1
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Yuan CU, Quah FX, Hemberg M. Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing. Mol Aspects Med 2024; 96:101255. [PMID: 38368637 DOI: 10.1016/j.mam.2024.101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Single-cell technologies have transformed biomedical research over the last decade, opening up new possibilities for understanding cellular heterogeneity, both at the genomic and transcriptomic level. In addition, more recent developments of spatial transcriptomics technologies have made it possible to profile cells in their tissue context. In parallel, there have been substantial advances in sequencing technologies, and the third generation of methods are able to produce reads that are tens of kilobases long, with error rates matching the second generation short reads. Long reads technologies make it possible to better map large genome rearrangements and quantify isoform specific abundances. This further improves our ability to characterize functionally relevant heterogeneity. Here, we show how researchers have begun to combine single-cell, spatial transcriptomics, and long-read technologies, and how this is resulting in powerful new approaches to profiling both the genome and the transcriptome. We discuss the achievements so far, and we highlight remaining challenges and opportunities.
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Affiliation(s)
- Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Hemberg
- Gene Lay Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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2
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Monette A, Niu M, Maldonado RK, Chang J, Lambert GS, Flanagan JM, Cochrane A, Parent LJ, Mouland AJ. Influence of HIV-1 Genomic RNA on the Formation of Gag Biomolecular Condensates. J Mol Biol 2023; 435:168190. [PMID: 37385580 PMCID: PMC10838171 DOI: 10.1016/j.jmb.2023.168190] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
Biomolecular condensates (BMCs) play an important role in the replication of a growing number of viruses, but many important mechanistic details remain to be elucidated. Previously, we demonstrated that the pan-retroviral nucleocapsid (NC) and HIV-1 pr55Gag (Gag) proteins phase separate into condensates, and that HIV-1 protease (PR)-mediated maturation of Gag and Gag-Pol precursor proteins yields self-assembling BMCs that have HIV-1 core architecture. Using biochemical and imaging techniques, we aimed to further characterize the phase separation of HIV-1 Gag by determining which of its intrinsically disordered regions (IDRs) influence the formation of BMCs, and how the HIV-1 viral genomic RNA (gRNA) could influence BMC abundance and size. We found that mutations in the Gag matrix (MA) domain or the NC zinc finger motifs altered condensate number and size in a salt-dependent manner. Gag BMCs were also bimodally influenced by the gRNA, with a condensate-promoting regime at lower protein concentrations and a gel dissolution at higher protein concentrations. Interestingly, incubation of Gag with CD4+ T cell nuclear lysates led to the formation of larger BMCs compared to much smaller ones observed in the presence of cytoplasmic lysates. These findings suggest that the composition and properties of Gag-containing BMCs may be altered by differential association of host factors in nuclear and cytosolic compartments during virus assembly. This study significantly advances our understanding of HIV-1 Gag BMC formation and provides a foundation for future therapeutic targeting of virion assembly.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Meijuan Niu
- Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Rebecca Kaddis Maldonado
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Jordan Chang
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Gregory S Lambert
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - John M Flanagan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Leslie J Parent
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.
| | - Andrew J Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, Québec H3T 1E2, Canada; Department of Medicine, McGill University, Montréal, Québec H4A 3J1, Canada.
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3
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van den Oord EJCG, Aberg KA. Fine-grained cell-type specific association studies with human bulk brain data using a large single-nucleus RNA sequencing based reference panel. Sci Rep 2023; 13:13004. [PMID: 37563216 PMCID: PMC10415334 DOI: 10.1038/s41598-023-39864-2] [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: 07/25/2022] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Brain disorders are leading causes of disability worldwide. Gene expression studies provide promising opportunities to better understand their etiology but it is critical that expression is studied on a cell-type level. Cell-type specific association studies can be performed with bulk expression data using statistical methods that capitalize on cell-type proportions estimated with the help of a reference panel. To create a fine-grained reference panel for the human prefrontal cortex, we performed an integrated analysis of the seven largest single nucleus RNA-seq studies. Our panel included 17 cell-types that were robustly detected across all studies, subregions of the prefrontal cortex, and sex and age groups. To estimate the cell-type proportions, we used an empirical Bayes estimator that substantially outperformed three estimators recommended previously after a comprehensive evaluation of methods to estimate cell-type proportions from brain transcriptome data. This is important as being able to precisely estimate the cell-type proportions may avoid unreliable results in downstream analyses particularly for the multiple cell-types that had low abundances. Transcriptome-wide association studies performed with permuted bulk expression data showed that it is possible to perform transcriptome-wide association studies for even the rarest cell-types without an increased risk of false positives.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, McGuire Hall, Room 216A, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA.
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, McGuire Hall, Room 216A, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
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4
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Monette A, Niu M, Maldonado RK, Chang J, Lambert GS, Flanagan JM, Cochrane A, Parent LJ, Mouland AJ. Influence of HIV-1 genomic RNA on the formation of Gag biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529585. [PMID: 36865181 PMCID: PMC9980109 DOI: 10.1101/2023.02.23.529585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Biomolecular condensates (BMCs) play an important role in the replication of a growing number of viruses, but many important mechanistic details remain to be elucidated. Previously, we demonstrated that pan-retroviral nucleocapsid (NC) and the HIV-1 pr55 Gag (Gag) proteins phase separate into condensates, and that HIV-1 protease (PR)-mediated maturation of Gag and Gag-Pol precursor proteins yield self-assembling BMCs having HIV-1 core architecture. Using biochemical and imaging techniques, we aimed to further characterize the phase separation of HIV-1 Gag by determining which of its intrinsically disordered regions (IDRs) influence the formation of BMCs and how the HIV-1 viral genomic RNA (gRNA) could influence BMC abundance and size. We found that mutations in the Gag matrix (MA) domain or the NC zinc finger motifs altered condensate number and size in a salt-dependent manner. Gag BMCs were also bimodally influenced by the gRNA, with a condensate-promoting regime at lower protein concentrations and a gel dissolution at higher protein concentrations. Interestingly, incubation of Gag with CD4 + T cell nuclear lysates led to the formation of larger BMCs as compared to much smaller ones observed in the presence of cytoplasmic lysates. These findings suggests that the composition and properties of Gag-containing BMCs may be altered by differential association of host factors in nuclear and cytosolic compartments during virus assembly. This study significantly advances our understanding of HIV-1 Gag BMC formation and provides a foundation for future therapeutic targeting of virion assembly.
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5
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Luo HY, Shen HY, Perkins RS, Wang YX. Adenosine Kinase on Deoxyribonucleic Acid Methylation: Adenosine Receptor-Independent Pathway in Cancer Therapy. Front Pharmacol 2022; 13:908882. [PMID: 35721189 PMCID: PMC9200284 DOI: 10.3389/fphar.2022.908882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Methylation is an important mechanism contributing to cancer pathology. Methylation of tumor suppressor genes and oncogenes has been closely associated with tumor occurrence and development. New insights regarding the potential role of the adenosine receptor-independent pathway in the epigenetic modulation of DNA methylation offer the possibility of new interventional strategies for cancer therapy. Targeting DNA methylation of cancer-related genes is a promising therapeutic strategy; drugs like 5-Aza-2′-deoxycytidine (5-AZA-CdR, decitabine) effectively reverse DNA methylation and cancer cell growth. However, current anti-methylation (or methylation modifiers) are associated with severe side effects; thus, there is an urgent need for safer and more specific inhibitors of DNA methylation (or DNA methylation modifiers). The adenosine signaling pathway is reported to be involved in cancer pathology and participates in the development of tumors by altering DNA methylation. Most recently, an adenosine metabolic clearance enzyme, adenosine kinase (ADK), has been shown to influence methylation on tumor suppressor genes and tumor development and progression. This review article focuses on recent updates on ADK and its two isoforms, and its actions in adenosine receptor-independent pathways, including methylation modification and epigenetic changes in cancer pathology.
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Affiliation(s)
- Hao-Yun Luo
- Chongqing Medical University, Chongqing, China.,Department of Gastrointestinal and Anorectal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Hai-Ying Shen
- Department of Neuroscience, Legacy Research Institute, Portland, OR, United States.,Integrative Physiology and Neuroscience, Washington State University, Vancouver, WA, United States
| | - R Serene Perkins
- Legacy Tumor Bank, Legacy Research Institute, Portland, OR, United States.,Mid-Columbia Medical Center, The Dalles, OR, United States
| | - Ya-Xu Wang
- Chongqing Medical University, Chongqing, China.,Department of Gastrointestinal and Anorectal Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
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6
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Oguchi Y, Ozaki Y, Abdelmoez MN, Shintaku H. NanoSINC-seq dissects the isoform diversity in subcellular compartments of single cells. SCIENCE ADVANCES 2021; 7:7/15/eabe0317. [PMID: 33827812 PMCID: PMC8026137 DOI: 10.1126/sciadv.abe0317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Alternative mRNA isoforms play a key role in generating diverse protein isoforms. To dissect isoform usage in the subcellular compartments of single cells, we introduced an novel approach, nanopore sequencing coupled with single-cell integrated nuclear and cytoplasmic RNA sequencing, that couples microfluidic fractionation, which separates cytoplasmic RNA from nuclear RNA, with full-length complementary DNA (cDNA) sequencing using a nanopore sequencer. Leveraging full-length cDNA reads, we found that the nuclear transcripts are notably more diverse than cytoplasmic transcripts. Our findings also indicated that transcriptional noise emanating from the nucleus is regulated across the nuclear membrane and then either attenuated or amplified in the cytoplasm depending on the function involved. Overall, our results provide the landscape that shows how the transcriptional noise arising from the nucleus propagates to the cytoplasm.
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Affiliation(s)
- Yusuke Oguchi
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuka Ozaki
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
| | | | - Hirofumi Shintaku
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan.
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7
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Zaghlool A, Niazi A, Björklund ÅK, Westholm JO, Ameur A, Feuk L. Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts. Sci Rep 2021; 11:4076. [PMID: 33603054 PMCID: PMC7893067 DOI: 10.1038/s41598-021-83541-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/20/2021] [Indexed: 12/23/2022] Open
Abstract
Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.
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Affiliation(s)
- Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden. .,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden.
| | - Adnan Niazi
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden.,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden
| | - Åsa K Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden.,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden. .,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden.
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8
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Fuchs A, Riegler S, Ayatollahi Z, Cavallari N, Giono LE, Nimeth BA, Mutanwad KV, Schweighofer A, Lucyshyn D, Barta A, Petrillo E, Kalyna M. Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing. Nucleic Acids Res 2021; 49:1133-1151. [PMID: 33406240 PMCID: PMC7826280 DOI: 10.1093/nar/gkaa1260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
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Affiliation(s)
- Armin Fuchs
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Stefan Riegler
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Zahra Ayatollahi
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Nicola Cavallari
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Barbara A Nimeth
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Krishna V Mutanwad
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | | | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Ezequiel Petrillo
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
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9
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Perlman K, Couturier CP, Yaqubi M, Tanti A, Cui QL, Pernin F, Stratton JA, Ragoussis J, Healy L, Petrecca K, Dudley R, Srour M, Hall JA, Kennedy TE, Mechawar N, Antel JP. Developmental trajectory of oligodendrocyte progenitor cells in the human brain revealed by single cell RNA sequencing. Glia 2020; 68:1291-1303. [PMID: 31958186 DOI: 10.1002/glia.23777] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022]
Abstract
Characterizing the developmental trajectory of oligodendrocyte progenitor cells (OPC) is of great interest given the importance of these cells in the remyelination process. However, studies of human OPC development remain limited by the availability of whole cell samples and material that encompasses a wide age range, including time of peak myelination. In this study, we apply single cell RNA sequencing to viable whole cells across the age span and link transcriptomic signatures of oligodendrocyte-lineage cells with stage-specific functional properties. Cells were isolated from surgical tissue samples of second-trimester fetal, 2-year-old pediatric, 13-year-old adolescent, and adult donors by mechanical and enzymatic digestion, followed by percoll gradient centrifugation. Gene expression was analyzed using droplet-based RNA sequencing (10X Chromium). Louvain clustering analysis identified three distinct cellular subpopulations based on 5,613 genes, comprised of an early OPC (e-OPC) group, a late OPC group (l-OPC), and a mature OL (MOL) group. Gene ontology terms enriched for e-OPCs included cell cycle and development, for l-OPCs included extracellular matrix and cell adhesion, and for MOLs included myelination and cytoskeleton. The e-OPCs were mostly confined to the premyelinating fetal group, and the l-OPCs were most highly represented in the pediatric age group, corresponding to the peak age of myelination. Cells expressing a signature characteristic of l-OPCs were identified in the adult brain in situ using RNAScope. These findings highlight the transcriptomic variability in OL-lineage cells before, during, and after peak myelination and contribute to identifying novel pathways required to achieve remyelination.
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Affiliation(s)
- Kelly Perlman
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.,Department of Psychiatry, Douglas Mental Health University Institute, Montreal, Canada
| | - Charles P Couturier
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Moein Yaqubi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Arnaud Tanti
- Department of Psychiatry, Douglas Mental Health University Institute, Montreal, Canada
| | - Qiao-Ling Cui
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Florian Pernin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Jo Anne Stratton
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics and Bioengineering, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Luke Healy
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Roy Dudley
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.,Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, Canada
| | - Myriam Srour
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.,Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, Canada
| | - Jeffrey A Hall
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Timothy E Kennedy
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Mental Health University Institute, Montreal, Canada
| | - Jack P Antel
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
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10
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Shamloo B, Kumar N, Owen RH, Reemmer J, Ost J, Perkins RS, Shen HY. Dysregulation of adenosine kinase isoforms in breast cancer. Oncotarget 2019; 10:7238-7250. [PMID: 31921385 PMCID: PMC6944449 DOI: 10.18632/oncotarget.27364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Dysregulated adenosine signaling pathway has been evidenced in the pathogenesis of breast cancer. However, the role of adenosine kinase (ADK) in tumorigenesis remains unclear while it crucially regulates the removal and availability of adenosine. ADK has two isoforms that localize to discrete subcellular spaces: i.e., nuclear, long-isoform (ADK-L) and cytosolic, short-isoform (ADK-S). We hypothesized that these two ADK isoforms would be differentially expressed in breast cancer and may contribute to divergent cellular actions in cancer. In this study, we examined the expression profiles of ADK isoforms in breast cancer tissues from 46 patient and followed up with an in vitro investigation by knocking down the expression of ADK-L or ADK-S using CRISPR gene editing to evaluate the role of ADK isoform in cancer progression and metastasis of cultured triple-negative breast cancer cell line MDA-MB-231. We demonstrated that (i) ADK-L expression level was significantly increased in breast cancer tissues versus paired normal tissues adjacent to tumor, whereas the ADK-S expression levels were not significantly different between cancerous and normal tissues; (ii) CRISPR/Cas9-mediated downregulation of ADK isoforms, led to suppressed cellular proliferation, division, and migration of cultured breast cancer cells; (iii) ADK-L knockdown significantly upregulated gene expression of matrix metalloproteinase (ADAM23, 9.93-fold; MMP9, 24.58-fold) and downregulated expression of cyclin D2 (CCND2, -30.76-fold), adhesive glycoprotein THBS1 (-8.28-fold), and cystatin E/M (CST6, -16.32-fold). Our findings suggest a potential role of ADK-L in mitogenesis, tumorigenesis, and tumor-associated tissue remodeling and invasion; and the manipulation of ADK-L holds promise as a therapeutic strategy for aggressive breast cancer.
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Affiliation(s)
- Bahar Shamloo
- Department of Translational Neuroscience, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
| | - Nandita Kumar
- Department of Translational Neuroscience, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
| | - Randall H Owen
- Department of Translational Neuroscience, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
| | - Jesica Reemmer
- Department of Translational Neuroscience, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
| | - John Ost
- Legacy Tumor Bank, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
| | - R Serene Perkins
- Legacy Tumor Bank, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA.,Mid-Columbia Medical Center, The Dalles, OR 97058, USA
| | - Hai-Ying Shen
- Department of Translational Neuroscience, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
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11
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Pont MJ, Oostvogels R, van Bergen CA, van der Meijden ED, Honders MW, Bliss S, Jongsma ML, Lokhorst HM, Falkenburg JF, Mutis T, Griffioen M, Spaapen RM. T Cells Specific for an Unconventional Natural Antigen Fail to Recognize Leukemic Cells. Cancer Immunol Res 2019; 7:797-804. [DOI: 10.1158/2326-6066.cir-18-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 12/21/2018] [Accepted: 03/14/2019] [Indexed: 11/16/2022]
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12
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Palovaara J, Weijers D. Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo. PLANT REPRODUCTION 2019; 32:113-121. [PMID: 30430248 DOI: 10.1007/s00497-018-0347-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 05/06/2023]
Abstract
In the early embryo of vascular plants, the different cell types and stem cells of the seedling are specified as the embryo develops from a zygote towards maturity. How the key steps in cell and tissue specification are instructed by genome-wide transcriptional activity is poorly understood. Progress in defining transcriptional regulation at the genome-wide level in plant embryos has been hampered by difficulties associated with capturing cell-type-specific transcriptomes in this small and inaccessible structure. We recently adapted a two-component genetic nucleus labelling system called INTACT to isolate nuclei from distinct cell types at different stages of Arabidopsis thaliana embryogenesis. We have used these to generate a transcriptomic atlas of embryo development following microarray-based expression profiling. Here, we present a general description of the adapted INTACT procedure, including the two-component labelling system, seed isolation, nuclei preparation and purification, as well as transcriptomic profiling. We also compare nuclear and cellular transcriptomes from the early Arabidopsis embryo to assess nucleocytoplasmic differences and discuss how these differences can be used to infer regulation of gene activity.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Molecular Genetics, University of Bremen, 28359, Bremen, Germany
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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Goldie BJ, Fitzsimmons C, Weidenhofer J, Atkins JR, Wang DO, Cairns MJ. miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif. Front Mol Neurosci 2017; 10:259. [PMID: 28878619 PMCID: PMC5573442 DOI: 10.3389/fnmol.2017.00259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022] Open
Abstract
While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons.
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Affiliation(s)
- Belinda J Goldie
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia.,World Premier International Research Center - Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyoto, Japan
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
| | - Judith Weidenhofer
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
| | - Dan O Wang
- World Premier International Research Center - Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyoto, Japan.,The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in ResearchKyoto, Japan
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
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14
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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15
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Li Z, Vuong JK, Zhang M, Stork C, Zheng S. Inhibition of nonsense-mediated RNA decay by ER stress. RNA (NEW YORK, N.Y.) 2017; 23:378-394. [PMID: 27940503 PMCID: PMC5311500 DOI: 10.1261/rna.058040.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 12/06/2016] [Indexed: 05/26/2023]
Abstract
Nonsense-mediated RNA decay (NMD) selectively degrades mutated and aberrantly processed transcripts that contain premature termination codons (PTC). Cellular NMD activity is typically assessed using exogenous PTC-containing reporters. We overcame some inherently problematic aspects of assaying endogenous targets and developed a broadly applicable strategy to reliably and easily monitor changes in cellular NMD activity. Our new method was genetically validated for distinguishing NMD regulation from transcriptional control and alternative splicing regulation, and unexpectedly disclosed a different sensitivity of NMD targets to NMD inhibition. Applying this robust method for screening, we identified NMD-inhibiting stressors but also found that NMD inactivation was not universal to cellular stresses. The high sensitivity and broad dynamic range of our method revealed a strong correlation between NMD inhibition, endoplasmic reticulum (ER) stress, and polysome disassembly upon thapsigargin treatment in a temporal and dose-dependent manner. We found little evidence of calcium signaling mediating thapsigargin-induced NMD inhibition. Instead, we discovered that of the three unfolded protein response (UPR) pathways activated by thapsigargin, mainly protein kinase RNA-like endoplasmic reticulum kinase (PERK) was required for NMD inhibition. Finally, we showed that ER stress compounded TDP-43 depletion in the up-regulation of NMD isoforms that had been implicated in the pathogenic mechanisms of amyotrophic lateral sclerosis and frontotemporal dementia, and that the additive effect of ER stress was completely blocked by PERK deficiency.
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Affiliation(s)
- Zhelin Li
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - John K Vuong
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - Min Zhang
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - Cheryl Stork
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
| | - Sika Zheng
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
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16
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Smith JE, Baker KE. Nonsense-mediated RNA decay--a switch and dial for regulating gene expression. Bioessays 2015; 37:612-23. [PMID: 25820233 DOI: 10.1002/bies.201500007] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Nonsense-mediated RNA decay (NMD) represents an established quality control checkpoint for gene expression that protects cells from consequences of gene mutations and errors during RNA biogenesis that lead to premature termination during translation. Characterization of NMD-sensitive transcriptomes has revealed, however, that NMD targets not only aberrant transcripts but also a broad array of mRNA isoforms expressed from many endogenous genes. NMD is thus emerging as a master regulator that drives both fine and coarse adjustments in steady-state RNA levels in the cell. Importantly, while NMD activity is subject to autoregulation as a means to maintain homeostasis, modulation of the pathway by external cues provides a means to reprogram gene expression and drive important biological processes. Finally, the unanticipated observation that transcripts predicted to lack protein-coding capacity are also sensitive to this translation-dependent surveillance mechanism implicates NMD in regulating RNA function in new and diverse ways.
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Affiliation(s)
- Jenna E Smith
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Kristian E Baker
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, USA
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17
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Joo JH, Ryu D, Peng Q, Sugrue SP. Role of Pnn in alternative splicing of a specific subset of lncRNAs of the corneal epithelium. Mol Vis 2014; 20:1629-42. [PMID: 25489234 PMCID: PMC4235046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/14/2014] [Indexed: 11/08/2022] Open
Abstract
PURPOSE GG-H whole transcriptome array analysis suggested involvement of PININ (PNN) in the alternative splicing of multiple long non-coding RNAs (lncRNAs). To further investigate PNN's role in regulating the alternative splicing of lncRNAs in a corneal epithelial context, we performed detailed analyses for detecting and identifying alternatively spliced lncRNAs. METHODS Total RNA was isolated from PNN knockdown human corneal epithelial (HCET) cells or Pnn-deficient mouse corneas, and subjected to real-time-PCR (RT-PCR) assays, and the alternatively spliced lncRNAs were counted. Alternatively spliced lncRNAs were detected with in situ hybridization with variant-specific RNA probes on human cornea sections. RESULTS Our analysis uncovered PNN's impact on the transcript levels of several lncRNAs including Linc00085 and HAS2-AS1. Interestingly, a mouse ortholog of HAS2-AS1, Has2as, clearly exhibited a differential splicing pattern among three major splice variants in the Pnn-deficient mouse cornea. The sequence analyses and quantification of splice variants of candidate lncRNAs, including RP11-295B20.2, RP11-18I14.1, and RP11-322M19.1, demonstrated complex configuration of their splicing changes, with a significant impact of PNN on the process. Knockdown of PNN in HCET cells led to specific changes in the inclusion of multiple cassette exons as well as in the use of alternative splice sites in RP11-322M19.1 and RP11-18I14.1, resulting in considerable net changes in the ratio between the splice variants. Finally, in situ hybridization analyses revealed the presence of RP11-295G20.2 in the nuclei of corneal epithelial cells, but not in the stromal cells of the human cornea, while RP11-322M19.1 was present in epithelial and non-epithelial cells. CONCLUSIONS The data suggest PNN's role in the alternative splicing of a specific subset of lncRNAs might have a significant impact on the corneal epithelium.
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Affiliation(s)
- Jeong Hoon Joo
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL
| | - Danny Ryu
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL
| | - Qian Peng
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL
| | - Stephen P Sugrue
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL
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18
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Abstract
We developed a robust computational statistical framework to identify RNA editing events from RNA-Seq data with high specificity. Our approach handles several outstanding challenges of genome-wide editing analyses, including the effect of editing on read alignment and the utilization of redundant reads. By applying this framework, we characterized the nuclear and cytosolic editomes of seven human cell lines. We found that 93.8-99.2% of the editing events are A-to-G (or A-to-I). Nuclear transcriptomes contain many more editing events than cytosolic transcriptomes. Most of the sites exhibiting nucleus-specific editing are in introns or novel intergenic transcripts that are preferentially localized in the nucleus regardless of their editing status, arguing against the role of editing in nuclear retention. In contrast, many sites that exhibit cytosol-specific editing show comparable nuclear and cytosolic expression, suggesting the differential subcellular compartmentalization of the edited and the unedited alleles. We found that RNA editing is globally associated with the modification of microRNA regulation in 3' untranslated regions, whereas editing events in coding regions are rare and tend to be synonymous. Interestingly, A-to-G editing at derived alleles in the human lineage tends to result in reversion back to the ancestral forms at the RNA level. This suggests that editing can mediate RNA memory on evolutionary time-scales to maintain ancestral genetic information.
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19
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Zheng S, Damoiseaux R, Chen L, Black DL. A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing. Genome Res 2013; 23:998-1007. [PMID: 23636947 PMCID: PMC3668367 DOI: 10.1101/gr.147546.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 03/21/2013] [Indexed: 01/17/2023]
Abstract
Most mammalian genes produce multiple mRNA isoforms derived from alternative pre-mRNA splicing, with each alternative exon controlled by a complex network of regulatory factors. The identification of these regulators can be laborious and is usually carried out one factor at a time. We have developed a broadly applicable high-throughput screening method that simultaneously identifies multiple positive and negative regulators of a particular exon. Two minigene reporters were constructed: One produces green fluorescent protein (GFP) from the mRNA including an exon, and red fluorescent protein (RFP) from the mRNA lacking the exon; the other switches these fluorescent products of exon inclusion and exclusion. Combining results from these two reporters eliminates many false positives and greatly enriches for true splicing regulators. After extensive optimization of this method, we performed a gain-of-function screen of 15,779 cDNA clones and identified 40 genes affecting exon 18 of Discs large homolog 4 (Dlg4; also known as post-synaptic density protein 95 [Psd-95]). We confirmed that 28 of the 34 recoverable clones alter reporter splicing in RT-PCR assays. Remarkably, 18 of the identified genes encode splicing factors or RNA binding proteins, including PTBP1, a previously identified regulator of this exon. Loss-of-function experiments examining endogenous Dlg4 transcripts validated the effects of five of eight genes tested in independent cell lines, and two genes were further confirmed to regulate Dlg4 splicing in primary neurons. These results identify multiple new regulators of Dlg4 splicing, and validate an approach to isolating splicing regulators for almost any cassette exon from libraries of cDNAs, shRNAs, or small molecules.
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Affiliation(s)
- Sika Zheng
- Howard Hughes Medical Institute, University of California at Los Angeles, California 90095, USA
| | - Robert Damoiseaux
- Molecular Screening Shared Resource, University of California at Los Angeles, California 90095, USA
| | - Liang Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Douglas L. Black
- Howard Hughes Medical Institute, University of California at Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, California 90095, USA
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20
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Zheng S, Gray EE, Chawla G, Porse BT, O'Dell TJ, Black DL. PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci 2012; 15:381-8, S1. [PMID: 22246437 PMCID: PMC3288398 DOI: 10.1038/nn.3026] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/14/2011] [Indexed: 11/09/2022]
Abstract
Postsynaptic density protein 95 (PSD-95) is essential for synaptic maturation and plasticity. Although its synaptic regulation has been widely studied, the control of PSD-95 cellular expression is not understood. We found that Psd-95 was controlled post-transcriptionally during neural development. Psd-95 was transcribed early in mouse embryonic brain, but most of its product transcripts were degraded. The polypyrimidine tract binding proteins PTBP1 and PTBP2 repressed Psd-95 (also known as Dlg4) exon 18 splicing, leading to premature translation termination and nonsense-mediated mRNA decay. The loss of first PTBP1 and then of PTBP2 during embryonic development allowed splicing of exon 18 and expression of PSD-95 late in neuronal maturation. Re-expression of PTBP1 or PTBP2 in differentiated neurons inhibited PSD-95 expression and impaired the development of glutamatergic synapses. Thus, expression of PSD-95 during early neural development is controlled at the RNA level by two PTB proteins whose sequential downregulation is necessary for synapse maturation.
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Affiliation(s)
- Sika Zheng
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California, USA
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21
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Pandey R, Mukerji M. From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus. Brief Funct Genomics 2011; 10:294-311. [DOI: 10.1093/bfgp/elr029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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22
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't Hoen PAC, Hirsch M, de Meijer EJ, de Menezes RX, van Ommen GJ, den Dunnen JT. mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance. Nucleic Acids Res 2010; 39:556-66. [PMID: 20852259 PMCID: PMC3025562 DOI: 10.1093/nar/gkq790] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Expression profiling experiments usually provide a static snapshot of messenger RNA (mRNA) levels. Improved understanding of the dynamics of mRNA synthesis and degradation will aid the development of sound bioinformatic models for control of gene expression. We studied mRNA stability in proliferating and differentiated myogenic cells using whole-genome exon arrays and reported the decay rates (half life) for ∼7000 mRNAs. We showed that the stability of many mRNAs strongly depends on the differentiation status and contributes to differences in abundance of these mRNAs. In addition, alternative splicing turns out to be coupled to mRNA degradation. Although different splice forms may be produced at comparable levels, their relative abundance is partly determined by their different stabilities in proliferating and differentiated cells. Where the 3'-untranslated region (3'-UTR) was previously thought to contain most RNA stabilizing and destabilizing elements, we showed that this also holds for transcript isoforms sharing the same 3'-UTR. There are two splice variants in Itga7, of which the isoform with an extra internal exon is highly stable in differentiated cells but preferentially degraded in the cytoplasm of proliferating cells. In conclusion, control of stability and degradation emerge as important determinants for differential expression of mRNA transcripts and splice variants.
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Affiliation(s)
- Peter A C 't Hoen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Whistler T, Chiang CF, Lonergan W, Hollier M, Unger ER. Implementation of exon arrays: alternative splicing during T-cell proliferation as determined by whole genome analysis. BMC Genomics 2010; 11:496. [PMID: 20840771 PMCID: PMC2996992 DOI: 10.1186/1471-2164-11-496] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 09/14/2010] [Indexed: 12/22/2022] Open
Abstract
Background The contribution of alternative splicing and isoform expression to cellular response is emerging as an area of considerable interest, and the newly developed exon arrays allow for systematic study of these processes. We use this pilot study to report on the feasibility of exon array implementation looking to replace the 3' in vitro transcription expression arrays in our laboratory. One of the most widely studied models of cellular response is T-cell activation from exogenous stimulation. Microarray studies have contributed to our understanding of key pathways activated during T-cell stimulation. We use this system to examine whole genome transcription and alternate exon usage events that are regulated during lymphocyte proliferation in an attempt to evaluate the exon arrays. Results Peripheral blood mononuclear cells form healthy donors were activated using phytohemagglutinin, IL2 and ionomycin and harvested at 5 points over a 7 day period. Flow cytometry measured cell cycle events and the Affymetrix exon array platform was used to identify the gene expression and alternate exon usage changes. Gene expression changes were noted in a total of 2105 transcripts, and alternate exon usage identified in 472 transcript clusters. There was an overlap of 263 transcripts which showed both differential expression and alternate exon usage over time. Gene ontology enrichment analysis showed a broader range of biological changes in biological processes for the differentially expressed genes, which include cell cycle, cell division, cell proliferation, chromosome segregation, cell death, component organization and biogenesis and metabolic process ontologies. The alternate exon usage ontological enrichments are in metabolism and component organization and biogenesis. We focus on alternate exon usage changes in the transcripts of the spliceosome complex. The real-time PCR validation rates were 86% for transcript expression and 71% for alternate exon usage. Conclusions This study illustrates that the Exon array technology has the potential to provide information on both transcript expression and isoform usage, with very little increase in expense.
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Affiliation(s)
- Toni Whistler
- Chronic Viral Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases (proposed), Centers for Disease Control and Prevention, Atlanta GA 30333, USA.
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