed: 11/27/2022]
Abstract
Idiopathic scoliosis is the most common pediatric spinal deformity affecting 1% to 3% of the population, and adolescent idiopathic scoliosis (AIS) accounts for approximately 80% of these cases; however, the etiology and pathogenesis of AIS are still uncertain. The current study aims to identify the relationship between G protein-coupled receptor 126 (GPR126) gene and AIS predisposition, to identify the relationship between the genotypes of the GPR126 SNPs and the clinical phenotypes of AIS. We conducted a case-control study and genotyped twenty SNPs of GPR126 gene including ten exonic SNPs and ten intronic polymorphisms in 352 Chinese sporadic AIS patients and 149 healthy controls. We provided evidence for strong association of three intronic SNPs of the GPR126 gene with AIS susceptibility: rs6570507 A > G (p =0 .0035, OR = 1.729), rs7774095 A > C (p = 0.0078, OR = 1.687), and rs7755109 A > G (p = 0.0078, OR = 1.687). However, we did not identify any significant association between ten exonic SNPs of GPR126 and AIS. Linkage disequilibrium analysis indicated that rs7774095 A > C and rs7755109 A > G could be parsed into one block. The association between the intronic haplotype and AIS was further confirmed in an independent population with 110 AIS individuals and 130 healthy controls (p = 0.046, OR = 1.680). Furthermore, molecular mechanisms underlying intronic SNP regulation of GPR126 gene were studied. Although intronic SNPs associated with AIS didn't influence GPR126 mRNA alternative splicing, there was a strong association of rs7755109 A > G with decreased GPR126 mRNA level and protein levels. Our findings indicate that genetic variants of GPR126 gene are associated with AIS susceptibility in Chinese populations. The genetic association of GPR126 gene and AIS might provide valuable insights into the pathogenesis of adolescent idiopathic scoliosis.
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Affiliation(s)
- Ji-Feng Xu
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China.
| | - Guang-hai Yang
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, PR China
| | - Xiao-Hong Pan
- Department of Cardiolopy, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, PR China
| | - Shui-Jun Zhang
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Chen Zhao
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Bin-Song Qiu
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Hai-Feng Gu
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Jian-Fei Hong
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Li Cao
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Yu Chen
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Bing Xia
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Qin Bi
- Department of Orthopedics and Joint Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Ya-Ping Wang
- Department of Cardiolopy, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, PR China.
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Fàbregas A, Sánchez-Hernández N, Ticó JR, García-Montoya E, Pérez-Lozano P, Suñé-Negre JM, Hernández-Munain C, Suñé C, Miñarro M. A new optimized formulation of cationic solid lipid nanoparticles intended for gene delivery: Development, characterization and DNA binding efficiency of TCERG1 expression plasmid. Int J Pharm 2014; 473:270-9. [DOI: 10.1016/j.ijpharm.2014.06.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
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Jali SS, Rosloski SM, Janakirama P, Steffen JG, Zhurov V, Berleth T, Clark RM, Grbic V. A plant-specific HUA2-LIKE (HULK) gene family in Arabidopsis thaliana is essential for development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:242-54. [PMID: 25070081 PMCID: PMC4283595 DOI: 10.1111/tpj.12629] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/11/2014] [Accepted: 07/21/2014] [Indexed: 05/23/2023]
Abstract
In Arabidopsis thaliana, the HUA2 gene is required for proper expression of FLOWERING LOCUS C (FLC) and AGAMOUS, key regulators of flowering time and reproductive development, respectively. Although HUA2 is broadly expressed, plants lacking HUA2 function have only moderately reduced plant stature, leaf initiation rate and flowering time. To better understand HUA2 activity, and to test whether redundancy with similar genes underlies the absence of strong phenotypes in HUA2 mutant plants, we identified and subsequently characterized three additional HUA2-LIKE (HULK) genes in Arabidopsis. These genes form two clades (HUA2/HULK1 and HULK2/HULK3), with members broadly conserved in both vascular and non-vascular plants, but not present outside the plant kingdom. Plants with progressively reduced HULK activity had increasingly severe developmental defects, and plants homozygous for loss-of-function mutations in all four HULK genes were not recovered. Multiple mutants displayed reproductive, embryonic and post-embryonic abnormalities, and provide detailed insights into the overlapping and unique functions of individual HULK genes. With regard to flowering time, opposing influences were apparent: hua2 hulk1 plants were early-flowering, while hulk2 hulk3 mutants were late-flowering, and hua2 acted epistatically to cause early flowering in all combinations. Genome-wide expression profiling of mutant combinations using RNA-Seq revealed complex transcriptional changes in seedlings, with FLC, a known target of HUA2, among the most affected. Our studies, which include characterization of HULK expression patterns and subcellular localization, suggest that the HULK genes encode conserved nuclear factors with partially redundant but essential functions associated with diverse genetic pathways in plants.
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Affiliation(s)
- Sathya S Jali
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
| | - Sarah M Rosloski
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
| | | | - Joshua G Steffen
- Department of Biology, University of UtahSalt Lake City, UT, 84112, USA
- Center for Cell and Genome Science, University of UtahSalt Lake City, UT, 84112, USA
| | - Vladimir Zhurov
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
| | - Thomas Berleth
- Department of Cell and Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
| | - Richard M Clark
- Department of Biology, University of UtahSalt Lake City, UT, 84112, USA
- Center for Cell and Genome Science, University of UtahSalt Lake City, UT, 84112, USA
| | - Vojislava Grbic
- Department of Biology, Western UniversityLondon, ON, N6A 5B7, Canada
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Recruitment of RED-SMU1 complex by Influenza A Virus RNA polymerase to control Viral mRNA splicing. PLoS Pathog 2014; 10:e1004164. [PMID: 24945353 PMCID: PMC4055741 DOI: 10.1371/journal.ppat.1004164] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/21/2014] [Indexed: 12/21/2022] Open
Abstract
Influenza A viruses are major pathogens in humans and in animals, whose genome consists of eight single-stranded RNA segments of negative polarity. Viral mRNAs are synthesized by the viral RNA-dependent RNA polymerase in the nucleus of infected cells, in close association with the cellular transcriptional machinery. Two proteins essential for viral multiplication, the exportin NS2/NEP and the ion channel protein M2, are produced by splicing of the NS1 and M1 mRNAs, respectively. Here we identify two human spliceosomal factors, RED and SMU1, that control the expression of NS2/NEP and are required for efficient viral multiplication. We provide several lines of evidence that in infected cells, the hetero-trimeric viral polymerase recruits a complex formed by RED and SMU1 through interaction with its PB2 and PB1 subunits. We demonstrate that the splicing of the NS1 viral mRNA is specifically affected in cells depleted of RED or SMU1, leading to a decreased production of the spliced mRNA species NS2, and to a reduced NS2/NS1 protein ratio. In agreement with the exportin function of NS2, these defects impair the transport of newly synthesized viral ribonucleoproteins from the nucleus to the cytoplasm, and strongly reduce the production of infectious influenza virions. Overall, our results unravel a new mechanism of viral subversion of the cellular splicing machinery, by establishing that the human splicing factors RED and SMU1 act jointly as key regulators of influenza virus gene expression. In addition, our data point to a central role of the viral RNA polymerase in coupling transcription and alternative splicing of the viral mRNAs.
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Napolitano G, Lania L, Majello B. RNA polymerase II CTD modifications: how many tales from a single tail. J Cell Physiol 2014; 229:538-44. [PMID: 24122273 DOI: 10.1002/jcp.24483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/30/2013] [Indexed: 12/31/2022]
Abstract
Eukaryote's RNA polymerases II (RNAPII) have the feature to contain, at the carbossi-terminal region of their largest subunit Rpb1, a unique CTD domain. Rpb1-CTD is composed of an increasing number of repetitions of the Y1 S2 P3 T4 S5 P6 S7 heptad that goes in parallel with the developmental level of organisms. Because of its composition, the CTD domain has a huge structural plasticity; virtually all the residues can be subjected to post-translational modifications and the two prolines can either be in cis or trans conformations. In light of these features, it is reasonable to think that different specific nuances of CTD modification and interacting factors take place not only on different gene promoters but also during different stages of the transcription cycle and reasonably might have a role even if the polymerase is on or off the DNA template. Rpb1-CTD domain is involved not only in regulating transcriptional rates, but also in all co-transcriptional processes, such as pre-mRNA processing, splicing, cleavage, and export. Moreover, recent studies highlight a role of CTD in DNA replication and in maintenance of genomic stability and specific CTD-modifications have been related to different CTD functions. In this paper, we examine results from the most recent CTD-related literature and give an overview of the general function of Rpb1-CTD in transcription, transcription-related and non transcription-related processes in which it has been recently shown to be involved in.
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Convertini P, Shen M, Potter PM, Palacios G, Lagisetti C, de la Grange P, Horbinski C, Fondufe-Mittendorf YN, Webb TR, Stamm S. Sudemycin E influences alternative splicing and changes chromatin modifications. Nucleic Acids Res 2014; 42:4947-61. [PMID: 24623796 PMCID: PMC4005683 DOI: 10.1093/nar/gku151] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sudemycin E is an analog of the pre-messenger RNA splicing modulator FR901464 and its derivative spliceostatin A. Sudemycin E causes the death of cancer cells through an unknown mechanism. We found that similar to spliceostatin A, sudemycin E binds to the U2 small nuclear ribonucleoprotein (snRNP) component SF3B1. Native chromatin immunoprecipitations showed that U2 snRNPs physically interact with nucleosomes. Sudemycin E induces a dissociation of the U2 snRNPs and decreases their interaction with nucleosomes. To determine the effect on gene expression, we performed genome-wide array analysis. Sudemycin E first causes a rapid change in alternative pre-messenger RNA splicing, which is later followed by changes in overall gene expression and arrest in the G2 phase of the cell cycle. The changes in alternative exon usage correlate with a loss of the H3K36me3 modification in chromatin encoding these exons. We propose that sudemycin E interferes with the ability of U2 snRNP to maintain an H3K36me3 modification in actively transcribed genes. Thus, in addition to the reversible changes in alternative splicing, sudemycin E causes changes in chromatin modifications that result in chromatin condensation, which is a likely contributing factor to cancer cell death.
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Affiliation(s)
- Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA and GenoSplice Technology, Hôpital Saint-Louis, Av Claude Vellefaux, 75010 Paris, France
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Abstract
SIGNIFICANCE Production of proteins requires the synthesis, maturation, and export of mRNAs before their translation in the cytoplasm. Endogenous and exogenous sources of DNA damage pose a challenge to the co-ordinated regulation of gene expression, because the integrity of the DNA template can be compromised by DNA lesions. Cells recognize and respond to this DNA damage through a variety of DNA damage responses (DDRs). Failure to deal with DNA damage appropriately can lead to genomic instability and cancer. RECENT ADVANCES The p53 tumor suppressor plays a dominant role in DDR-dependent changes in gene expression, but this transcription factor is not solely responsible for all changes. Recent evidence indicates that RNA metabolism is integral to DDRs as well. In particular, post-transcriptional processes are emerging as important contributors to these complex responses. CRITICAL ISSUES Transcriptional, post-transcriptional, and translational regulation of gene expression is subject to changes in response to DNA damage. How these processes are intertwined in the unfolding of DDR is not fully understood. FUTURE DIRECTIONS Many complex regulatory responses combine to determine cell fate after DNA damage. Understanding how transcriptional, post-transcriptional, and translational processes interdigitate to create a web of regulatory interactions will be one of the key challenges to fully understand DDRs.
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Affiliation(s)
- Bruce C McKay
- Department of Biology, Institute of Biochemistry, Carleton University , Ottawa, Canada
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Yadav SP, Hao H, Yang HJ, Kautzmann MAI, Brooks M, Nellissery J, Klocke B, Seifert M, Swaroop A. The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. Hum Mol Genet 2013; 23:2132-44. [PMID: 24301678 DOI: 10.1093/hmg/ddt609] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Phototransduction machinery in vertebrate photoreceptors is contained within the membrane discs of outer segments. Daily renewal of 10% of photoreceptor outer segments requires stringent control of gene expression. Rhodopsin constitutes over 90% of the protein in rod discs, and its altered expression or transport is associated with photoreceptor dysfunction and/or death. Two cis-regulatory sequences have been identified upstream of the rhodopsin transcription start site. While the proximal promoter binds to specific transcription factors, including NRL and CRX, the rhodopsin enhancer region (RER) reportedly contributes to precise and high-level expression of rhodopsin in vivo. Here, we report the identification of RER-bound proteins by mass spectrometry. We validate the binding of NonO (p54(nrb)), a protein implicated in coupling transcription to splicing, and three NonO-interacting proteins-hnRNP M, Ywhaz and Ppp1ca. NonO and its interactors can activate rhodopsin promoter in HEK293 cells and function synergistically with NRL and CRX. DNA-binding domain of NonO is critical for rhodopsin promoter activation. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analysis demonstrates high occupancy of NonO at rhodopsin and a subset of phototransduction genes. Furthermore, shRNA knockdown of NonO in mouse retina leads to loss of rhodopsin expression and rod cell death, which can be partially rescued by a C-terminal NonO construct. RNA-seq analysis of the NonO shRNA-treated retina revealed splicing defects and altered expression of genes, specifically those associated with phototransduction. Our studies identify an important contribution of NonO and its interacting modulator proteins in enhancing rod-specific gene expression and controlling rod homeostasis.
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Affiliation(s)
- Sharda P Yadav
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Cotter KA, Yershov A, Novillo A, Callard GV. Multiple structurally distinct ERα mRNA variants in zebrafish are differentially expressed by tissue type, stage of development and estrogen exposure. Gen Comp Endocrinol 2013; 194:217-29. [PMID: 24090614 PMCID: PMC3862120 DOI: 10.1016/j.ygcen.2013.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/04/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
It is well established that estrogen-like environmental chemicals interact with the ligand-binding site of estrogen receptors (ERs) to disrupt transcriptional control of estrogen responsive targets. Here we investigate the possibility that estrogens also impact splicing decisions on estrogen responsive genes, such as that encoding ERα itself. Targeted PCR cloning was applied to identify six ERα mRNA variants in zebrafish. Sequencing revealed alternate use of transcription and translation start sites, multiple exon deletions, intron retention and alternate polyadenylation. As determined by quantitative (q)PCR, N-terminal mRNA variants predicting long (ERαA(L)) and short (ERα(S)) isoforms were differentially expressed by tissue-type, sex, stage of development and estrogen exposure. Whereas ERα(L) mRNA was diffusely distributed in liver, brain, heart, eye, and gonads, ERα(S) mRNA was preferentially expressed in liver (female>male) and ovary. Neither ERα(L) nor ERα(S) transcripts varied significantly during development, but 17β-estradiol selectively increased accumulation of ERα(S) mRNA (∼170-fold by 120 hpf), an effect mimicked by bisphenol-A and diethylstilbestrol. Significantly, a C-truncated variant (ERα(S)-Cx) lacking most of the ligand binding and AF-2 domains was transcribed exclusively from the short isoform promoter and was similar to ERα(S) in its tissue-, stage- and estrogen inducible expression. These results support the idea that promoter choice and alternative splicing of the esr1 gene of zebrafish are part of the autoregulatory mechanism by which estrogen modulates subsequent ERα expression, and further suggest that environmental estrogens could exert some of their toxic effects by altering the relative abundance of structurally and functionally distinct ERα isoforms.
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Affiliation(s)
- Kellie A. Cotter
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
| | - Anya Yershov
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
| | - Apolonia Novillo
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
| | - Gloria V. Callard
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
- Corresponding author: (617-353-8980)
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Guzeloglu-Kayisli O, Lalioti MD, Babayev E, Torrealday S, Karakaya C, Seli E. Human embryonic poly(A)-binding protein (EPAB) alternative splicing is differentially regulated in human oocytes and embryos. Mol Hum Reprod 2013; 20:59-65. [PMID: 24002949 DOI: 10.1093/molehr/gat061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Oocyte maturation is associated with suppression of transcriptional activity. Consequently, gene expression during oocyte maturation, fertilization and early embryo development, until zygotic genome activation (ZGA) is primarily regulated by translational activation of maternally derived mRNAs. Embryonic poly(A)-binding protein (EPAB) is the predominant poly(A)-binding protein in Xenopus, mouse and human oocytes and early embryos prior to ZGA. EPAB plays a key role in polyadenylation-dependent translational activation of mRNAs by stabilizing polyadenylated mRNAs and by stimulating their translation. Epab-knockout female mice are sterile, fail to generate mature oocytes and display impaired cumulus expansion and ovulation. Consistent with its role during gametogenesis and early embryo development, Xenopus and mouse Epab mRNA is expressed exclusively in oocytes and early embryos, and is undetectable following ZGA or in somatic tissues. Herein, we demonstrate that although EPAB is expressed in human somatic tissues, its transcripts largely consist of an alternatively spliced form lacking the first 58 bp of exon 8, which leads to the formation of a premature stop codon 6 amino acids downstream on exon 8, and omission of the functionally critical poly(A)-binding domain. Moreover, 8-cell and blastocyst stage human embryos also express only the alternatively spliced form of EPAB. On the other hand, the full-length form of EPAB mRNA is exclusively expressed in oocytes. In conclusion, in contrast with the transcriptional regulation in Xenopus and mouse, oocyte- and early embryo-specific expression of EPAB in human is regulated by a post-transcriptional mechanism.
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Affiliation(s)
- Ozlem Guzeloglu-Kayisli
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 310 Cedar Street, LSOG 304B, New Haven, CT 06520-8063, USA
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Mattioli C, Pianigiani G, Pagani F. A competitive regulatory mechanism discriminates between juxtaposed splice sites and pri-miRNA structures. Nucleic Acids Res 2013; 41:8680-91. [PMID: 23863840 PMCID: PMC3794580 DOI: 10.1093/nar/gkt614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We have explored the functional relationships between spliceosome and Microprocessor complex activities in a novel class of microRNAs (miRNAs), named Splice site Overlapping (SO) miRNAs, whose pri-miRNA hairpins overlap splice sites. We focused on the evolutionarily conserved SO miR-34b, and we identified two indispensable elements for recognition of its 3′ splice site: a branch point located in the hairpin and a downstream purine-rich exonic splicing enhancer. In minigene systems, splicing inhibition owing to exonic splicing enhancer deletion or AG 3′ss mutation increases miR-34b levels. Moreover, small interfering-mediated silencing of Drosha and/or DGCR8 improves splicing efficiency and abolishes miR-34b production. Thus, the processing of this 3′ SO miRNA is regulated in an antagonistic manner by the Microprocessor and the spliceosome owing to competition between these two machineries for the nascent transcript. We propose that this novel mechanism is commonly used to regulate the relative amount of SO miRNA and messenger RNA produced from primary transcripts.
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Affiliation(s)
- Chiara Mattioli
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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Rittore C, Sanchez E, Soler S, Barat-Houari M, Albers M, Obici L, McDermott MF, Touitou I, Grandemange S. Identification of a new exon 2-skipped TNFR1 transcript: regulation by three functional polymorphisms of the TNFR-associated periodic syndrome (TRAPS) gene. Ann Rheum Dis 2013; 73:290-7. [PMID: 23505244 DOI: 10.1136/annrheumdis-2012-203023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mutations in the TNFRSF1A gene encoding the tumour necrosis factor α cell surface receptor, TNFR1, cause TNFR-associated periodic syndrome (TRAPS) and polymorphisms in TNFRSF1A, including rs4149570, rs767455 and rs1800692, are associated with inflammatory diseases. OBJECTIVES To describe a new exon 2-spliced transcript-TNFR1-d2-and the impact of these three single nucleotide polymorphisms on exon 2 splicing, transcriptional activity of TNFRSF1A and TRAPS phenotype. METHODS Expression of TNFRSF1A transcripts was performed by reverse-transcription-PCR in a range of human cells and tissues. Exon 2 splicing and transcriptional activity were analysed in HEK293T and SW480 cells by in vitro alternative splicing and luciferase assays, respectively. We constructed haplotypes containing rs4149570, rs767455 and rs1800692 in controls (n=72), patients with TRAPS (n=111) and in TRAPS-like patients (n=450) to compare their distribution and association with clinical features of TRAPS. RESULTS TNFR1-d2 was expressed in a tissue-specific manner, whereas TNFR1 expression was ubiquitous. Alternative splicing assays showed that the T-A-T haplotype at rs4149570-rs767455-rs1800692 had a significantly higher expression of exon 2-skipping product (p=0.02) compared with the G-G-C haplotype. Transcriptional activity from the T-T haplotype at rs4149570-rs1800692 was increased compared with the G-C haplotype (p=0.03). In patients with TRAPS, rs1800692 T/T homozygotes were excessively rare (p<10(-4)) and TRAPS-like patients with this genotype experienced less fever. CONCLUSIONS Our study provides a new mechanism of TNFRSF1A regulation whereby three polymorphisms in the promoter, exon 1 and intron 4 have a functional and combined effect on exon 2 splicing, via a coupling mechanism between transcription and splicing. These polymorphisms may affect the phenotype of TRAPS and TRAPS-like patients.
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Affiliation(s)
- Cécile Rittore
- Génétique des maladies Autoinflammatoires et des ostéoarthropathies chroniques, INSERM U844, Hôpital Saint Eloi, Bâtiment INM, , Montpellier, France
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Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 2013; 14:153-65. [PMID: 23385723 DOI: 10.1038/nrm3525] [Citation(s) in RCA: 569] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alternative splicing was discovered simultaneously with splicing over three decades ago. Since then, an enormous body of evidence has demonstrated the prevalence of alternative splicing in multicellular eukaryotes, its key roles in determining tissue- and species-specific differentiation patterns, the multiple post- and co-transcriptional regulatory mechanisms that control it, and its causal role in hereditary disease and cancer. The emerging evidence places alternative splicing in a central position in the flow of eukaryotic genetic information, between transcription and translation, in that it can respond not only to various signalling pathways that target the splicing machinery but also to transcription factors and chromatin structure.
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Affiliation(s)
- Alberto R Kornblihtt
- Departamento de Fisiología, Biología Molecular y Celular e Instituto de Fisiología, Biología Molecular y Neurociencias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina.
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Gui YX, Xu ZP, Lv W, Liu HM, Zhao JJ, Hu XY. Association of mitochondrial DNA polymerase γ gene POLG1 polymorphisms with parkinsonism in Chinese populations. PLoS One 2012; 7:e50086. [PMID: 23251356 PMCID: PMC3519471 DOI: 10.1371/journal.pone.0050086] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
Background Mitochondrial DNA polymerase gamma (POLG1) mutations were associated with levodopa-responsive Parkinsonism. POLG1 gene contains a number of common nonsynonymous SNPs and intronic regulatory SNPs which may have functional consequences. It is of great interest to discover polymorphisms variants associated with Parkinson's disease (PD), both in isolation and in combination with specific SNPs. Materials and Methods We conducted a case-control study and genotyped twenty SNPs and poly-Q polymorphisms of POLG1 gene including in 344 Chinese sporadic PD patients and 154 healthy controls. All the polymorphisms of POLG1 we found in this study were sequenced by PCR products with dye terminator methods using an ABI-3100 sequencer. Hardy-Weinberg equilibrium and linkage disequilibrium (LD) for association between twenty POLG1 SNPs and PD were calculated using the program Haploview. Principal Results We provided evidence for strong association of four intronic SNPs of the POLG1 gene (new report: c.2070-12T>A and rs2307439: c.2070-64G>A in intron 11, P = 0.00011, OR = 1.727; rs2302084: c.3105-11T>C and rs2246900: c.3105-36A>G in intron 19, P = 0.00031, OR = 1.648) with PD. However, we did not identify any significant association between ten exonic SNPs of POLG1 and PD. Linkage disequilibrium analysis indicated that c.2070-12T>A and c.2070-64G>A could be parsed into one block as Haplotype 1 as well as c.3105-11T>C and c.3105-36A>G in Haplotype 2. In addition, case and control study on association of POLG1 CAG repeat (poly-Q) alleles with PD showed a significant association (P = 0.03, OR = 2.16) of the non-10/11Q variants with PD. Although intronic SNPs associated with PD didn't influence POLG1 mRNA alternative splicing, there was a strong association of c.2070-12T>A and c.2070-64G>A with decreased POLG1 mRNA level and protein levels. Conclusions Our findings indicate that POLG1 may play a role in the pathogenesis of PD in Chinese populations.
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Affiliation(s)
- Ya-xing Gui
- Department of Neurology, Sir Run Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Miura K, Fujibuchi W, Unno M. Splice isoforms as therapeutic targets for colorectal cancer. Carcinogenesis 2012; 33:2311-9. [PMID: 23118106 DOI: 10.1093/carcin/bgs347] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Alternative pre-mRNA splicing allows exons of pre-mRNA to be spliced in different arrangements to produce functionally distinct mRNAs. More than 95% of human genes encode splice isoforms, some of which exert antagonistic functions. Recent studies revealed that alterations of the splicing machinery can cause the development of neoplasms, and understanding the splicing machinery is crucial for developing novel therapeutic strategies for malignancies. Colorectal cancer patients need novel strategies not only to enhance the efficacy of the currently available agents but also to utilize newly identified therapeutic targets. This review summarizes the current knowledge about the splice isoforms of VEGFA, UGT1A, PXR, cyclin D1, BIRC5 (survivin), DPD, K-RAS, SOX9, SLC39A14 and other genes, which may be possible therapeutic targets for colorectal cancer. Among them, the VEGFA splice isoforms are classified into VEGFAxxx and VEGFAxxxb, which have proangiogenic and antiangiogenic properties, respectively; UGT1A is alternatively spliced into UGT1A1 and other isoforms, which are regulated by pregnane X receptor isoforms and undergo further splicing modifications. Recently, the splicing machinery has been extensively investigated and novel discoveries in this research field are being reported at a rapid pace. The information contained in this review also provides suggestions for how therapeutic strategies targeting alternative splicing can be further developed.
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Affiliation(s)
- Koh Miura
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan.
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