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Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Getting the Entire Message: Progress in Isoform Sequencing. Front Genet 2019; 10:709. [PMID: 31475029 PMCID: PMC6706457 DOI: 10.3389/fgene.2019.00709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/04/2019] [Indexed: 01/31/2023] Open
Abstract
The advent of second-generation sequencing and its application to RNA sequencing have revolutionized the field of genomics by allowing quantification of gene expression, as well as the definition of transcription start/end sites, exons, splice sites and RNA editing sites. However, due to the sequencing of fragments of cDNAs, these methods have not given a reliable picture of complete RNA isoforms. Third-generation sequencing has filled this gap and allows end-to-end sequencing of entire RNA/cDNA molecules. This approach to transcriptomics has been a "niche" technology for a couple of years but now is becoming mainstream with many different applications. Here, we review the background and progress made to date in this rapidly growing field. We start by reviewing the progressive realization that alternative splicing is omnipresent. We then focus on long-noncoding RNA isoforms and the distinct combination patterns of exons in noncoding and coding genes. We consider the implications of the recent technologies of direct RNA sequencing and single-cell isoform RNA sequencing. Finally, we discuss the parameters that define the success of long-read RNA sequencing experiments and strategies commonly used to make the most of such data.
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Affiliation(s)
- Simon A. Hardwick
- Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Anoushka Joglekar
- Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Hagen U. Tilgner
- Brain and Mind Research Institute, Weill Cornell Medicine, NY, United States
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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53
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Cibi DM, Mia MM, Guna Shekeran S, Yun LS, Sandireddy R, Gupta P, Hota M, Sun L, Ghosh S, Singh MK. Neural crest-specific deletion of Rbfox2 in mice leads to craniofacial abnormalities including cleft palate. eLife 2019; 8:45418. [PMID: 31241461 PMCID: PMC6663295 DOI: 10.7554/elife.45418] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/25/2019] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) creates proteomic diversity from a limited size genome by generating numerous transcripts from a single protein-coding gene. Tissue-specific regulators of AS are essential components of the gene regulatory network, required for normal cellular function, tissue patterning, and embryonic development. However, their cell-autonomous function in neural crest development has not been explored. Here, we demonstrate that splicing factor Rbfox2 is expressed in the neural crest cells (NCCs), and deletion of Rbfox2 in NCCs leads to cleft palate and defects in craniofacial bone development. RNA-Seq analysis revealed that Rbfox2 regulates splicing and expression of numerous genes essential for neural crest/craniofacial development. We demonstrate that Rbfox2-TGF-β-Tak1 signaling axis is deregulated by Rbfox2 deletion. Furthermore, restoration of TGF-β signaling by Tak1 overexpression can rescue the proliferation defect seen in Rbfox2 mutants. We also identified a positive feedback loop in which TGF-β signaling promotes expression of Rbfox2 in NCCs. Abnormalities affecting the head and face – such as a cleft lip or palate – are among the most common of all birth defects. These tissues normally develop from cells in the embryo known as the neural crest cells, and specifically a subset of these cells called the cranial neural crest cells. Most cases of cleft lip or palate are linked back to genes that affect the biology of this group of cells. The list of genes implicated in the impaired development of cranial neural crest cells code for proteins with a wide range of different activities. Some encode transcription factors – proteins that switch genes on or off. Others code for chromatin remodeling factors, which control how the DNA is packed inside cells. However, the role of another group of proteins – the splicing factors – remains unclear and warrants further investigation. When a gene is switched on its genetic code is first copied into a short-lived molecule called a transcript. These transcripts are then edited to form templates to build proteins. Splicing is one way that a transcript can be edited, which involves different pieces of the transcript being cut out and the remaining pieces being pasted together to form alternative versions of the final template. Splicing factors control this process. Cibi et al. now show that neural crest cells from mice make a splicing factor called Rbfox2 and that deleting this gene for this protein from only these cells leads to mice with a cleft palate and defects in the bones of their head and face. Further analysis helped to identify the transcripts that are spliced by Rbfox2, and the effects that these splicing events have on gene activity in mouse tissues that develop from cranial neural crest cells. Cibi et al. went on to find a signaling pathway that was impaired in the mutant cells that lacked Rbfox2. Forcing the mutant cells to over-produce one of the proteins involved in this signaling pathway (a protein named Tak1) was enough to compensate for the some of the defects caused by a lack of Rbfox2, suggesting it acts downstream of the splicing regulator. Lastly, Cibi et al. showed that another protein in this signaling pathway, called TGF-β, acted to increase how much Rbfox2 was made by neural crest cells. Together these findings may be relevant in human disease studies, given that altered TGF-β signaling is a common feature in many birth defects seen in humans.
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Affiliation(s)
- Dasan Mary Cibi
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Masum M Mia
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Shamini Guna Shekeran
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Lim Sze Yun
- National Heart Research Institute, National Heart Center, Singapore, Singapore
| | - Reddemma Sandireddy
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Priyanka Gupta
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Monalisa Hota
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Lei Sun
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Sujoy Ghosh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Manvendra K Singh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.,National Heart Research Institute, National Heart Center, Singapore, Singapore
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Sharma V, Nandan A, Singh H, Agarwal S, Tripathi R, Sinha DN, Mehrotra R. Events of alternative splicing in head and neck cancer via RNA sequencing - an update. BMC Genomics 2019; 20:442. [PMID: 31159745 PMCID: PMC6545735 DOI: 10.1186/s12864-019-5794-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 05/10/2019] [Indexed: 12/28/2022] Open
Abstract
Background Alternative splicing (AS) is a regulatory mechanism used to create many forms of mature messengers RNAs (mRNAs) from the same gene. Sequencing of RNA (RNA-Seq) is an advanced technology, which has been utilized by different studies to find AS mechanisms in head and neck cancer (HNC). Hitherto, there is no available review that could inform us of the major findings from these studies. Hence, we aim to perform a systematic literature search following PRISMA guidelines to study AS events in HNC identified through RNA-Seq studies. Results A total of five records were identified that utilized RNA-Seq data for identifying AS events in HNC. Five software was used in these records to identify AS events. Two genes influenced by AS i.e. MLL3 and RPS9 were found to be common in 4 out of 5 records. Likewise, 38 genes were identified to be similar in at least 3 records. Conclusions Alternative splicing in HNC is a multifaceted regulatory mechanism of gene expression. It can be studied via RNA-Seq using different bioinformatics tools. Genes MLL3, as well as RPS9, were repeatedly found to be associated with HNC, however needs further functional validation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5794-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vishwas Sharma
- Department of Health Research, National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Amrita Nandan
- Society for Life Science and Human Health, Allahabad, Uttar Pradesh, India
| | - Harpreet Singh
- ICMR Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India.,Informatics, Systems and Research Management, Indian Council of Medical Research, New Delhi, 110029, India
| | - Suyash Agarwal
- ICMR Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India.,Informatics, Systems and Research Management, Indian Council of Medical Research, New Delhi, 110029, India
| | - Richa Tripathi
- Division of Molecular Cytology, National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Dhirendra Narain Sinha
- WHO FCTC Global Knowledge Hub on Smokeless Tobacco, National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Ravi Mehrotra
- Department of Health Research, National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India.
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Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing. BMC Med Genomics 2019; 12:66. [PMID: 31118097 PMCID: PMC6532208 DOI: 10.1186/s12920-019-0529-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background In cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a major therapeutic challenge. The characterization of molecular mechanisms underlying impaired immune responses in CF may reveal novel targets with therapeutic potential. Therefore, we utilized simultaneous RNA sequencing targeted at identifying differentially expressed genes, transcripts, and miRNAs that characterize impaired immune responses triggered by CF and its phenotypes. Methods Peripheral blood mononuclear cells (PBMCs) extracted from a healthy donor were stimulated with plasma from CF patients (n = 9) and healthy controls (n = 3). The PBMCs were cultured (1 × 105 cells/well) for 9 h at 37 ° C in 5% CO2. After culture, total RNA was extracted from each sample and used for simultaneous total RNA and miRNA sequencing. Results Analysis of expression signatures from peripheral blood mononuclear cells induced by plasma of CF patients and healthy controls identified 151 genes, 154 individual transcripts, and 41 miRNAs differentially expressed in CF compared to HC while the expression signatures of 285 genes, 241 individual transcripts, and seven miRNAs differed due to CF phenotypes. Top immune pathways influenced by CF included agranulocyte adhesion, diapedesis signaling, and IL17 signaling, while those influenced by CF phenotypes included natural killer cell signaling and PI3K signaling in B lymphocytes. Upstream regulator analysis indicated dysregulation of CCL5, NF-κB and IL1A due to CF while dysregulation of TREM1 and TP53 regulators were associated with CF phenotype. Five miRNAs showed inverse expression patterns with three target genes relevant in CF-associated impaired immune pathways while two miRNAs showed inverse expression patterns with two target genes relevant to a dysregulated immune pathway associated with CF phenotypes. Conclusions Our results indicate that miRNAs and individual transcript variants are relevant molecular targets contributing to impaired immune cell responses in CF. Electronic supplementary material The online version of this article (10.1186/s12920-019-0529-0) contains supplementary material, which is available to authorized users.
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56
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Pacini C, Koziol MJ. Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0073. [PMID: 29685977 PMCID: PMC5915717 DOI: 10.1098/rstb.2017.0073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2017] [Indexed: 02/07/2023] Open
Abstract
It is widely known that epigenetic modifications are important in regulating transcription, but several have also been reported in alternative splicing. The regulation of pre-mRNA splicing is important to explain proteomic diversity and the misregulation of splicing has been implicated in many diseases. Here, we give a brief overview of the role of epigenetics in alternative splicing and disease. We then discuss the bioinformatics methods that can be used to model interactions between epigenetic marks and regulators of splicing. These models can be used to identify alternative splicing and epigenetic changes across different phenotypes. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.
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Affiliation(s)
- Clare Pacini
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Magdalena J Koziol
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK .,Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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57
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Abstract
Alternative splicing is a major contributor to transcriptome and proteome diversity in eukaryotes. Comparing to normal samples, about 30% more alternative splicing events were recently identified in 32 cancer types included in The Cancer Genome Atlas database. Some alternative splicing isoforms and their encoded proteins contribute to specific cancer hallmarks. In this review, we will discuss recent progress regarding the contributions of alternative splicing to breast cancer metastasis. We plan to dissect the role of MTDH, CD44 and their interaction with other mRNA splicing factors. We believe an in-depth understanding of the mechanism underlying the contribution of splicing to breast cancer metastasis will provide novel strategies to the management of breast cancer.
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Affiliation(s)
- Xiangbing Meng
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Shujie Yang
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Jun Zhang
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Huimin Yu
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Department of Pathogenic Biology, Shenzhen University School of medicine, Shenzhen 518060, China
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58
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Ideozu JE, Zhang X, McColley S, Levy H. Transcriptome Profiling and Molecular Therapeutic Advances in Cystic Fibrosis: Recent Insights. Genes (Basel) 2019; 10:genes10030180. [PMID: 30813620 PMCID: PMC6470978 DOI: 10.3390/genes10030180] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
In cystic fibrosis (CF), mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene disrupt the capacity of the encoded protein to function as a channel to transport chloride ions and water across cell membranes. The consequences are deleterious, system-wide, and immensely variable, even among patients with the same CFTR genotype. This underscores the need to characterize the mechanisms contributing to CF pathophysiology. Gene replacement and gene editing therapies have been pursued intensively and are expected to provide a one-time treatment for CF. However, gene replacement therapy is limited by the lack of efficient vectors to deliver functional copies of CFTR to cells without immunological complications, while gene editing technologies such as CRISPR/Cas9 are still in their infancy, mainly useful in somatic cells and limited by off-target insertions. Small molecule treatments targeted at potentiating or correcting CFTR have shown clinical benefits, but they are limited to a few CFTR mutations and insufficient to overcome challenges related to clinical heterogeneity. Transcriptome profiling approaches have emerged as robust tools capable of characterizing phenotypic variability and revealing novel molecular targets with therapeutic potential for CF. We summarize current insights gained through transcriptome profiling approaches in CF studies and recent advances in molecular therapeutics.
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Affiliation(s)
- Justin E Ideozu
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL 60614, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
| | - Xi Zhang
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL 60614, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
| | - Susanna McColley
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
| | - Hara Levy
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL 60614, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
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Hornbeck PV, Kornhauser JM, Latham V, Murray B, Nandhikonda V, Nord A, Skrzypek E, Wheeler T, Zhang B, Gnad F. 15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. Nucleic Acids Res 2019; 47:D433-D441. [PMID: 30445427 PMCID: PMC6324072 DOI: 10.1093/nar/gky1159] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/26/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
For 15 years the mission of PhosphoSitePlus® (PSP, https://www.phosphosite.org) has been to provide comprehensive information and tools for the study of mammalian post-translational modifications (PTMs). The number of unique PTMs in PSP is now more than 450 000 from over 22 000 articles and thousands of MS datasets. The most important areas of growth in PSP are in disease and isoform informatics. Germline mutations associated with inherited diseases and somatic cancer mutations have been added to the database and can now be viewed along with PTMs and associated quantitative information on novel 'lollipop' plots. These plots enable researchers to interactively visualize the overlap between disease variants and PTMs, and to identify mutations that may alter phenotypes by rewiring signaling networks. We are expanding the sequence space to include over 30 000 human and mouse isoforms to enable researchers to explore the important but understudied biology of isoforms. This represents a necessary expansion of sequence space to accommodate the growing precision and depth of coverage enabled by ongoing advances in mass spectrometry. Isoforms are aligned using a new algorithm. Exploring the worlds of PTMs and disease mutations in the entire isoform space will hopefully lead to new biomarkers, therapeutic targets, and insights into isoform biology.
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Affiliation(s)
- Peter V Hornbeck
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Jon M Kornhauser
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Vaughan Latham
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Beth Murray
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Vidhisha Nandhikonda
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Alex Nord
- University of Montana, Missoula, MT, USA
| | - Elżbieta Skrzypek
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | | | - Bin Zhang
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
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60
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Affiliation(s)
- Arthur A Levin
- From Research and Development, Avidity Biosciences, La Jolla, CA
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61
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Rawcliffe DFR, Österman L, Nordin A, Holmberg M. PTBP1 acts as a dominant repressor of the aberrant tissue-specific splicing of ISCU in hereditary myopathy with lactic acidosis. Mol Genet Genomic Med 2018; 6:887-897. [PMID: 30209894 PMCID: PMC6305642 DOI: 10.1002/mgg3.413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/23/2018] [Accepted: 04/17/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hereditary myopathy with lactic acidosis (HML) is an autosomal recessive disease caused by an intron mutation in the iron-sulfur cluster assembly (ISCU) gene. The mutation results in aberrant splicing, where part of the intron is retained in the final mRNA transcript, giving rise to a truncated nonfunctional ISCU protein. Using an ISCU mini-gene system, we have previously shown that PTBP1 can act as a repressor of the mis-splicing of ISCU, where overexpression of PTBP1 resulted in a decrease of the incorrect splicing. In this study, we wanted to, in more detail, analyze the role of PTBP1 in the regulation of endogenous ISCU mis-splicing. METHODS Overexpression and knockdown of PTBP1 was performed in myoblasts from two HML patients and a healthy control. Quantification of ISCU mis-splicing was done by qRTPCR. Biotinylated ISCU RNA, representing wildtype and mutant intron sequence, was used in a pull-down assay with nuclear extracts from myoblasts. Levels of PTBP1 in human cell lines and mice tissues were analyzed by qRTPCR and western blot. RESULTS PTBP1 overexpression in HML patient myoblasts resulted in a substantial decrease of ISCU mis-splicing while knockdown of PTBP1 resulted in a drastic increase. The effect could be observed in both patient and control myoblasts. We could also show that PTBP1 interacts with both the mutant and wild-type ISCU intron sequence, but with a higher affinity to the mutant sequence. Furthermore, low levels of PTBP1 among examined mouse tissues correlated with high levels of incorrect splicing of ISCU. CONCLUSION Our results show that PTBP1 acts as a dominant repressor of ISCU mis-splicing. We also show an inverse correlation between the levels of PTBP1 and ISCU mis-splicing, suggesting that the high level of mis-splicing in the skeletal muscle is primarily due to the low levels of PTBP1.
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Affiliation(s)
- Denise F. R. Rawcliffe
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
| | - Lennart Österman
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
| | - Angelica Nordin
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
| | - Monica Holmberg
- Unit for Medical and Clinical GeneticsDepartment of Medical BiosciencesUmeå UniversityUmeåSweden
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Roovers J, De Jonghe P, Weckhuysen S. The therapeutic potential of RNA regulation in neurological disorders. Expert Opin Ther Targets 2018; 22:1017-1028. [PMID: 30372655 DOI: 10.1080/14728222.2018.1542429] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Gene regulation is the term used to describe the mechanisms by which a cell increases or decreases the amount of a gene product (RNA or protein). In complex organs such as the brain, gene regulation is of the utmost importance; aberrations in the regulation of specific genes can lead to neurological disorders. Understanding these mechanisms can create new strategies for targeting these disorders and progress is being made. Two drugs that function at the RNA level (nusinersen and eteplirsen) have now been approved by the FDA for the treatment of Spinomuscular atrophy and Duchenne muscular dystrophy, respectively; several other compounds for neurological disease are currently being investigated in preclinical studies and clinical trials. Areas covered: We highlight how gene regulation at the level of RNA molecules can be used as a therapeutic strategy to treat neurological disorders. We provide examples of how such an approach is being studied or used and discuss the current hurdles. Expert opinion: Targeting gene expression at the RNA level is a promising strategy to treat genetic neurological disorders. Safe administration, long-term efficacy, and potential side effects, however, still need careful evaluation before RNA therapeutics can be applied on a larger scale.
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Affiliation(s)
- Jolien Roovers
- a Neurogenetics Group , Center for Molecular Neurology, VIB , Antwerp , Belgium.,b Laboratory of Neurogenetics, Institute Born-Bunge , University of Antwerp , Antwerp , Belgium
| | - Peter De Jonghe
- a Neurogenetics Group , Center for Molecular Neurology, VIB , Antwerp , Belgium.,b Laboratory of Neurogenetics, Institute Born-Bunge , University of Antwerp , Antwerp , Belgium.,c Department of Neurology , University Hospital Antwerp , Antwerp , Belgium
| | - Sarah Weckhuysen
- a Neurogenetics Group , Center for Molecular Neurology, VIB , Antwerp , Belgium.,b Laboratory of Neurogenetics, Institute Born-Bunge , University of Antwerp , Antwerp , Belgium.,c Department of Neurology , University Hospital Antwerp , Antwerp , Belgium
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Zhao L, Yi S. Transcriptional landscape of alternative splicing during peripheral nerve injury. J Cell Physiol 2018; 234:6876-6885. [PMID: 30362529 DOI: 10.1002/jcp.27446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Abstract
Alternative splicing (AS) regulates a variety of biological activities in numerous tissues and organs, including the nervous system. However, the existence and specific roles of AS events during peripheral nerve repair and regeneration remain largely undetermined. In the current study, by mapping splice-crossing sequence reads, we identified AS events and relevant spliced genes in rat sciatic nerve stumps following sciatic nerve crush. AS-related genes at 1, 4, 7, and 14 days post nerve crush were compared with those at 0 day to discover alternatively spliced genes induced by sciatic nerve crush. These injury-induced alternatively spliced genes were then categorized to diseases and biological functions, genetic networks, and canonical signaling pathways. Bioinformatic analysis indicated that these alternatively spliced genes were mainly correlated to immune response, cellular growth, and cellular function maintenance. Our study elucidated AS events following peripheral nerve injury and might help deepen our understanding of the molecular mechanisms underlying peripheral nerve regeneration.
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Affiliation(s)
- Lili Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Sheng Yi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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Harvey SE, Xu Y, Lin X, Gao XD, Qiu Y, Ahn J, Xiao X, Cheng C. Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT. RNA (NEW YORK, N.Y.) 2018; 24:1326-1338. [PMID: 30042172 PMCID: PMC6140460 DOI: 10.1261/rna.066712.118] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The epithelial-mesenchymal transition (EMT) is a fundamental developmental process that is abnormally activated in cancer metastasis. Dynamic changes in alternative splicing occur during EMT. ESRP1 and hnRNPM are splicing regulators that promote an epithelial splicing program and a mesenchymal splicing program, respectively. The functional relationships between these splicing factors in the genome scale remain elusive. Comparing alternative splicing targets of hnRNPM and ESRP1 revealed that they coregulate a set of cassette exon events, with the majority showing discordant splicing regulation. Discordant splicing events regulated by hnRNPM show a positive correlation with splicing during EMT; however, concordant events do not, indicating the role of hnRNPM in regulating alternative splicing during EMT is more complex than previously understood. Motif enrichment analysis near hnRNPM-ESRP1 coregulated exons identifies guanine-uridine rich motifs downstream from hnRNPM-repressed and ESRP1-enhanced exons, supporting a general model of competitive binding to these cis-elements to antagonize alternative splicing. The set of coregulated exons are enriched in genes associated with cell migration and cytoskeletal reorganization, which are pathways associated with EMT. Splicing levels of coregulated exons are associated with breast cancer patient survival and correlate with gene sets involved in EMT and breast cancer subtyping. This study identifies complex modes of interaction between hnRNPM and ESRP1 in regulation of splicing in disease-relevant contexts.
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Affiliation(s)
- Samuel E Harvey
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Yilin Xu
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Xiaodan Lin
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Xin D Gao
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Yushan Qiu
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Jaegyoon Ahn
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Chonghui Cheng
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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65
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Guo X, Zhao Y, Nguyen H, Liu T, Wang Z, Lou H. Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay. J Vis Exp 2018. [PMID: 30199013 DOI: 10.3791/57889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Alternative splicing (AS) occurs in more than 90% of human genes. The expression pattern of an alternatively spliced exon is often regulated in a cell type-specific fashion. AS expression patterns are typically analyzed by RT-PCR and RNA-seq using RNA samples isolated from a population of cells. In situ examination of AS expression patterns for a particular biological structure can be carried out by RNA in situ hybridization (ISH) using exon-specific probes. However, this particular use of ISH has been limited because alternative exons are generally too short to design exon-specific probes. In this report, the use of BaseScope, a recently developed technology that employs short antisense oligonucleotides in RNA ISH, is described to analyze AS expression patterns in mouse brain sections. Exon 23a of neurofibromatosis type 1 (Nf1) is used as an example to illustrate that short exon-exon junction probes exhibit robust hybridization signals with high specificity in RNA ISH analysis on mouse brain sections. More importantly, signals detected with exon inclusion- and skipping-specific probes can be used to reliably calculate the percent spliced in values of Nf1 exon 23a expression in different anatomical areas of a mouse brain. The experimental protocol and calculation method for AS analysis are presented. The results indicate that BaseScope provides a powerful new tool to assess AS expression patterns in situ.
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Affiliation(s)
- Xuan Guo
- Department of Genetics and Genome Sciences, Case Western Reserve University; Department of Endocrinology, Dongfang Hospital of Beijing University of Chinese Medicine
| | - Yiqing Zhao
- Department of Genetics and Genome Sciences, Case Western Reserve University; Case Comprehensive Cancer Center, Case Western Reserve University
| | - Hieu Nguyen
- Department of Genetics and Genome Sciences, Case Western Reserve University
| | - Tonghua Liu
- Department of Endocrinology, Dongfang Hospital of Beijing University of Chinese Medicine
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University; Case Comprehensive Cancer Center, Case Western Reserve University
| | - Hua Lou
- Department of Genetics and Genome Sciences, Case Western Reserve University; Case Comprehensive Cancer Center, Case Western Reserve University; Center for RNA Science and Therapeutics, Case Western Reserve University;
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66
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Guo J, Jia R. Splicing factor poly(rC)-binding protein 1 is a novel and distinctive tumor suppressor. J Cell Physiol 2018; 234:33-41. [PMID: 30132844 DOI: 10.1002/jcp.26873] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 12/20/2022]
Abstract
A lot of evidence has been found on the link between tumorigenesis and the aberrant expression of splicing factors. A number of splicing factors have been reported to be either oncogenic or overexpressed in cancer cells. However, splicing factors can also play negative roles in tumorigenesis. In the current review, we focus on splicing factor poly(rC)-binding protein 1 (PCBP1), a novel tumor suppressor that is characterized by downregulation in many cancer types and shows inhibition of tumor formation and metastasis. Notably, the messenger RNA levels of PCBP1 are not significantly decreased in most cancer types. In fact, PCBP1 protein is often degraded or shows a loss-of-function through phosphorylation in cancer cells. PCBP1 is highly homologous to its family member, PCBP2. Interestingly, PCBP2 appears to be an oncogenic splicing factor. A growing body of evidence has shown that PCBP1 regulates alternative splicing, translation, and RNA stability of many cancer-related genes. Taking together, PCBP1 has distinctive tumor suppressive functions, and increasing PCBP1 expression may represent a new approach for cancer treatment.
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Affiliation(s)
- Jihua Guo
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Rong Jia
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
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67
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Handschuh L, Wojciechowski P, Kazmierczak M, Marcinkowska-Swojak M, Luczak M, Lewandowski K, Komarnicki M, Blazewicz J, Figlerowicz M, Kozlowski P. NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome. J Transl Med 2018; 16:232. [PMID: 30126426 PMCID: PMC6102803 DOI: 10.1186/s12967-018-1608-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/14/2018] [Indexed: 11/29/2022] Open
Abstract
Background Expression of the NPM1 gene, encoding nucleophosmin, is upregulated in cancers. Although more than ten NPM1 transcripts are known, the reports were usually limited to one predominant transcript. In leukemia, the NPM1 expression has not been widely studied so far. In acute myeloid leukemia (AML), the mutational status of the gene seems to play a pivotal role in carcinogenesis. Therefore, the aim of the study was to quantify alternative NPM1 transcripts in two types of acute leukemia, AML and ALL (acute lymphoblastic leukemia). Methods Using droplet digital PCR, we analyzed the levels of three protein-coding NPM1 transcripts in 66 samples collected from AML and ALL patients and 16 control samples. Using RNA-seq, we detected 8 additional NPM1 transcripts, including non-coding splice variants with retained introns. For data analysis, Welch two sample t-test, Pearson’s correlation and Kaplan–Meier analysis were applied. Results The levels of the particular NPM1 transcripts were significantly different but highly correlated with each other in both leukemia and control samples. Transcript NPM1.1, encoding the longest protein (294 aa), had the highest level of accumulation and was one of the most abundant transcripts in the cell. Comparing to NPM1.1, the levels of the NPM1.2 and NPM1.3 transcripts, encoding a 265-aa and 259-aa proteins, were 30 and 3 times lower, respectively. All three NPM1 transcripts were proportionally upregulated in both types of leukemia compared to control samples. In AML, the levels of NPM1 transcripts decreased in complete remission and increased again with relapse of the disease. Low levels of NPM1.1 and NPM1.3 were associated with better prognosis. The contribution of non-coding transcripts to the total level of NPM1 gene seemed to be marginal, except for one short 5-end transcript accumulated at high levels in AML and control cells. Aberrant proportions of particular NPM1 splice variants could be linked to abnormal expression of genes encoding alternative splicing factors. Conclusions The levels of the studied NPM1 transcripts were different but highly correlated with each other. Their upregulation in AML and ALL, decrease after therapy and association with patient outcome suggests the involvement of elevated NPM1 expression in the acute leukemia pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12967-018-1608-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiza Handschuh
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland.
| | - Pawel Wojciechowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Maciej Kazmierczak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland
| | - Malgorzata Marcinkowska-Swojak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Magdalena Luczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, Poznan, Poland
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland
| | - Mieczyslaw Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Szamarzewskiego 84, 60-569, Poznan, Poland
| | - Jacek Blazewicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Marek Figlerowicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Piotr Kozlowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, Poznan, Poland
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Miyamoto T, Mizuno N, Kosaka M, Fujitani Y, Ohno E, Ohtsuka A. Conclusive Evidence for OCT4
Transcription in Human Cancer Cell Lines: Possible Role of a Small OCT4-Positive Cancer Cell Population. Stem Cells 2018; 36:1341-1354. [DOI: 10.1002/stem.2851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 06/17/2018] [Accepted: 05/01/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Tomoyuki Miyamoto
- Department of Human Morphology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Kita, Okayama Japan
- Faculty of Medical Bioscience, Department of Medical Life Science; Kyushu University of Health and Welfare/Cancer Cell Institute of Kyushu University of Health and Welfare, , Yoshino; Nobeoka, Miyazaki Japan
| | - Nobuhiko Mizuno
- Department of Human Morphology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Kita, Okayama Japan
| | - Mitsuko Kosaka
- Department of Human Morphology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Kita, Okayama Japan
| | - Yoko Fujitani
- Department of Human Morphology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Kita, Okayama Japan
| | - Eiji Ohno
- Faculty of Medical Bioscience, Department of Medical Life Science; Kyushu University of Health and Welfare/Cancer Cell Institute of Kyushu University of Health and Welfare, , Yoshino; Nobeoka, Miyazaki Japan
| | - Aiji Ohtsuka
- Department of Human Morphology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Kita, Okayama Japan
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69
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Li J, Tseng CS, Federico A, Ivankovic F, Huang YS, Ciccodicola A, Swanson MS, Yu P. SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4161772. [PMID: 29220461 PMCID: PMC5737203 DOI: 10.1093/database/bax071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023]
Abstract
Although the number of RNA-Seq datasets deposited publicly has increased over the past few years, incomplete annotation of the associated metadata limits their potential use. Because of the importance of RNA splicing in diseases and biological processes, we constructed a database called SFMetaDB by curating datasets related with RNA splicing factors. Our effort focused on the RNA-Seq datasets in which splicing factors were knocked-down, knocked-out or over-expressed, leading to 75 datasets corresponding to 56 splicing factors. These datasets can be used in differential alternative splicing analysis for the identification of the potential targets of these splicing factors and other functional studies. Surprisingly, only ∼15% of all the splicing factors have been studied by loss- or gain-of-function experiments using RNA-Seq. In particular, splicing factors with domains from a few dominant Pfam domain families have not been studied. This suggests a significant gap that needs to be addressed to fully elucidate the splicing regulatory landscape. Indeed, there are already mouse models available for ∼20 of the unstudied splicing factors, and it can be a fruitful research direction to study these splicing factors in vitro and in vivo using RNA-Seq. Database URL:http://sfmetadb.ece.tamu.edu/
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Affiliation(s)
- Jin Li
- Department of Electrical and Computer Engineering.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Ching-San Tseng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Antonio Federico
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - Franjo Ivankovic
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Alfredo Ciccodicola
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
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70
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Zhang Q, Fan X, Wang Y, Sun MA, Shao J, Guo D. BPP: a sequence-based algorithm for branch point prediction. Bioinformatics 2018. [PMID: 28633445 DOI: 10.1093/bioinformatics/btx401] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Motivation Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results We here propose a novel branch point prediction algorithm that utilizes information on the branch point sequence and the polypyrimidine tract. Using experimentally validated data, we demonstrate that our proposed method outperforms existing methods. Availability and implementation: https://github.com/zhqingit/BPP. Contact djguo@cuhk.edu.hk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qing Zhang
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yejun Wang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Ming-An Sun
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology
| | - Jianlin Shao
- First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dianjing Guo
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology
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72
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Lee PH, Lee C, Li X, Wee B, Dwivedi T, Daly M. Principles and methods of in-silico prioritization of non-coding regulatory variants. Hum Genet 2018; 137:15-30. [PMID: 29288389 PMCID: PMC5892192 DOI: 10.1007/s00439-017-1861-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Over a decade of genome-wide association, studies have made great strides toward the detection of genes and genetic mechanisms underlying complex traits. However, the majority of associated loci reside in non-coding regions that are functionally uncharacterized in general. Now, the availability of large-scale tissue and cell type-specific transcriptome and epigenome data enables us to elucidate how non-coding genetic variants can affect gene expressions and are associated with phenotypic changes. Here, we provide an overview of this emerging field in human genomics, summarizing available data resources and state-of-the-art analytic methods to facilitate in-silico prioritization of non-coding regulatory mutations. We also highlight the limitations of current approaches and discuss the direction of much-needed future research.
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Affiliation(s)
- Phil H Lee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA.
- Quantitative Genomics Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Christian Lee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- Department of Life Sciences, Harvard University, Cambridge, MA, USA
| | - Xihao Li
- Quantitative Genomics Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brian Wee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
| | - Tushar Dwivedi
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Mark Daly
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0474. [PMID: 27994117 DOI: 10.1098/rstb.2015.0474] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Lu Chen
- West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, People's Republic of China
| | | | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK .,Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
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74
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Gu L, Wang H, Wang J, Guo Y, Tang Y, Mao Y, Chen L, Lou H, Ji G. Reconstitution of HuR-Inhibited CUGBP1 Expression Protects Cardiomyocytes from Acute Myocardial Infarction-Induced Injury. Antioxid Redox Signal 2017; 27:1013-1026. [PMID: 28350193 DOI: 10.1089/ars.2016.6880] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIM Myocardial infarction (MI) is one of the leading causes of death in elderly people. Expanding the knowledge of the molecular mechanisms underlying MI is of profound importance to developing a cure for MI. The CUGBP- and ETR-3-like factor (CELF) proteins, a family of RNA-binding proteins, play key roles in RNA metabolism. To determine the functions and molecular mechanisms of CELF proteins in MI, an animal model of acute myocardial infarction (AMI) was used in our study. RESULTS We found that the CUG triplet repeat RNA-binding protein 1 (CUGBP1)/CELF1 expression levels were decreased in AMI-injured hearts, and further studies showed that two highly conserved adenylate-uridylate-rich (AU-rich) elements in the 3'UTR of CUGBP1 were responsible for the decreased CUGBP1 expression. Upon AMI, human antigen R (HuR) was relocated to the cytoplasm from the nucleus and interacted with these AU-rich elements to affect the expression of CUGBP1. Reintroduction of CUGBP1 via gene delivery by recombinant adenovirus improved cardiac function in AMI mice. Our studies also indicated that CUGBP1 protected cardiomyocytes from ischemia-induced injury through the promotion of angiogenesis and inhibition of apoptosis by regulating the vascular endothelial growth factor-A gene. Innovation and Conclusion: Our studies indicate a role for CUGBP1 in cardiac disease and reveal a novel MI post-transcriptional gene regulatory mechanism. The reconstitution of CUGBP1 could be developed as a potential therapeutic option for the management of MI. Antioxid. Redox Signal. 27, 1013-1026.
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Affiliation(s)
- Lei Gu
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China .,2 University of the Chinese Academy of Sciences , Beijing, China
| | - Huiwen Wang
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China
| | - Jun Wang
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China .,2 University of the Chinese Academy of Sciences , Beijing, China
| | - Yuting Guo
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China .,2 University of the Chinese Academy of Sciences , Beijing, China
| | - Yinglong Tang
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China
| | - Yang Mao
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China .,2 University of the Chinese Academy of Sciences , Beijing, China
| | - Lijuan Chen
- 3 Beijing Institutes of Life Science , Chinese Academy of Sciences, Beijing, China
| | - Hua Lou
- 4 Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University , Cleveland, Ohio
| | - Guangju Ji
- 1 National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China
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75
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Rohacek AM, Bebee TW, Tilton RK, Radens CM, McDermott-Roe C, Peart N, Kaur M, Zaykaner M, Cieply B, Musunuru K, Barash Y, Germiller JA, Krantz ID, Carstens RP, Epstein DJ. ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development. Dev Cell 2017; 43:318-331.e5. [PMID: 29107558 PMCID: PMC5687886 DOI: 10.1016/j.devcel.2017.09.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 08/15/2017] [Accepted: 08/26/2017] [Indexed: 12/30/2022]
Abstract
Alternative splicing contributes to gene expression dynamics in many tissues, yet its role in auditory development remains unclear. We performed whole-exome sequencing in individuals with sensorineural hearing loss (SNHL) and identified pathogenic mutations in Epithelial Splicing-Regulatory Protein 1 (ESRP1). Patient-derived induced pluripotent stem cells showed alternative splicing defects that were restored upon repair of an ESRP1 mutant allele. To determine how ESRP1 mutations cause hearing loss, we evaluated Esrp1-/- mouse embryos and uncovered alterations in cochlear morphogenesis, auditory hair cell differentiation, and cell fate specification. Transcriptome analysis revealed impaired expression and splicing of genes with essential roles in cochlea development and auditory function. Aberrant splicing of Fgfr2 blocked stria vascularis formation due to erroneous ligand usage, which was corrected by reducing Fgf9 gene dosage. These findings implicate mutations in ESRP1 as a cause of SNHL and demonstrate the complex interplay between alternative splicing, inner ear development, and auditory function.
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Affiliation(s)
- Alex M Rohacek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Thomas W Bebee
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard K Tilton
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Caleb M Radens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Chris McDermott-Roe
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natoya Peart
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maninder Kaur
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael Zaykaner
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin Cieply
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran Musunuru
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - John A Germiller
- Division of Pediatric Otolaryngology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian D Krantz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Russ P Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA.
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Henning LM, Santos KF, Sticht J, Jehle S, Lee CT, Wittwer M, Urlaub H, Stelzl U, Wahl MC, Freund C. A new role for FBP21 as regulator of Brr2 helicase activity. Nucleic Acids Res 2017; 45:7922-7937. [PMID: 28838205 PMCID: PMC5570060 DOI: 10.1093/nar/gkx535] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/19/2017] [Indexed: 02/01/2023] Open
Abstract
Splicing of eukaryotic pre-mRNA is carried out by the spliceosome, which assembles stepwise on each splicing substrate. This requires the concerted action of snRNPs and non-snRNP accessory proteins, the functions of which are often not well understood. Of special interest are B complex factors that enter the spliceosome prior to catalytic activation and may alter splicing kinetics and splice site selection. One of these proteins is FBP21, for which we identified several spliceosomal binding partners in a yeast-two-hybrid screen, among them the RNA helicase Brr2. Biochemical and biophysical analyses revealed that an intrinsically disordered region of FBP21 binds to an extended surface of the C-terminal Sec63 unit of Brr2. Additional contacts in the C-terminal helicase cassette are required for allosteric inhibition of Brr2 helicase activity. Furthermore, the direct interaction between FBP21 and the U4/U6 di-snRNA was found to reduce the pool of unwound U4/U6 di-snRNA. Our results suggest FBP21 as a novel key player in the regulation of Brr2.
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Affiliation(s)
- Lisa M Henning
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Karine F Santos
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Jana Sticht
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany.,BioSupraMol Gerätezentrum, Freie Universität Berlin, Takustr. 3, Berlin 14195, Germany
| | - Stefanie Jehle
- Max-Planck-Insitute for Molecular Genetics, Ihnestraße 63-74, Berlin 14195, Germany
| | - Chung-Tien Lee
- Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, Göttingen 37077, Germany.,University Medical Center Goettingen, Bioanalytics, Department of Clinical Chemistry, Robert Koch Strasse 40, Göttingen 37075, Germany
| | - Malte Wittwer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Henning Urlaub
- Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, Göttingen 37077, Germany.,University Medical Center Goettingen, Bioanalytics, Department of Clinical Chemistry, Robert Koch Strasse 40, Göttingen 37075, Germany
| | - Ulrich Stelzl
- Max-Planck-Insitute for Molecular Genetics, Ihnestraße 63-74, Berlin 14195, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert- Einstein-Straße 15, Berlin 12489, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
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77
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Greening DW, Kapp EA, Simpson RJ. The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome. Enzymes 2017; 42:27-64. [PMID: 29054270 DOI: 10.1016/bs.enz.2017.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases. The identification of circulating peptides in the context of disease constitutes a hitherto source of new clinical biomarkers. The field of peptidomics can be defined as the identification and comprehensive analysis of physiological and pathological peptides. Like proteomics, peptidomics has been advanced by the development of new separation strategies, analytical detection methods such as mass spectrometry, and bioinformatic technologies. Unlike proteomics, peptidomics is targeted toward identifying endogenous protein and peptide fragments, defining proteolytic enzyme substrate specificity, as well as protease cleavage recognition (degradome). Peptidomics employs "top-down proteomics" strategies where mass spectrometry is applied at the proteoform level to analyze intact proteins and large endogenous peptide fragments. With recent advances in prefractionation workflows for separating peptides, mass spectrometry instrumentation, and informatics, peptidomics is an important field that promises to impact on translational medicine. This review covers the current advances in peptidomics, including top-down and imaging mass spectrometry, comprehensive quantitative peptidome analyses (developments in reproducibility and coverage), peptide prefractionation and enrichment workflows, peptidomic data analyses, and informatic tools. The application of peptidomics in cancer biomarker discovery will be discussed.
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Affiliation(s)
- David W Greening
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
| | - Eugene A Kapp
- Systems Biology & Personalised Medicine Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Florey Institute of Neuroscience, Parkville, Victoria, Australia; University of Melbourne, Parkville, Victoria, Australia
| | - Richard J Simpson
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
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78
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Ranwez V, Serra A, Pot D, Chantret N. Domestication reduces alternative splicing expression variations in sorghum. PLoS One 2017; 12:e0183454. [PMID: 28886042 PMCID: PMC5590825 DOI: 10.1371/journal.pone.0183454] [Citation(s) in RCA: 7] [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: 04/19/2017] [Accepted: 08/06/2017] [Indexed: 01/09/2023] Open
Abstract
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
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Affiliation(s)
| | - Audrey Serra
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
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79
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Balbinot C, Vanier M, Armant O, Nair A, Penichon J, Soret C, Martin E, Saandi T, Reimund JM, Deschamps J, Beck F, Domon-Dell C, Gross I, Duluc I, Freund JN. Fine-tuning and autoregulation of the intestinal determinant and tumor suppressor homeobox gene CDX2 by alternative splicing. Cell Death Differ 2017; 24:2173-2186. [PMID: 28862703 DOI: 10.1038/cdd.2017.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
On the basis of phylogenetic analyses, we uncovered a variant of the CDX2 homeobox gene, a major regulator of the development and homeostasis of the gut epithelium, also involved in cancer. This variant, miniCDX2, is generated by alternative splicing coupled to alternative translation initiation, and contains the DNA-binding homeodomain but is devoid of transactivation domain. It is predominantly expressed in crypt cells, whereas the CDX2 protein is present in crypt cells but also in differentiated villous cells. Functional studies revealed a dominant-negative effect exerted by miniCDX2 on the transcriptional activity of CDX2, and conversely similar effects regarding several transcription-independent functions of CDX2. In addition, a regulatory role played by the CDX2 and miniCDX2 homeoproteins on their pre-mRNA splicing is displayed, through interactions with splicing factors. Overexpression of miniCDX2 in the duodenal Brunner glands leads to the expansion of the territory of these glands and ultimately to brunneroma. As a whole, this study characterized a new and original variant of the CDX2 homeobox gene. The production of this variant represents not only a novel level of regulation of this gene, but also a novel way to fine-tune its biological activity through the versatile functions exerted by the truncated variant compared to the full-length homeoprotein. This study highlights the relevance of generating protein diversity through alternative splicing in the gut and its diseases.
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Affiliation(s)
- Camille Balbinot
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Marie Vanier
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Olivier Armant
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Postfach 3640, Karlsruhe 76021, Germany
| | - Asmaa Nair
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Julien Penichon
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Christine Soret
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Elisabeth Martin
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Thoueiba Saandi
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Marie Reimund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jacqueline Deschamps
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Felix Beck
- Barts and The London School of Medicine and Dentistry, London E1 2ES, UK
| | - Claire Domon-Dell
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Gross
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Duluc
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Noël Freund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
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80
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Yi J, Shen HF, Qiu JS, Huang MF, Zhang WJ, Ding JC, Zhu XY, Zhou Y, Fu XD, Liu W. JMJD6 and U2AF65 co-regulate alternative splicing in both JMJD6 enzymatic activity dependent and independent manner. Nucleic Acids Res 2017; 45:3503-3518. [PMID: 27899633 PMCID: PMC5389685 DOI: 10.1093/nar/gkw1144] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 11/02/2016] [Indexed: 12/11/2022] Open
Abstract
JMJD6, a jumonji C (Jmj C) domain-containing protein demethylase and hydroxylase, has been implicated in an array of biological processes. It has been shown that JMJD6 interacts with and hydroxylates multiple serine/arginine-rich (SR) proteins and SR related proteins, including U2AF65, all of which are known to function in alternative splicing regulation. However, whether JMJD6 is widely involved in alternative splicing and the molecular mechanism underlying JMJD6-regulated alternative splicing have remained incompletely understood. Here, by using RASL-Seq, we investigated the functional impact of RNA-dependent interaction between JMJD6 and U2AF65, revealing that JMJD6 and U2AF65 co-regulated a large number of alternative splicing events. We further demonstrated the JMJD6 function in alternative splicing in jmjd6 knockout mice. Mechanistically, we showed that the enzymatic activity of JMJD6 was required for a subset of JMJD6-regulated splicing, and JMJD6-mediated lysine hydroxylation of U2AF65 could account for, at least partially, their co-regulated alternative splicing events, suggesting both JMJD6 enzymatic activity-dependent and independent control of alternative splicing. These findings reveal an intimate link between JMJD6 and U2AF65 in alternative splicing regulation, which has important implications in development and disease processes.
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Affiliation(s)
- Jia Yi
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Hai-Feng Shen
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jin-Song Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Ming-Feng Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Wen-Juan Zhang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jian-Cheng Ding
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Xiao-Yan Zhu
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0648, USA
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Wen Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
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81
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Abstract
Alternative splicing (AS) greatly expands the coding capacities of genomes by allowing the generation of multiple mature mRNAs from a limited number of genes. Although the massive switch in AS profiles that often accompanies variations in gene expression patterns occurring during cell differentiation has been characterized for a variety of models, their causes and mechanisms remain largely unknown. Here, we integrate foundational and recent studies indicating the AS switches that govern the processes of cell fate determination. We include some distinct AS events in pluripotent cells and somatic reprogramming and discuss new progresses on alternative isoform expression in adipogenesis, myogenic differentiation and stimulation of immune cells. Finally, we cover novel insights on AS mechanisms during neuronal differentiation, paying special attention to the role of chromatin structure.
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Affiliation(s)
- Ana Fiszbein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
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82
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Tranchevent LC, Aubé F, Dulaurier L, Benoit-Pilven C, Rey A, Poret A, Chautard E, Mortada H, Desmet FO, Chakrama FZ, Moreno-Garcia MA, Goillot E, Janczarski S, Mortreux F, Bourgeois CF, Auboeuf D. Identification of protein features encoded by alternative exons using Exon Ontology. Genome Res 2017; 27:1087-1097. [PMID: 28420690 PMCID: PMC5453322 DOI: 10.1101/gr.212696.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/28/2017] [Indexed: 12/16/2022]
Abstract
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.
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Affiliation(s)
- Léon-Charles Tranchevent
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fabien Aubé
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Louis Dulaurier
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Clara Benoit-Pilven
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Amandine Rey
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Arnaud Poret
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Emilie Chautard
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, INRIA Erable, Villeurbanne, F-69622, France
| | - Hussein Mortada
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - François-Olivier Desmet
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Fatima Zahra Chakrama
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Maira Alejandra Moreno-Garcia
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Evelyne Goillot
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, F-69007 France
| | - Stéphane Janczarski
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Franck Mortreux
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
| | - Didier Auboeuf
- Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France
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83
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Suñé-Pou M, Prieto-Sánchez S, Boyero-Corral S, Moreno-Castro C, El Yousfi Y, Suñé-Negre JM, Hernández-Munain C, Suñé C. Targeting Splicing in the Treatment of Human Disease. Genes (Basel) 2017; 8:genes8030087. [PMID: 28245575 PMCID: PMC5368691 DOI: 10.3390/genes8030087] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023] Open
Abstract
The tightly regulated process of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is a key mechanism in the regulation of gene expression. Defects in this regulatory process affect cellular functions and are the cause of many human diseases. Recent advances in our understanding of splicing regulation have led to the development of new tools for manipulating splicing for therapeutic purposes. Several tools, including antisense oligonucleotides and trans-splicing, have been developed to target and alter splicing to correct misregulated gene expression or to modulate transcript isoform levels. At present, deregulated AS is recognized as an important area for therapeutic intervention. Here, we summarize the major hallmarks of the splicing process, the clinical implications that arise from alterations in this process, and the current tools that can be used to deliver, target, and correct deficiencies of this key pre-mRNA processing event.
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Affiliation(s)
- Marc Suñé-Pou
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
- Drug Development Service, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII, s/n 08028 Barcelona, Spain.
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Sofía Boyero-Corral
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Younes El Yousfi
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Josep Mª Suñé-Negre
- Drug Development Service, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII, s/n 08028 Barcelona, Spain.
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
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84
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EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression. Mol Cancer 2017; 16:8. [PMID: 28137272 PMCID: PMC5282733 DOI: 10.1186/s12943-016-0579-2] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/25/2016] [Indexed: 12/17/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is associated with metastasis formation as well as with generation and maintenance of cancer stem cells. In this way, EMT contributes to tumor invasion, heterogeneity and chemoresistance. Morphological and functional changes involved in these processes require robust reprogramming of gene expression, which is only partially accomplished at the transcriptional level. Alternative splicing is another essential layer of gene expression regulation that expands the cell proteome. This step in post-transcriptional regulation of gene expression tightly controls cell identity between epithelial and mesenchymal states and during stem cell differentiation. Importantly, dysregulation of splicing factor function and cancer-specific splicing isoform expression frequently occurs in human tumors, suggesting the importance of alternative splicing regulation for cancer biology. In this review, we briefly discuss the role of EMT programs in development, stem cell differentiation and cancer progression. Next, we focus on selected examples of key factors involved in EMT and stem cell differentiation that are regulated post-transcriptionally through alternative splicing mechanisms. Lastly, we describe relevant oncogenic splice-variants that directly orchestrate cancer stem cell biology and tumor EMT, which may be envisioned as novel targets for therapeutic intervention.
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85
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The impact of RABL2B gene (rs144944885) on human male infertility in patients with oligoasthenoteratozoospermia and immotile short tail sperm defects. J Assist Reprod Genet 2017; 34:505-510. [PMID: 28138870 DOI: 10.1007/s10815-016-0863-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Male infertility is a multifactorial disorder with impressively genetic basis; besides, sperm abnormalities are the cause of numerous cases of male infertility. In this study, we evaluated the genetic variants in exons 4 and 5 and their intron-exon boundaries in RABL2B gene in infertile men with oligoasthenoteratozoospermia (OAT) and immotile short tail sperm (ISTS) defects to define if there is any association between these variants and human male infertility. METHODS To this purpose, DNA was extracted from peripheral blood and after PCR reaction and sequencing, the results of sequenced segments were analyzed. In the present study, 30 infertile men with ISTS defect and 30 oligoasthenoteratozoospermic infertile men were recruited. All men were of Iranian origin and it took 3 years to collect patient's samples with ISTS defect. RESULTS As a result, the 50776482 delC intronic variant (rs144944885) was identified in five patients with oligoasthenoteratozoospermia defect and one patient with ISTS defect in heterozygote form. This variant was not identified in controls. The allelic frequency of the 50776482 delC variant was significantly statistically higher in oligoasthenoteratozoospermic infertile men (p < 0.05). Bioinformatics studies suggested that the 50776482 delC allele would modify the splicing of RABL2B pre-mRNA. In addition, we identified a new genetic variant in RABL2B gene. CONCLUSIONS According to the present study, 50776482 delC allele in the RABL2B gene could be a risk factor in Iranian infertile men with oligoasthenoteratozoospermia defect, but more genetic studies are required to understand the accurate role of this variant in pathogenesis of human male infertility.
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86
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BCAS2 is involved in alternative mRNA splicing in spermatogonia and the transition to meiosis. Nat Commun 2017; 8:14182. [PMID: 28128212 PMCID: PMC5290162 DOI: 10.1038/ncomms14182] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022] Open
Abstract
Breast cancer amplified sequence 2 (BCAS2) is involved in multiple biological processes, including pre-mRNA splicing. However, the physiological roles of BCAS2 are still largely unclear. Here we report that BCAS2 is specifically enriched in spermatogonia of mouse testes. Conditional disruption of Bcas2 in male germ cells impairs spermatogenesis and leads to male mouse infertility. Although the spermatogonia appear grossly normal, spermatocytes in meiosis prophase I and meiosis events (recombination and synapsis) are rarely observed in the BCAS2-depleted testis. In BCAS2 null testis, 245 genes are altered in alternative splicing forms; at least three spermatogenesis-related genes (Dazl, Ehmt2 and Hmga1) can be verified. In addition, disruption of Bcas2 results in a significant decrease of the full-length form and an increase of the short form (lacking exon 8) of DAZL protein. Altogether, our results suggest that BCAS2 regulates alternative splicing in spermatogonia and the transition to meiosis initiation, and male fertility. Breast cancer amplified sequence 2 (BCAS2) is involved in pre-mRNA splicing but its physiological role is unclear. Here, the authors find BCAS2 enriched in mice spermatogonia in the testes, and BCAS2 deletion in germ cells alters alternative splicing of spermatogenesis-related genes, causing male infertility.
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87
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Carlini F, Picard C, Garulli C, Piquemal D, Roubertoux P, Chiaroni J, Chanez P, Gras D, Di Cristofaro J. Bronchial Epithelial Cells from Asthmatic Patients Display Less Functional HLA-G Isoform Expression. Front Immunol 2017; 8:6. [PMID: 28303134 PMCID: PMC5333864 DOI: 10.3389/fimmu.2017.00006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/03/2017] [Indexed: 11/13/2022] Open
Abstract
Not all asthmatic patients adequately respond to current available treatments, such as inhaled corticosteroids or omalizumab®. New treatments will aim to target the bronchial epithelium-immune response interaction using different pathways. HLA-G is involved in immunomodulation and may promote epithelial cell differentiation and proliferation. HLA-G protein has several isoforms generated by alternative splicing that might have differential functionalities. HLA-G protein expression and genetic polymorphisms have been reported to be associated with asthma. Our hypothesis is that bronchial epithelium from asthmatic patients displays less functional HLA-G isoforms. HLA-G transcriptional isoforms were quantified by real-time PCR in human bronchial epithelium cells (HBEC) grown in air-liquid interface culture obtained from five healthy controls (HC), seven patients with mild asthma (MA), and seven patients with severe asthma (SA). They were re-differentiated, and IL-13 exposure was used as a proxy for a pro-inflammatory cytokine. HLA-G protein expression was assessed by western blot analysis. HLA-G allele was typed by direct sequencing. Our results showed that both MA and SA display less functional HLA-G isoforms than HC (p < 0.05); in vitro HBEC re-differentiation from SA displays a particular isoform expression profile compared to MA and HC (p = 0.03); HLA-G*01:06 frequency in MA and SA was significantly higher than in the healthy population (p = 0.03 and p < 0.001, respectively); and IL-13 exposure had no impact on HLA-G expression. Our results support that an impaired expression of HLA-G isoforms in asthmatic patients could contribute to the loss of inflammation control and epithelium structural remodeling. Therefore, HLA-G might be an interesting alternative target for asthmatic patients not adequately responding to current drugs.
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Affiliation(s)
- Federico Carlini
- Etablissement Français du Sang Alpes Méditerranée , Marseille , France
| | - Christophe Picard
- Etablissement Français du Sang Alpes Méditerranée, Marseille, France; Aix-Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Céline Garulli
- Aix-Marseille Univ, INSERM U1067 CNRS UMR 7333 , Marseille , France
| | | | - Pierre Roubertoux
- INSERM U491, Génétique Médicale et Développement, Aix-Marseille Université , Marseille , France
| | - Jacques Chiaroni
- Etablissement Français du Sang Alpes Méditerranée, Marseille, France; Aix-Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Pascal Chanez
- Aix-Marseille Univ, INSERM U1067 CNRS UMR 7333, Marseille, France; Clinique des Bronches, Allergie et Sommeil, AP-HM Hôpital Nord, Marseille, France
| | - Delphine Gras
- Aix-Marseille Univ, INSERM U1067 CNRS UMR 7333 , Marseille , France
| | - Julie Di Cristofaro
- Etablissement Français du Sang Alpes Méditerranée, Marseille, France; Aix-Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
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88
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Chen Y, Liu D, Liu P, Chen Y, Yu H, Zhang Q. Identification of biomarkers of intrahepatic cholangiocarcinoma via integrated analysis of mRNA and miRNA microarray data. Mol Med Rep 2017; 15:1051-1056. [PMID: 28098904 PMCID: PMC5367350 DOI: 10.3892/mmr.2017.6123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/07/2016] [Indexed: 01/06/2023] Open
Abstract
The present study aimed to identify potential therapeutic targets of intrahepatic cholangiocarcinoma (ICC) via integrated analysis of gene (transcript version) and microRNA (miRNA/miR) expression. The miRNA microarray dataset GSE32957 contained miRNA expression data from 16 ICC, 7 mixed type of combined hepatocellular-cholangiocarcinoma (CHC), 2 hepatic adenoma, 3 focal nodular hyperplasia (FNH) and 5 healthy liver tissue samples, and 2 cholangiocarcinoma cell lines. In addition, the mRNA microarray dataset GSE32879 contained mRNA expression data from 16 ICC, 7 CHC, 2 hepatic adenoma, 5 FNH and 7 healthy liver tissue samples. The datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and miRNAs (DEMs) in ICC samples compared with healthy liver tissues were identified via the limma package, following data preprocessing. Genes that exhibited alternative splicing (AS) in ICC samples were identified via AltAnalyze software. Functional enrichment analysis of DEGs was performed using the Database for Annotation, Visualization and Integrated Analysis. Target genes of DEMs were identified using the TargetScan database. The regulatory association between DEMs and any overlaps among DEGs, alternative splicing genes (ASGs) and target genes of DEMs were retrieved, and a network was visualized using the Cytoscape software. A total of 2,327 DEGs, 70 DEMs and 623 ASGs were obtained. Functional enrichment analysis indicated that DEGs were primarily enriched in biological processes and pathways associated with cell activity or the immune system. A total of 63 overlaps were obtained among DEGs, ASGs and target genes of DEMs, and a regulation network that contained 243 miRNA-gene regulation pairs was constructed between these overlaps and DEMs. The overlapped genes, including sprouty-related EVH1 domain containing 1, protein phosphate 1 regulatory subunit 12A, chromosome 20 open reading frame 194, and DEMs, including hsa-miR-96, hsa-miR-1 and hsa-miR-25, may be potential therapeutic targets for the future treatment of ICC.
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Affiliation(s)
- Yaqing Chen
- Department of VIP Ward, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Dan Liu
- Department of Ultrasonic Imaging, Zhuhai People's Hospital, Zhuhai, Guangdong 519000, P.R. China
| | - Pengfei Liu
- Department of Lymphoma, Sino‑US Center of Lymphoma and Leukemia, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Yajing Chen
- Department of Internal Medicine, Baoding Xiongxian County Hospital, Baoding, Hebei 071000, P.R. China
| | - Huiling Yu
- Department of Gastroenterology, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Quan Zhang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
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Resveratrol limits epithelial to mesenchymal transition through modulation of KHSRP/hnRNPA1-dependent alternative splicing in mammary gland cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:291-298. [PMID: 28088441 DOI: 10.1016/j.bbagrm.2017.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/29/2022]
Abstract
Resveratrol (RESV) is a natural polyphenolic compound endowed with anti-inflammatory, anti-proliferative, as well as pro-apoptotic activities that make it a potential anti-tumor compound. Here we show that RESV counteracts the TGF-β-induced Epithelial to Mesenchymal Transition (EMT) phenotype in mammary gland cells and affects the alternative exon usage of pre-mRNAs that encode crucial factors in adhesion and migration -including CD44, ENAH, and FGFR2- in a panel of immortalized and transformed mammary gland cells. RESV causes a shift from the mesenchymal-specific forms of these factors to the respective epithelial forms and increases the expression of the RNA-binding proteins KHSRP and hnRNPA1. From a mechanistic point of view, we show that the combined silencing of KHSRP and hnRNPA1 prevents the RESV-dependent inclusion of the epithelial-type exons in the Cd44 pre-mRNA. Our findings support an unexpected regulatory mechanism where RESV limits EMT by controlling gene expression at post-transcriptional level.
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90
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Park JY, Yun Y, Chung KY. Conformations of JNK3α splice variants analyzed by hydrogen/deuterium exchange mass spectrometry. J Struct Biol 2016; 197:271-278. [PMID: 27998708 DOI: 10.1016/j.jsb.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family that regulate apoptosis, inflammation, cytokine production, and metabolism. MAPKs undergo various splicing within their kinase domains. Unlike other MAPKs, JNKs have alternative splicing at the C-terminus, resulting in long and short variants. Functional or conformational effects due to the elongated C-terminal tail in the long splice variants have not been investigated nor has the conformation of the C-terminal tail been analyzed. Here, we analyzed the conformation of the elongated C-terminal tail and investigated conformational differences between long and short splice variants of JNKs using JNK3α2 and JNK3α1 as models. We adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to analyze the conformation. HDX-MS revealed that the C-terminal tail is mostly intrinsically disordered, and that the conformation of the kinase domain of JNK3α2 is more dynamic than that of JNK3α1. The different conformation dynamics between long and short splice variants of JNK3α might affect the cellular functions of JNK3.
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Affiliation(s)
- Ji Young Park
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Youngjoo Yun
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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91
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Cui Y, Liu J, Irudayaraj J. Beyond quantification: in situ analysis of transcriptome and pre-mRNA alternative splicing at the nanoscale. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27813271 DOI: 10.1002/wnan.1443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/02/2016] [Accepted: 10/02/2016] [Indexed: 11/08/2022]
Abstract
In situ analysis offers a venue for dissecting the complex transcriptome in its natural context to tap into cellular processes that could explain the phenotypic physiology and pathology yet to be understood. Over the past decades, enormous progress has been made to improve the resolution, sensitivity, and specificity of single-cell technologies. The continued efforts in RNA research not only facilitates mechanistic studies of molecular biology but also provides state-of-the-art strategies for diagnostic purposes. The implementation of novel bio-imaging platforms has yielded valuable information for inspecting gene expression, mapping regulatory networks, and classifying cell types. In this article, we discuss the merits and technical challenges in single-molecule in situ RNA profiling. Advanced in situ hybridization methodologies developed for a variety of detection modalities are reviewed. Considering the fact that in mammalian cells the number of protein products immensely exceeds that of the actual coding genes due to pre-mRNA alternative splicing, tools capable of elucidating this process in intact cells are highlighted. To conclude, we point out future directions for in situ transcriptome analysis and expect a plethora of opportunities and discoveries in this field. WIREs Nanomed Nanobiotechnol 2017, 9:e1443. doi: 10.1002/wnan.1443 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.,Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jing Liu
- Department of Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD, USA
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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92
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miRNA-Mediated KHSRP Silencing Rewires Distinct Post-transcriptional Programs during TGF-β-Induced Epithelial-to-Mesenchymal Transition. Cell Rep 2016; 16:967-978. [DOI: 10.1016/j.celrep.2016.06.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/12/2016] [Accepted: 06/12/2016] [Indexed: 12/17/2022] Open
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93
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Lin J, Hu Y, Nunez S, Foulkes AS, Cieply B, Xue C, Gerelus M, Li W, Zhang H, Rader DJ, Musunuru K, Li M, Reilly MP. Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. Arterioscler Thromb Vasc Biol 2016; 36:1434-47. [PMID: 27230130 PMCID: PMC4919157 DOI: 10.1161/atvbaha.116.307573] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Human macrophages can shift phenotype across the inflammatory M1 and reparative M2 spectrum in response to environmental challenges, but the mechanisms promoting inflammatory and cardiometabolic disease-associated M1 phenotypes remain incompletely understood. Alternative splicing (AS) is emerging as an important regulator of cellular function, yet its role in macrophage activation is largely unknown. We investigated the extent to which AS occurs in M1 activation within the cardiometabolic disease context and validated a functional genomic cell model for studying human macrophage-related AS events. APPROACH AND RESULTS From deep RNA-sequencing of resting, M1, and M2 primary human monocyte-derived macrophages, we found 3860 differentially expressed genes in M1 activation and detected 233 M1-induced AS events; the majority of AS events were cell- and M1-specific with enrichment for pathways relevant to macrophage inflammation. Using genetic variant data for 10 cardiometabolic traits, we identified 28 trait-associated variants within the genomic loci of 21 alternatively spliced genes and 15 variants within 7 differentially expressed regulatory splicing factors in M1 activation. Knockdown of 1 such splicing factor, CELF1, in primary human macrophages led to increased inflammatory response to M1 stimulation, demonstrating CELF1's potential modulation of the M1 phenotype. Finally, we demonstrated that an induced pluripotent stem cell-derived macrophage system recapitulates M1-associated AS events and provides a high-fidelity macrophage AS model. CONCLUSIONS AS plays a role in defining macrophage phenotype in a cell- and stimulus-specific fashion. Alternatively spliced genes and splicing factors with trait-associated variants may reveal novel pathways and targets in cardiometabolic diseases.
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Affiliation(s)
- Jennie Lin
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
| | - Yu Hu
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Sara Nunez
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Andrea S Foulkes
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Benjamin Cieply
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Chenyi Xue
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mark Gerelus
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Wenjun Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Hanrui Zhang
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Daniel J Rader
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Kiran Musunuru
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mingyao Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Muredach P Reilly
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
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Ning P, Zhou Y, Liang W, Zhang Y. Different RNA splicing mechanisms contribute to diverse infective outcome of classical swine fever viruses of differing virulence: insights from the deep sequencing data in swine umbilical vein endothelial cells. PeerJ 2016; 4:e2113. [PMID: 27330868 PMCID: PMC4906664 DOI: 10.7717/peerj.2113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/17/2016] [Indexed: 11/20/2022] Open
Abstract
Molecular mechanisms underlying RNA splicing regulation in response to viral infection are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen and C strains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen and C strains disturbed ‘RNA splicing’ of SUVEC, resulting in differential ‘gene expression’ in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance.
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Affiliation(s)
- Pengbo Ning
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi; School of Life Science and Technology, Xidian University, Xi'an, China
| | - Yulu Zhou
- College of Science, Northwest A&F University , Yangling , China
| | - Wulong Liang
- College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi
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95
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Abstract
Examples of associations between human disease and defects in pre-messenger RNA splicing/alternative splicing are accumulating. Although many alterations are caused by mutations in splicing signals or regulatory sequence elements, recent studies have noted the disruptive impact of mutated generic spliceosome components and splicing regulatory proteins. This review highlights recent progress in our understanding of how the altered splicing function of RNA-binding proteins contributes to myelodysplastic syndromes, cancer, and neuropathologies.
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Affiliation(s)
- Benoit Chabot
- Centre of Excellence in RNA Biology, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Lulzim Shkreta
- Centre of Excellence in RNA Biology, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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96
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Lv D, Wang X, Dong J, Zhuang Y, Huang S, Ma B, Chen P, Li X, Zhang B, Li Z, Jin B. Systematic characterization of lncRNAs' cell-to-cell expression heterogeneity in glioblastoma cells. Oncotarget 2016; 7:18403-14. [PMID: 26918340 PMCID: PMC4951297 DOI: 10.18632/oncotarget.7580] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/11/2016] [Indexed: 12/30/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant adult brain tumor generally associated with high level of cellular heterogeneity and a dismal prognosis. Long noncoding RNAs (lncRNAs) are emerging as novel mediators of tumorigenesis. Recently developed single-cell RNA-seq provides an unprecedented way for analysis of the cell-to-cell variability in lncRNA expression profiles. Here we comprehensively examined the expression patterns of 2,003 lncRNAs in 380 cells from five primary GBMs and two glioblastoma stem-like cell (GSC) lines. Employing the self-organizing maps, we displayed the landscape of the lncRNA expression dynamics for individual cells. Further analyses revealed heterogeneous nature of lncRNA in abundance and splicing patterns. Moreover, lncRNA expression variation is also ubiquitously present in the established GSC lines composed of seemingly identical cells. Through comparative analysis of GSC and corresponding differentiated cell cultures, we defined a stemness signature by the set of 31 differentially expressed lncRNAs, which can disclose stemness gradients in five tumors. Additionally, based on known classifier lncRNAs for molecular subtypes, each tumor was found to comprise individual cells representing four subtypes. Our systematic characterization of lncRNA expression heterogeneity lays the foundation for future efforts to further understand the function of lncRNA, develop valuable biomarkers, and enhance knowledge of GBM biology.
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Affiliation(s)
- Dekang Lv
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Jun Dong
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Yan Zhuang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Shuyu Huang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Binbin Ma
- Department of Neurosurgery, The Second Hospital of Dalian Medical University, Dalian, 116023, Liaoning, P.R. China
| | - Puxiang Chen
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, P.R. China
| | - Xiaodong Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Bo Zhang
- Department of Neurosurgery, The Second Hospital of Dalian Medical University, Dalian, 116023, Liaoning, P.R. China
| | - Zhiguang Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
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97
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Cieply B, Park JW, Nakauka-Ddamba A, Bebee TW, Guo Y, Shang X, Lengner CJ, Xing Y, Carstens RP. Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins. Cell Rep 2016; 15:247-55. [PMID: 27050523 DOI: 10.1016/j.celrep.2016.03.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/17/2015] [Accepted: 03/04/2016] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing (AS) plays a critical role in cell fate transitions, development, and disease. Recent studies have shown that AS also influences pluripotency and somatic cell reprogramming. We profiled transcriptome-wide AS changes that occur during reprogramming of fibroblasts to pluripotency. This analysis revealed distinct phases of AS, including a splicing program that is unique to transgene-independent induced pluripotent stem cells (iPSCs). Changes in the expression of AS factors Zcchc24, Esrp1, Mbnl1/2, and Rbm47 were demonstrated to contribute to phase-specific AS. RNA-binding motif enrichment analysis near alternatively spliced exons provided further insight into the combinatorial regulation of AS during reprogramming by different RNA-binding proteins. Ectopic expression of Esrp1 enhanced reprogramming, in part by modulating the AS of the epithelial specific transcription factor Grhl1. These data represent a comprehensive temporal analysis of the dynamic regulation of AS during the acquisition of pluripotency.
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Affiliation(s)
- Benjamin Cieply
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA; KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Angela Nakauka-Ddamba
- Department of Biomedical Sciences and Institute for Regenerative Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas W Bebee
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yang Guo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; School of Computer Science, Northwestern Polytechnical University, Xian 710072, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xian 710072, China
| | - Christopher J Lengner
- Department of Biomedical Sciences and Institute for Regenerative Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Russ P Carstens
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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98
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Wei N, Cheng Y, Wang Z, Liu Y, Luo C, Liu L, Chen L, Xie Z, Lu Y, Feng Y. SRSF10 Plays a Role in Myoblast Differentiation and Glucose Production via Regulation of Alternative Splicing. Cell Rep 2015; 13:1647-57. [DOI: 10.1016/j.celrep.2015.10.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 10/12/2015] [Indexed: 12/26/2022] Open
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99
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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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100
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Bebee TW, Park JW, Sheridan KI, Warzecha CC, Cieply BW, Rohacek AM, Xing Y, Carstens RP. The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development. eLife 2015; 4. [PMID: 26371508 PMCID: PMC4566030 DOI: 10.7554/elife.08954] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/18/2015] [Indexed: 12/13/2022] Open
Abstract
Tissue- and cell-type-specific regulators of alternative splicing (AS) are essential components of posttranscriptional gene regulation, necessary for normal cellular function, patterning, and development. Mice with ablation of Epithelial splicing regulatory protein (Esrp1) develop cleft lip and palate. Loss of both Esrp1 and its paralog Esrp2 results in widespread developmental defects with broad implications to human disease. Deletion of the Esrps in the epidermis revealed their requirement for establishing a proper skin barrier, a primary function of epithelial cells comprising the epidermis. We profiled the global Esrp-mediated splicing regulatory program in epidermis, which revealed large-scale programs of epithelial cell-type-specific splicing required for epithelial cell functions. These mice represent a valuable model for evaluating the essential role for AS in development and function of epithelial cells, which play essential roles in tissue homeostasis in numerous organs, and provide a genetic tool to evaluate important functional properties of epithelial-specific splice variants in vivo. DOI:http://dx.doi.org/10.7554/eLife.08954.001 Genes are turned into their protein products via two steps. The first, transcription, produces an intermediate RNA molecule or ‘transcript’; the second step, translation, turns the transcript into a protein. Most genes in mammals contain stretches of DNA called exons, which code for protein, interspersed with sequences called introns that do not. Therefore, a transcript must be ‘spliced’ before translation—the introns are removed and the exons joined. In some genes, certain exons can be optionally included or excluded from a transcript to produce different versions of the same protein that can often have very different functions. This is known as alternative splicing, and is essential for normal development. A large number of regulatory proteins control this process, many of which are only made in specific types of cells or tissues. Esrp1 and Esrp2 are two proteins that regulate alternative splicing in epithelial cells. These specialized cells form sheets that line most organs in the body and are found in the epidermis, the outermost layer of the skin. Although Esrp1 and Esrp2 have previously been studied in the laboratory using cultured cell lines, their roles have not been investigated in living animals. Bebee, Park et al. have now examined mice that are unable to produce one or both of these proteins. Mice that only lacked Esrp1 developed a cleft lip and palate. In mice that lacked both proteins, many organs failed to develop correctly and in some cases did not form at all. In the epidermis, the loss of Esrp1 and Esrp2 disrupted the splicing of the transcripts from genes that give epithelial cells many of their specialized characteristics, such as the ability to form sheets of cells with well formed junctions between them. This meant that epidermis that lacked Esrp1 and Esrp2 could not form a proper barrier layer, which is a crucial role of epithelia in skin as well as in other organs. In future, the mutant mice will be valuable for exploring how alternative splicing affects the development of epithelial cells and their properties. DOI:http://dx.doi.org/10.7554/eLife.08954.002
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Affiliation(s)
- Thomas W Bebee
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Juw Won Park
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Katherine I Sheridan
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Claude C Warzecha
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Benjamin W Cieply
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Alex M Rohacek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Yi Xing
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Russ P Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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