201
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Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell 2016; 164:805-17. [PMID: 26871637 PMCID: PMC4882190 DOI: 10.1016/j.cell.2016.01.029] [Citation(s) in RCA: 396] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/12/2015] [Accepted: 01/20/2016] [Indexed: 12/11/2022]
Abstract
While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms").
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Affiliation(s)
- Xinping Yang
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | | | - Shuli Kang
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gloria M. Sheynkman
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tong Hao
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron Richardson
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Song Sun
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada,Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Fan Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yun A. Shen
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan R. Murray
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kerstin Spirohn
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bridget E. Begg
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Miquel Duran-Frigola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Andrew MacWilliams
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel J. Pevzner
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Boston University School of Medicine, Boston, MA 02118, USA
| | - Quan Zhong
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shelly A. Trigg
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley Tam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nidhi Sahni
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Song Yi
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Maria D. Rodriguez
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dawit Balcha
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Guihong Tan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Brenda Andrews
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Xianghong J. Zhou
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kourosh Salehi-Ashtiani
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Benoit Charloteaux
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alyce A. Chen
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A. Calderwood
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Catalonia, Spain
| | - Frederick P. Roth
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada,Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - David E. Hill
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA,Correspondence: (M.V.), (Y.X.), (L.M.I.)
| | - Yu Xia
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.
| | - Marc Vidal
- Genomic Analysis of Network Perturbations Center of Excellence in Genomic Science (CEGS), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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202
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Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y. A new view of transcriptome complexity and regulation through the lens of local splicing variations. eLife 2016; 5:e11752. [PMID: 26829591 PMCID: PMC4801060 DOI: 10.7554/elife.11752] [Citation(s) in RCA: 295] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/31/2016] [Indexed: 12/29/2022] Open
Abstract
Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing variations remains a challenge. Here, we propose a new approach to define and quantify mRNA splicing in units of local splicing variations (LSVs). LSVs capture previously defined types of alternative splicing as well as more complex transcript variations. Building the first genome wide map of LSVs from twelve mouse tissues, we find complex LSVs constitute over 30% of tissue dependent transcript variations and affect specific protein families. We show the prevalence of complex LSVs is conserved in humans and identify hundreds of LSVs that are specific to brain subregions or altered in Alzheimer's patients. Amongst those are novel isoforms in the Camk2 family and a novel poison exon in Ptbp1, a key splice factor in neurogenesis. We anticipate the approach presented here will advance the ability to relate tissue-specific splice variation to genetic variation, phenotype, and disease.
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Affiliation(s)
- Jorge Vaquero-Garcia
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, United States
| | - Alejandro Barrera
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, United States
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Juan González-Vallinas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, United States
| | - Nicholas F Lahens
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - John B Hogenesch
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Kristen W Lynch
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, United States
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203
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Li HD, Omenn GS, Guan Y. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. Brief Bioinform 2016; 17:1024-1031. [PMID: 26740460 DOI: 10.1093/bib/bbv109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/03/2015] [Indexed: 01/23/2023] Open
Abstract
The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions. It is therefore essential to differentiate and annotate functions for individual isoforms. Computational approaches provide an efficient complement to expensive and time-consuming experimental studies. The input data of these methods range from DNA sequence, to RNA selection pressure, to expressed sequence tags, to full-length complementary DNA, to exon array, to RNA-seq expression, to proteomic data. Notably, RNA-seq technology generates quantitative profiling of transcript expression at the genome scale, with an unprecedented amount of expression data available for developing isoform function prediction methods. Integrative analysis of these data at different molecular levels enables a proteogenomic approach to systematically interrogate isoform functions. Here, we briefly review the state-of-the-art methods according to their input data sources, discuss their advantages and limitations and point out potential ways to improve prediction accuracies.
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204
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Yan J, Dunker AK, Uversky VN, Kurgan L. Molecular recognition features (MoRFs) in three domains of life. MOLECULAR BIOSYSTEMS 2016; 12:697-710. [DOI: 10.1039/c5mb00640f] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MoRFs are widespread intrinsically disordered protein-binding regions that have similar abundance and amino acid composition across the three domains of life.
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Affiliation(s)
- Jing Yan
- Department of Electrical and Computer Engineering
- University of Alberta
- Edmonton
- Canada
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics
- Indiana University School of Medicine
- Indianapolis
- USA
- Indiana University School of Informatics
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering
- University of Alberta
- Edmonton
- Canada
- Department of Computer Science
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205
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Licatalosi DD. Roles of RNA-binding Proteins and Post-transcriptional Regulation in Driving Male Germ Cell Development in the Mouse. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:123-51. [PMID: 27256385 DOI: 10.1007/978-3-319-29073-7_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tissue development and homeostasis are dependent on highly regulated gene expression programs in which cell-specific combinations of regulatory factors determine which genes are expressed and the post-transcriptional fate of the resulting RNA transcripts. Post-transcriptional regulation of gene expression by RNA-binding proteins has critical roles in tissue development-allowing individual genes to generate multiple RNA and protein products, and the timing, location, and abundance of protein synthesis to be finely controlled. Extensive post-transcriptional regulation occurs during mammalian gametogenesis, including high levels of alternative mRNA expression, stage-specific expression of mRNA variants, broad translational repression, and stage-specific activation of mRNA translation. In this chapter, an overview of the roles of RNA-binding proteins and the importance of post-transcriptional regulation in male germ cell development in the mouse is presented.
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Affiliation(s)
- Donny D Licatalosi
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, 44106, USA.
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206
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Inoue K, Fry EA. Aberrant Splicing of Estrogen Receptor, HER2, and CD44 Genes in Breast Cancer. GENETICS & EPIGENETICS 2015; 7:19-32. [PMID: 26692764 PMCID: PMC4669075 DOI: 10.4137/geg.s35500] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) is the most common cause of cancer-related death among women under the age of 50 years. Established biomarkers, such as hormone receptors (estrogen receptor [ER]/progesterone receptor) and human epidermal growth factor receptor 2 (HER2), play significant roles in the selection of patients for endocrine and trastuzumab therapies. However, the initial treatment response is often followed by tumor relapse with intrinsic resistance to the first-line therapy, so it has been expected to identify novel molecular markers to improve the survival and quality of life of patients. Alternative splicing of pre-messenger RNAs is a ubiquitous and flexible mechanism for the control of gene expression in mammalian cells. It provides cells with the opportunity to create protein isoforms with different, even opposing, functions from a single genomic locus. Aberrant alternative splicing is very common in cancer where emerging tumor cells take advantage of this flexibility to produce proteins that promote cell growth and survival. While a number of splicing alterations have been reported in human cancers, we focus on aberrant splicing of ER, HER2, and CD44 genes from the viewpoint of BC development. ERα36, a splice variant from the ER1 locus, governs nongenomic membrane signaling pathways triggered by estrogen and confers 4-hydroxytamoxifen resistance in BC therapy. The alternative spliced isoform of HER2 lacking exon 20 (Δ16HER2) has been reported in human BC; this isoform is associated with transforming ability than the wild-type HER2 and recapitulates the phenotypes of endocrine therapy-resistant BC. Although both CD44 splice isoforms (CD44s, CD44v) play essential roles in BC development, CD44v is more associated with those with favorable prognosis, such as luminal A subtype, while CD44s is linked to those with poor prognosis, such as HER2 or basal cell subtypes that are often metastatic. Hence, the detection of splice variants from these loci will provide keys to understand the pathogenesis, predict the prognosis, and choose specific therapies for BC.
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Affiliation(s)
- Kazushi Inoue
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Elizabeth A. Fry
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC, USA
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207
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Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Curr Opin Struct Biol 2015; 35:125-34. [PMID: 26658741 DOI: 10.1016/j.sbi.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/07/2023]
Abstract
Structure has traditionally been interrelated with sequence, usually in the framework of comparing sequences across species sharing a common fold. However, the nature of information within the sequence and structure databases is evolving, changing the type of comparisons possible. In particular, we now have a vast amount of personal genome sequences from human populations and a greater fraction of new structures contain interacting proteins within large complexes. Consequently, we have to recast our conception of sequence conservation and its relation to structure-for example, focusing more on selection within the human population. Moreover, within structural biology there is less emphasis on the discovery of novel folds and more on relating structures to networks of protein interactions. We cover this changing mindset here.
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Affiliation(s)
- Anurag Sethi
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Declan Clarke
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Jieming Chen
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Sushant Kumar
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Timur R Galeev
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Lynne Regan
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States
| | - Mark Gerstein
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States.
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208
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Cropley VL, Scarr E, Fornito A, Klauser P, Bousman CA, Scott R, Cairns MJ, Tooney PA, Pantelis C, Dean B. The effect of a muscarinic receptor 1 gene variant on grey matter volume in schizophrenia. Psychiatry Res 2015; 234:182-7. [PMID: 26481978 DOI: 10.1016/j.pscychresns.2015.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/20/2015] [Accepted: 09/01/2015] [Indexed: 11/18/2022]
Abstract
Previous research has demonstrated that individuals with schizophrenia who are homozygous at the c.267C>A single nucleotide polymorphism (rs2067477) within the cholinergic muscarinic M1 receptor (CHRM1) perform less well on the Wisconsin Card Sorting Test (WCST) than those who are heterozygous. This study sought to determine whether variation in the rs2067477 genotype was associated with differential changes in brain structure. Data from 227 patients with established schizophrenia or schizoaffective disorder were obtained from the Australian Schizophrenia Research Bank. Whole-brain voxel-based morphometry was performed to compare regional grey matter volume (GMV) between the 267C/C (N=191) and 267C/A (N=36) groups. Secondary analyses tested for an effect of genotype on cognition (the WCST was not available). Individuals who were homozygous (267C/C) demonstrated significantly reduced GMV in the right precentral gyrus compared to those who were heterozygous (267C/A). These preliminary results suggest that the rs2067477 genotype is associated with brain structure in the right precentral gyrus in individuals with schizophrenia/schizoaffective disorder. Future studies are required to replicate these results and directly link the volumetric reductions with specific cognitive processes.
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Affiliation(s)
- Vanessa L Cropley
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria 3053, Australia; Department of Psychiatry, The University of Melbourne, Parkville, Victoria 3052, Australia.
| | - Elizabeth Scarr
- Department of Psychiatry, The University of Melbourne, Parkville, Victoria 3052, Australia; Molecular Psychiatry Laboratory, Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
| | - Alex Fornito
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria 3053, Australia; Brain and Mental Health Laboratory, Institute of Cognitive and Clinical Neuroscience, Monash University, Clayton, Victoria 3168, Australia
| | - Paul Klauser
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria 3053, Australia; Brain and Mental Health Laboratory, Institute of Cognitive and Clinical Neuroscience, Monash University, Clayton, Victoria 3168, Australia
| | - Chad A Bousman
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria 3053, Australia; Department of Psychiatry, The University of Melbourne, Parkville, Victoria 3052, Australia; Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
| | - Rodney Scott
- The School of Biomedical Sciences and Pharmacy and the Priority Research Centre for Translational Neuroscience and Mental Health, The University of Newcastle, Callaghan, New South Wales 3208, Australia; Neurobehavioural Genetics Unit, Hunter Medical Research Institute, New Lambton, New South Wales 2305, Australia
| | - Murray J Cairns
- The School of Biomedical Sciences and Pharmacy and the Priority Research Centre for Translational Neuroscience and Mental Health, The University of Newcastle, Callaghan, New South Wales 3208, Australia; Neurobehavioural Genetics Unit, Hunter Medical Research Institute, New Lambton, New South Wales 2305, Australia
| | - Paul A Tooney
- The School of Biomedical Sciences and Pharmacy and the Priority Research Centre for Translational Neuroscience and Mental Health, The University of Newcastle, Callaghan, New South Wales 3208, Australia; Neurobehavioural Genetics Unit, Hunter Medical Research Institute, New Lambton, New South Wales 2305, Australia
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria 3053, Australia; Department of Psychiatry, The University of Melbourne, Parkville, Victoria 3052, Australia; Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
| | - Brian Dean
- Department of Psychiatry, The University of Melbourne, Parkville, Victoria 3052, Australia; Molecular Psychiatry Laboratory, Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
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209
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Gibson TJ, Dinkel H, Van Roey K, Diella F. Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal 2015; 13:42. [PMID: 26581338 PMCID: PMC4652402 DOI: 10.1186/s12964-015-0121-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/13/2015] [Indexed: 12/17/2022] Open
Abstract
It has become clear in outline though not yet in detail how cellular regulatory and signalling systems are constructed. The essential machines are protein complexes that effect regulatory decisions by undergoing internal changes of state. Subcomponents of these cellular complexes are assembled into molecular switches. Many of these switches employ one or more short peptide motifs as toggles that can move between one or more sites within the switch system, the simplest being on-off switches. Paradoxically, these motif modules (termed short linear motifs or SLiMs) are both hugely abundant but difficult to research. So despite the many successes in identifying short regulatory protein motifs, it is thought that only the “tip of the iceberg” has been exposed. Experimental and bioinformatic motif discovery remain challenging and error prone. The advice presented in this article is aimed at helping researchers to uncover genuine protein motifs, whilst avoiding the pitfalls that lead to reports of false discovery.
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany. .,Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
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210
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Will T, Helms V. PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. Bioinformatics 2015; 32:571-8. [PMID: 26508756 DOI: 10.1093/bioinformatics/btv620] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Protein-protein interaction networks are an important component of modern systems biology. Yet, comparatively few efforts have been made to tailor their topology to the actual cellular condition being studied. Here, we present a network construction method that exploits expression data at the transcript-level and thus reveals alterations in protein connectivity not only caused by differential gene expression but also by alternative splicing. We achieved this by establishing a direct correspondence between individual protein interactions and underlying domain interactions in a complete but condition-unspecific protein interaction network. This knowledge was then used to infer the condition-specific presence of interactions from the dominant protein isoforms. When we compared contextualized interaction networks of matched normal and tumor samples in breast cancer, our transcript-based construction identified more significant alterations that affected proteins associated with cancerogenesis than a method that only uses gene expression data. The approach is provided as the user-friendly tool PPIXpress. AVAILABILITY AND IMPLEMENTATION PPIXpress is available at https://sourceforge.net/projects/ppixpress/.
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Affiliation(s)
- Thorsten Will
- Center for Bioinformatics and Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
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211
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Gupta MK, Jayaram S, Reddy DN, Polisetty RV, Sirdeshmukh R. Transcriptomic and Proteomic Data Integration and Two-Dimensional Molecular Maps with Regulatory and Functional Linkages: Application to Cell Proliferation and Invasion Networks in Glioblastoma. J Proteome Res 2015; 14:5017-27. [DOI: 10.1021/acs.jproteome.5b00765] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Institute of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Savita Jayaram
- Institute of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Divijendra Natha Reddy
- Neuro-Oncology,
Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical
Foundation, Narayana Health, Bangalore 560099, India
| | | | - Ravi Sirdeshmukh
- Institute of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Neuro-Oncology,
Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical
Foundation, Narayana Health, Bangalore 560099, India
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212
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RNA Binding Protein Ptbp2 Is Essential for Male Germ Cell Development. Mol Cell Biol 2015; 35:4030-42. [PMID: 26391954 DOI: 10.1128/mcb.00676-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/14/2015] [Indexed: 11/20/2022] Open
Abstract
RNA binding proteins (RBPs) are increasingly recognized as essential factors in tissue development and homeostasis. The polypyrimidine tract binding (PTB) protein family of RBPs are important posttranscriptional regulators of gene expression. In the nervous system, the function and importance of PTB protein 2 (Ptbp2) as a key alternative splicing regulator is well established. Ptbp2 is also abundantly expressed during spermatogenesis, but its role in this developmental program has not been explored. Additionally, the importance of alternative splicing regulation in spermatogenesis is unclear. Here, we demonstrate that Ptbp2 is essential for spermatogenesis. We also describe an improved dual fluorescence flow cytometry strategy to discriminate, quantify, and collect germ cells in different stages of development. Using this approach, in combination with traditional histological methods, we show that Ptbp2 ablation results in germ cell loss due to increased apoptosis of meiotic spermatocytes and postmeiotic arrest of spermatid differentiation. Furthermore, we show that Ptbp2 is required for alternative splicing regulation in the testis, as in brain. Strikingly, not all of the alternatively spliced RNAs examined were sensitive to Ptbp2 loss in both tissues. Collectively, the data provide evidence for an important role for alternative splicing regulation in germ cell development and a central role for Ptbp2 in this process.
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213
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214
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Yeger-Lotem E, Sharan R. Human protein interaction networks across tissues and diseases. Front Genet 2015; 6:257. [PMID: 26347769 PMCID: PMC4541328 DOI: 10.3389/fgene.2015.00257] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/17/2015] [Indexed: 11/13/2022] Open
Abstract
Protein interaction networks are an important framework for studying protein function, cellular processes, and genotype-to-phenotype relationships. While our view of the human interaction network is constantly expanding, less is known about networks that form in biologically important contexts such as within distinct tissues or in disease conditions. Here we review efforts to characterize these networks and to harness them to gain insights into the molecular mechanisms underlying human disease.
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Affiliation(s)
- Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev Beer-Sheva, Israel
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University Tel Aviv, Israel
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215
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Trepte P, Buntru A, Klockmeier K, Willmore L, Arumughan A, Secker C, Zenkner M, Brusendorf L, Rau K, Redel A, Wanker EE. DULIP: A Dual Luminescence-Based Co-Immunoprecipitation Assay for Interactome Mapping in Mammalian Cells. J Mol Biol 2015; 427:3375-88. [PMID: 26264872 DOI: 10.1016/j.jmb.2015.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 12/30/2022]
Abstract
Mapping of protein-protein interactions (PPIs) is critical for understanding protein function and complex biological processes. Here, we present DULIP, a dual luminescence-based co-immunoprecipitation assay, for systematic PPI mapping in mammalian cells. DULIP is a second-generation luminescence-based PPI screening method for the systematic and quantitative analysis of co-immunoprecipitations using two different luciferase tags. Benchmarking studies with positive and negative PPI reference sets revealed that DULIP allows the detection of interactions with high sensitivity and specificity. Furthermore, the analysis of a PPI reference set with known binding affinities demonstrated that both low- and high-affinity interactions can be detected with DULIP assays. Finally, using the well-characterized interaction between Syntaxin-1 and Munc18, we found that DULIP is capable of detecting the effects of point mutations on interaction strength. Taken together, our studies demonstrate that DULIP is a sensitive and reliable method of great utility for systematic interactome research. It can be applied for interaction screening and validation of PPIs in mammalian cells. Moreover, DULIP permits the specific analysis of mutation-dependent binding patterns.
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Affiliation(s)
- Philipp Trepte
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Konrad Klockmeier
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Lindsay Willmore
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Anup Arumughan
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Lydia Brusendorf
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Kirstin Rau
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Alexandra Redel
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Straße 10, 13125 Berlin, Germany.
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216
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Krasnov GS, Dmitriev AA, Kudryavtseva AV, Shargunov AV, Karpov DS, Uroshlev LA, Melnikova NV, Blinov VM, Poverennaya EV, Archakov AI, Lisitsa AV, Ponomarenko EA. PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics. J Proteome Res 2015; 14:3729-37. [DOI: 10.1021/acs.jproteome.5b00490] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- George Sergeevich Krasnov
- Engelhardt
Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111991 Russia
- Orekhovich
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121 Russia
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | | | - Anna Viktorovna Kudryavtseva
- Engelhardt
Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111991 Russia
- Herzen
Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow, 125284 Russia
| | - Alexander Valerievich Shargunov
- Orekhovich
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121 Russia
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - Dmitry Sergeevich Karpov
- Engelhardt
Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111991 Russia
- Orekhovich
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121 Russia
| | | | | | - Vladimir Mikhailovich Blinov
- Orekhovich
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121 Russia
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | | | | | - Andrey Valerievich Lisitsa
- Orekhovich
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121 Russia
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217
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Parikshak NN, Gandal MJ, Geschwind DH. Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders. Nat Rev Genet 2015; 16:441-58. [PMID: 26149713 PMCID: PMC4699316 DOI: 10.1038/nrg3934] [Citation(s) in RCA: 307] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic and genomic approaches have implicated hundreds of genetic loci in neurodevelopmental disorders and neurodegeneration, but mechanistic understanding continues to lag behind the pace of gene discovery. Understanding the role of specific genetic variants in the brain involves dissecting a functional hierarchy that encompasses molecular pathways, diverse cell types, neural circuits and, ultimately, cognition and behaviour. With a focus on transcriptomics, this Review discusses how high-throughput molecular, integrative and network approaches inform disease biology by placing human genetics in a molecular systems and neurobiological context. We provide a framework for interpreting network biology studies and leveraging big genomics data sets in neurobiology.
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Affiliation(s)
- Neelroop N Parikshak
- 1] Program in Neurobehavioral Genetics, Semel Institute, and Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [2] Interdepartmental Program in Neuroscience, University of California, Los Angeles, California 90095, USA
| | - Michael J Gandal
- 1] Program in Neurobehavioral Genetics, Semel Institute, and Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [2] Center for Autism Treatment and Research, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Daniel H Geschwind
- 1] Program in Neurobehavioral Genetics, Semel Institute, and Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [2] Interdepartmental Program in Neuroscience, University of California, Los Angeles, California 90095, USA. [3] Center for Autism Treatment and Research, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [4] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
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218
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Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level. Methods 2015; 93:110-8. [PMID: 26238263 DOI: 10.1016/j.ymeth.2015.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 07/29/2015] [Indexed: 12/23/2022] Open
Abstract
In past decades, the experimental determination of protein functions was expensive and time-consuming, so numerous computational methods were developed to speed up and guide the process. However, most of these methods predict protein functions at the gene level and do not consider the fact that protein isoforms (translated from alternatively spliced transcripts), not genes, are the actual function carriers. Now, high-throughput RNA-seq technology is providing unprecedented opportunities to unravel protein functions at the isoform level. In this article, we review recent progress in the high-resolution functional annotations of protein isoforms, focusing on two methods developed by the authors. Both methods can integrate multiple RNA-seq datasets for comprehensively characterizing functions of protein isoforms.
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219
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Pundhir S, Gorodkin J. Differential and coherent processing patterns from small RNAs. Sci Rep 2015; 5:12062. [PMID: 26166713 PMCID: PMC4499813 DOI: 10.1038/srep12062] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/16/2015] [Indexed: 12/16/2022] Open
Abstract
Post-transcriptional processing events related to short RNAs are often reflected in their read profile patterns emerging from high-throughput sequencing data. MicroRNA arm switching across different tissues is a well-known example of what we define as differential processing. Here, short RNAs from the nine cell lines of the ENCODE project, irrespective of their annotation status, were analyzed for genomic loci representing differential or coherent processing. We observed differential processing predominantly in RNAs annotated as miRNA, snoRNA or tRNA. Four out of five known cases of differentially processed miRNAs that were in the input dataset were recovered and several novel cases were discovered. In contrast to differential processing, coherent processing is observed widespread in both annotated and unannotated regions. While the annotated loci predominantly consist of ~24 nt short RNAs, the unannotated loci comparatively consist of ~17 nt short RNAs. Furthermore, these ~17 nt short RNAs are significantly enriched for overlap to transcription start sites and DNase I hypersensitive sites (p-value < 0.01) that are characteristic features of transcription initiation RNAs. We discuss how the computational pipeline developed in this study has the potential to be applied to other forms of RNA-seq data for further transcriptome-wide studies of differential and coherent processing.
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Affiliation(s)
- Sachin Pundhir
- Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
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220
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Raj B, Blencowe B. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron 2015; 87:14-27. [DOI: 10.1016/j.neuron.2015.05.004] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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221
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Latysheva NS, Flock T, Weatheritt RJ, Chavali S, Babu MM. How do disordered regions achieve comparable functions to structured domains? Protein Sci 2015; 24:909-22. [PMID: 25752799 PMCID: PMC4456105 DOI: 10.1002/pro.2674] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
Abstract
The traditional structure to function paradigm conceives of a protein's function as emerging from its structure. In recent years, it has been established that unstructured, intrinsically disordered regions (IDRs) in proteins are equally crucial elements for protein function, regulation and homeostasis. In this review, we provide a brief overview of how IDRs can perform similar functions to structured proteins, focusing especially on the formation of protein complexes and assemblies and the mediation of regulated conformational changes. In addition to highlighting instances of such functional equivalence, we explain how differences in the biological and physicochemical properties of IDRs allow them to expand the functional and regulatory repertoire of proteins. We also discuss studies that provide insights into how mutations within functional regions of IDRs can lead to human diseases.
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Affiliation(s)
| | - Tilman Flock
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | | | - Sreenivas Chavali
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridge, CB2 0QH, United Kingdom
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222
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Chabot B. My road to alternative splicing control: from simple paths to loops and interconnections. Biochem Cell Biol 2015; 93:171-9. [PMID: 25759250 DOI: 10.1139/bcb-2014-0161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With the functional importance of alternative splicing being validated in nearly every mammalian biological system and implicated in many human diseases, it is now crucial to identify the molecular programs that control the production of splice variants. In this article, I will survey how our knowledge of the basic principles of alternative splicing control evolved over the last 25 years. I will also describe how investigation of the splicing control of an apoptotic regulator led us to identify novel effectors and revealed the existence of converging pathways linking splicing decisions to DNA damage. Finally, I will review how our efforts at developing tools designed to monitor and redirect splicing helped assess the impact of misregulated splicing in cancer.
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Affiliation(s)
- Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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223
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Ma X, Gao L, Karamanlidis G, Gao P, Lee CF, Garcia-Menendez L, Tian R, Tan K. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS Comput Biol 2015; 11:e1004332. [PMID: 26083688 PMCID: PMC4471235 DOI: 10.1371/journal.pcbi.1004332] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023] Open
Abstract
Development of heart diseases is driven by dynamic changes in both the activity and connectivity of gene pathways. Understanding these dynamic events is critical for understanding pathogenic mechanisms and development of effective treatment. Currently, there is a lack of computational methods that enable analysis of multiple gene networks, each of which exhibits differential activity compared to the network of the baseline/healthy condition. We describe the iMDM algorithm to identify both unique and shared gene modules across multiple differential co-expression networks, termed M-DMs (multiple differential modules). We applied iMDM to a time-course RNA-Seq dataset generated using a murine heart failure model generated on two genotypes. We showed that iMDM achieves higher accuracy in inferring gene modules compared to using single or multiple co-expression networks. We found that condition-specific M-DMs exhibit differential activities, mediate different biological processes, and are enriched for genes with known cardiovascular phenotypes. By analyzing M-DMs that are present in multiple conditions, we revealed dynamic changes in pathway activity and connectivity across heart failure conditions. We further showed that module dynamics were correlated with the dynamics of disease phenotypes during the development of heart failure. Thus, pathway dynamics is a powerful measure for understanding pathogenesis. iMDM provides a principled way to dissect the dynamics of gene pathways and its relationship to the dynamics of disease phenotype. With the exponential growth of omics data, our method can aid in generating systems-level insights into disease progression.
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Affiliation(s)
- Xiaoke Ma
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Long Gao
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Georgios Karamanlidis
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Peng Gao
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Chi Fung Lee
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lorena Garcia-Menendez
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Rong Tian
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kai Tan
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
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224
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Quesnel-Vallières M, Irimia M, Cordes SP, Blencowe BJ. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes Dev 2015; 29:746-59. [PMID: 25838543 PMCID: PMC4387716 DOI: 10.1101/gad.256115.114] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Quesnel-Vallières et al. show that loss of the vertebrate- and neural-specific Ser/Arg repeat-related protein of 100 kDa (nSR100/SRRM4) impairs development of the central and peripheral nervous systems. Accompanying these developmental defects are widespread changes in alternative splicing (AS) that primarily result in shifts to nonneural patterns for different classes of splicing events. The main component of the altered AS program comprises 3- to 27-nt neural microexons, and inclusion of a 6-nt nSR100-activated microexon in Unc13b transcripts is sufficient to rescue a neuritogenesis defect in nSR100 mutant primary neurons. Alternative splicing (AS) generates vast transcriptomic complexity in the vertebrate nervous system. However, the extent to which trans-acting splicing regulators and their target AS regulatory networks contribute to nervous system development is not well understood. To address these questions, we generated mice lacking the vertebrate- and neural-specific Ser/Arg repeat-related protein of 100 kDa (nSR100/SRRM4). Loss of nSR100 impairs development of the central and peripheral nervous systems in part by disrupting neurite outgrowth, cortical layering in the forebrain, and axon guidance in the corpus callosum. Accompanying these developmental defects are widespread changes in AS that primarily result in shifts to nonneural patterns for different classes of splicing events. The main component of the altered AS program comprises 3- to 27-nucleotide (nt) neural microexons, an emerging class of highly conserved AS events associated with the regulation of protein interaction networks in developing neurons and neurological disorders. Remarkably, inclusion of a 6-nt, nSR100-activated microexon in Unc13b transcripts is sufficient to rescue a neuritogenesis defect in nSR100 mutant primary neurons. These results thus reveal critical in vivo neurodevelopmental functions of nSR100 and further link these functions to a conserved program of neuronal microexon splicing.
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Affiliation(s)
- Mathieu Quesnel-Vallières
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Manuel Irimia
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Sabine P Cordes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada;
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225
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Chiurillo MA. Role of the Wnt/β-catenin pathway in gastric cancer: An in-depth literature review. World J Exp Med 2015; 5:84-102. [PMID: 25992323 PMCID: PMC4436943 DOI: 10.5493/wjem.v5.i2.84] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/05/2014] [Accepted: 03/20/2015] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer remains one of the most common cancers worldwide and one of the leading cause for cancer-related deaths. Gastric adenocarcinoma is a multifactorial disease that is genetically, cytologically and architecturally more heterogeneous than other gastrointestinal carcinomas. The aberrant activation of the Wnt/β-catenin signaling pathway is involved in the development and progression of a significant proportion of gastric cancer cases. This review focuses on the participation of the Wnt/β-catenin pathway in gastric cancer by offering an analysis of the relevant literature published in this field. Indeed, it is discussed the role of key factors in Wnt/β-catenin signaling and their downstream effectors regulating processes involved in tumor initiation, tumor growth, metastasis and resistance to therapy. Available data indicate that constitutive Wnt signalling resulting from Helicobacter pylori infection and inactivation of Wnt inhibitors (mainly by inactivating mutations and promoter hypermethylation) play an important role in gastric cancer. Moreover, a number of recent studies confirmed CTNNB1 and APC as driver genes in gastric cancer. The identification of specific membrane, intracellular, and extracellular components of the Wnt pathway has revealed potential targets for gastric cancer therapy. High-throughput “omics” approaches will help in the search for Wnt pathway antagonist in the near future.
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226
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Tay AP, Pang CNI, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR. Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J Proteome Res 2015; 14:3541-54. [PMID: 25961807 DOI: 10.1021/pr5011394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ∼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
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Affiliation(s)
- Aidan P Tay
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Chi Nam Ignatius Pang
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Natalie A Twine
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Linda Harkness
- Endocrine Research Laboratory (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital & University of Southern Denmark , Odense 5230, Denmark
| | - Moustapha Kassem
- Endocrine Research Laboratory (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital & University of Southern Denmark , Odense 5230, Denmark
| | - Marc R Wilkins
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
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227
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Neural differentiation modulates the vertebrate brain specific splicing program. PLoS One 2015; 10:e0125998. [PMID: 25993117 PMCID: PMC4438066 DOI: 10.1371/journal.pone.0125998] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/27/2015] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing patterns are known to vary between tissues but these patterns have been found to be predominantly peculiar to one species or another, implying only a limited function in fundamental neural biology. Here we used high-throughput RT-PCR to monitor the expression pattern of all the annotated simple alternative splicing events (ASEs) in the Reference Sequence Database, in different mouse tissues and identified 93 brain-specific events that shift from one isoform to another (switch-like) between brain and other tissues. Consistent with an important function, regulation of a core set of 9 conserved switch-like ASEs is highly conserved, as they have the same pattern of tissue-specific splicing in all vertebrates tested: human, mouse and zebrafish. Several of these ASEs are embedded within genes that encode proteins associated with the neuronal microtubule network, and show a dramatic and concerted shift within a short time window of human neural stem cell differentiation. Similarly these exons are dynamically regulated in zebrafish development. These data demonstrate that although alternative splicing patterns often vary between species, there is nonetheless a core set of vertebrate brain-specific ASEs that are conserved between species and associated with neural differentiation.
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228
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Cui H, Dhroso A, Johnson N, Korkin D. The variation game: Cracking complex genetic disorders with NGS and omics data. Methods 2015; 79-80:18-31. [PMID: 25944472 DOI: 10.1016/j.ymeth.2015.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/27/2015] [Accepted: 04/17/2015] [Indexed: 12/14/2022] Open
Abstract
Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.
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Affiliation(s)
- Hongzhu Cui
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
| | - Andi Dhroso
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
| | - Nathan Johnson
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
| | - Dmitry Korkin
- Department of Computer Science, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States; Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, United States
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229
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Abstract
Intrinsically disordered proteins (IDPs) are important components of the cellular signalling machinery, allowing the same polypeptide to undertake different interactions with different consequences. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and providing a mechanism for tissue-specific signalling. These proteins participate in the assembly of signalling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles. Experimental, computational and bioinformatic analyses combine to identify and characterize disordered regions of proteins, leading to a greater appreciation of their widespread roles in biological processes.
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230
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Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing. Proc Natl Acad Sci U S A 2015; 112:E1307-16. [PMID: 25737553 DOI: 10.1073/pnas.1500536112] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The synthesis and processing of mRNA, from transcription to translation initiation, often requires splicing of intragenic material. The final mRNA composition varies based on proteins that modulate splice site selection. EWS-FLI1 is an Ewing sarcoma (ES) oncoprotein with an interactome that we demonstrate to have multiple partners in spliceosomal complexes. We evaluate the effect of EWS-FLI1 on posttranscriptional gene regulation using both exon array and RNA-seq. Genes that potentially regulate oncogenesis, including CLK1, CASP3, PPFIBP1, and TERT, validate as alternatively spliced by EWS-FLI1. In a CLIP-seq experiment, we find that EWS-FLI1 RNA-binding motifs most frequently occur adjacent to intron-exon boundaries. EWS-FLI1 also alters splicing by directly binding to known splicing factors including DDX5, hnRNP K, and PRPF6. Reduction of EWS-FLI1 produces an isoform of γ-TERT that has increased telomerase activity compared with wild-type (WT) TERT. The small molecule YK-4-279 is an inhibitor of EWS-FLI1 oncogenic function that disrupts specific protein interactions, including helicases DDX5 and RNA helicase A (RHA) that alters RNA-splicing ratios. As such, YK-4-279 validates the splicing mechanism of EWS-FLI1, showing alternatively spliced gene patterns that significantly overlap with EWS-FLI1 reduction and WT human mesenchymal stem cells (hMSC). Exon array analysis of 75 ES patient samples shows similar isoform expression patterns to cell line models expressing EWS-FLI1, supporting the clinical relevance of our findings. These experiments establish systemic alternative splicing as an oncogenic process modulated by EWS-FLI1. EWS-FLI1 modulation of mRNA splicing may provide insight into the contribution of splicing toward oncogenesis, and, reciprocally, EWS-FLI1 interactions with splicing proteins may inform the splicing code.
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231
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Niklas KJ, Bondos SE, Dunker AK, Newman SA. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Front Cell Dev Biol 2015; 3:8. [PMID: 25767796 PMCID: PMC4341551 DOI: 10.3389/fcell.2015.00008] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/26/2015] [Indexed: 11/16/2022] Open
Abstract
Models for genetic regulation and cell fate specification characteristically assume that gene regulatory networks (GRNs) are essentially deterministic and exhibit multiple stable states specifying alternative, but pre-figured cell fates. Mounting evidence shows, however, that most eukaryotic precursor RNAs undergo alternative splicing (AS) and that the majority of transcription factors contain intrinsically disordered protein (IDP) domains whose functionalities are context dependent as well as subject to post-translational modification (PTM). Consequently, many transcription factors do not have fixed cis-acting regulatory targets, and developmental determination by GRNs alone is untenable. Modeling these phenomena requires a multi-scale approach to explain how GRNs operationally interact with the intra- and intercellular environments. Evidence shows that AS, IDP, and PTM complicate gene expression and act synergistically to facilitate and promote time- and cell-specific protein modifications involved in cell signaling and cell fate specification and thereby disrupt a strict deterministic GRN-phenotype mapping. The combined effects of AS, IDP, and PTM give proteomes physiological plasticity, adaptive responsiveness, and developmental versatility without inefficiently expanding genome size. They also help us understand how protein functionalities can undergo major evolutionary changes by buffering mutational consequences.
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Affiliation(s)
- Karl J Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College Station, TX, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University Indianapolis, IN, USA
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College Valhalla, NY, USA
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232
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Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJE, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 2015; 159:1511-23. [PMID: 25525873 DOI: 10.1016/j.cell.2014.11.035] [Citation(s) in RCA: 470] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/20/2014] [Accepted: 11/18/2014] [Indexed: 12/16/2022]
Abstract
Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However, which of the myriad of detected AS events provide important biological functions is not well understood. Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals. Relative to all other types of AS within this program, 3-15 nucleotide "microexons" display the most striking evolutionary conservation and switch-like regulation. These microexons modulate the function of interaction domains of proteins involved in neurogenesis. Most neural microexons are regulated by the neuronal-specific splicing factor nSR100/SRRM4, through its binding to adjacent intronic enhancer motifs. Neural microexons are frequently misregulated in the brains of individuals with autism spectrum disorder, and this misregulation is associated with reduced levels of nSR100. The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein-interaction networks during neurogenesis, the misregulation of which is linked to autism.
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Affiliation(s)
- Manuel Irimia
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain.
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan D Ellis
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Neelroop N Parikshak
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | | | - Mariana Babor
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | | | - Javier Tapial
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain
| | - Bushra Raj
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada; Canadian Institute For Advanced Research, 180 Dundas Street West, Toronto, ON M5G 1Z8, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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233
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Tseng YT, Li W, Chen CH, Zhang S, Chen JJW, Zhou X, Liu CC. IIIDB: a database for isoform-isoform interactions and isoform network modules. BMC Genomics 2015; 16 Suppl 2:S10. [PMID: 25707505 PMCID: PMC4331710 DOI: 10.1186/1471-2164-16-s2-s10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "proteins" of currently known PPIs generally refer to "genes." It is known that alternative splicing often impacts PPI by either directly affecting protein interacting domains, or by indirectly impacting other domains, which, in turn, impacts the PPI binding. Thus, proteins translated from different isoforms of the same gene can have different interaction partners. RESULTS Due to the limitations of current experimental capacities, little data is available for PPIs at the resolution of isoforms, although such high-resolution data is crucial to map pathways and to understand protein functions. In fact, alternative splicing can often change the internal structure of a pathway by rearranging specific PPIs. To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs. Furthermore, we constructed an III database (IIIDB) that is a resource for studying PPIs at isoform resolution. To discover functional modules in the III network, we performed III network clustering, and then obtained 1025 isoform modules. To evaluate the module functionality, we performed the GO/pathway enrichment analysis for each isoform module. CONCLUSIONS The IIIDB provides predictions of human protein-protein interactions at the high resolution of transcript isoforms that can facilitate detailed understanding of protein functions and biological pathways. The web interface allows users to search for IIIs or III network modules. The IIIDB is freely available at http://syslab.nchu.edu.tw/IIIDB.
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234
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Yang J, Hung LH, Licht T, Kostin S, Looso M, Khrameeva E, Bindereif A, Schneider A, Braun T. RBM24 is a major regulator of muscle-specific alternative splicing. Dev Cell 2015; 31:87-99. [PMID: 25313962 DOI: 10.1016/j.devcel.2014.08.025] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 06/23/2014] [Accepted: 08/27/2014] [Indexed: 11/29/2022]
Abstract
Cell-type-specific splicing generates numerous alternatively spliced transcripts playing important roles for organ development and homeostasis, but only a few tissue-specific splicing factors have been identified. We found that RBM24 governs a large number of muscle-specific splicing events that are critically involved in cardiac and skeletal muscle development and disease. Targeted inactivation of RBM24 in mice disrupted cardiac development and impaired sarcomerogenesis in striated muscles. In vitro splicing assays revealed that recombinant RBM24 is sufficient to promote muscle-specific exon inclusion in nuclear extracts of nonmuscle cells. Furthermore, we demonstrate that binding of RBM24 to an intronic splicing enhancer (ISE) is essential and sufficient to overcome repression of exon inclusion by an exonic splicing silencer (ESS) containing PTB and hnRNP A1/A2 binding sites. Introduction of ESS and ISE converted a constitutive exon into an RMB24-dependent alternative exon. We reason that RBM24 is a major regulator of alternative splicing in striated muscles.
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Affiliation(s)
- Jiwen Yang
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Thomas Licht
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Sawa Kostin
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Mario Looso
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Ekaterina Khrameeva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, Moscow 127994, Russia
| | - Albrecht Bindereif
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Andre Schneider
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany.
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany.
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235
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Tsugeki R, Tanaka-Sato N, Maruyama N, Terada S, Kojima M, Sakakibara H, Okada K. CLUMSY VEIN, the Arabidopsis DEAH-box Prp16 ortholog, is required for auxin-mediated development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:183-97. [PMID: 25384462 DOI: 10.1111/tpj.12721] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 05/25/2023]
Abstract
Pre-messenger RNA (pre-mRNA) splicing is essential in eukaryotic cells. In animals and yeasts, the DEAH-box RNA-dependent ATPase Prp16 mediates conformational change of the spliceosome, thereby facilitating pre-mRNA splicing. In yeasts, Prp16 also plays an important role in splicing fidelity. Conversely, PRP16 orthologs in Chlamydomonas reinhardtii and nematode do not have an important role in general pre-mRNA splicing, but are required for gene silencing and sex determination, respectively. Functions of PRP16 orthologs in higher plants have not been described until now. Here we show that the CLUMSY VEIN (CUV) gene encoding the unique Prp16 ortholog in Arabidopsis thaliana facilitates auxin-mediated development including male-gametophyte transmission, apical-basal patterning of embryonic and gynoecium development, stamen development, phyllotactic flower positioning, and vascular development. cuv-1 mutation differentially affects splicing and expression of genes involved in auxin biosynthesis, polar auxin transport, auxin perception and auxin signaling. The cuv-1 mutation does not have an equal influence on pre-mRNA substrates. We propose that Arabidopsis PRP16/CUV differentially facilitates expression of genes, which include genes involved in auxin biosynthesis, transport, perception and signaling, thereby collectively influencing auxin-mediated development.
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Affiliation(s)
- Ryuji Tsugeki
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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236
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Chen FC. Alternative RNA structure-coupled gene regulations in tumorigenesis. Int J Mol Sci 2014; 16:452-75. [PMID: 25551597 PMCID: PMC4307256 DOI: 10.3390/ijms16010452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative RNA structures (ARSs), or alternative transcript isoforms, are critical for regulating cellular phenotypes in humans. In addition to generating functionally diverse protein isoforms from a single gene, ARS can alter the sequence contents of 5'/3' untranslated regions (UTRs) and intronic regions, thus also affecting the regulatory effects of these regions. ARS may introduce premature stop codon(s) into a transcript, and render the transcript susceptible to nonsense-mediated decay, which in turn can influence the overall gene expression level. Meanwhile, ARS can regulate the presence/absence of upstream open reading frames and microRNA targeting sites in 5'UTRs and 3'UTRs, respectively, thus affecting translational efficiencies and protein expression levels. Furthermore, since ARS may alter exon-intron structures, it can influence the biogenesis of intronic microRNAs and indirectly affect the expression of the target genes of these microRNAs. The connections between ARS and multiple regulatory mechanisms underline the importance of ARS in determining cell fate. Accumulating evidence indicates that ARS-coupled regulations play important roles in tumorigenesis. Here I will review our current knowledge in this field, and discuss potential future directions.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan.
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237
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Affiliation(s)
- Claudia Scheckel
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute The Rockefeller University, New York, NY, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute The Rockefeller University, New York, NY, USA New York Genome Center, New York, NY, USA
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238
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Li HD, Menon R, Omenn GS, Guan Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics 2014; 14:2709-18. [PMID: 25265570 DOI: 10.1002/pmic.201400170] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/11/2014] [Accepted: 09/23/2014] [Indexed: 01/08/2023]
Abstract
Canonical isoforms in different databases have been defined as the most prevalent, most conserved, most expressed, longest, or the one with the clearest description of domains or posttranslational modifications. In this article, we revisit these definitions of canonical isoforms based on functional genomics and proteomics evidence, focusing on mouse data. We report a novel functional relationship network-based approach for identifying the highest connected isoforms (HCIs). We show that 46% of these HCIs are not the longest transcripts. In addition, this approach revealed many genes that have more than one highly connected isoforms. Averaged across 175 RNA-seq datasets covering diverse tissues and conditions, 65% of the HCIs show higher expression levels than nonhighest connected isoforms at the transcript level. At the protein level, these HCIs highly overlap with the expressed splice variants, based on proteomic data from eight different normal tissues. These results suggest that a more confident definition of canonical isoforms can be made through integration of multiple lines of evidence, including HCIs defined by biological processes and pathways, expression prevalence at the transcript level, and relative or absolute abundance at the protein level. This integrative proteogenomics approach can successfully identify principal isoforms that are responsible for the canonical functions of genes.
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Affiliation(s)
- Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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239
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Wu T, Baumgart T. BIN1 membrane curvature sensing and generation show autoinhibition regulated by downstream ligands and PI(4,5)P2. Biochemistry 2014; 53:7297-309. [PMID: 25350771 PMCID: PMC4245986 DOI: 10.1021/bi501082r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In striated muscles, invaginations
from the plasma membrane, termed
transverse tubules (T-tubule), function in the excitation–contraction
coupling machinery. BIN1 (isoform8) plays a critical role in the biogenesis
of T-tubules. BIN1 contains an N-terminal BAR domain to sense and
induce membrane curvature, an isoform8-specific polybasic motif (exon10)
as the phosphoinositide binding module and a C-terminal Src homology
3 (SH3) domain for the recruitment of downstream proteins such as
dynamin 2. Previous studies of N-BAR domains focused on elucidating
mechanisms of membrane curvature sensing and generation (MC-S&G).
Less is known about how MC-S&G is regulated. We found that the
SH3 domain binds to the exon10 motif more strongly compared to the
proline-rich domain (PRD) of dynamin 2. Furthermore, we found that
the MC-S&G ability of full-length BIN1 is inhibited on membranes
lacking PI(4,5)P2. Addition of PI(4,5)P2 in
the membrane activates BIN1 to sense and induce membrane curvature.
Co-presence of the SH3 domain and exon10 motif leads to the strongest
phosphoinositide-mediated control of BIN1 function. Addition of SH3
domain ligand (such as PRD peptides), as well as addition of the water-soluble
PI(4,5)P2 analogue, can both enhance the MC-S&G ability
of BIN1 on membranes without PI(4,5)P2, indicating that
the key to activate BIN1 is to disrupt the exon10–SH3 interaction.
The nonsense mutation K436X, found in centronuclear myopathy (CNM)
patients, abolishes SH3 domain binding with either exon10 or the PRD
motif, resulting in increased membrane deformation capacity. Our results
suggest an autoinhibition model for BIN1 that involves a synergistic
regulation by membrane composition and protein–protein interactions.
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Affiliation(s)
- Tingting Wu
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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240
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A million peptide motifs for the molecular biologist. Mol Cell 2014; 55:161-9. [PMID: 25038412 DOI: 10.1016/j.molcel.2014.05.032] [Citation(s) in RCA: 384] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/24/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
Abstract
A molecular description of functional modules in the cell is the focus of many high-throughput studies in the postgenomic era. A large portion of biomolecular interactions in virtually all cellular processes is mediated by compact interaction modules, referred to as peptide motifs. Such motifs are typically less than ten residues in length, occur within intrinsically disordered regions, and are recognized and/or posttranslationally modified by structured domains of the interacting partner. In this review, we suggest that there might be over a million instances of peptide motifs in the human proteome. While this staggering number suggests that peptide motifs are numerous and the most understudied functional module in the cell, it also holds great opportunities for new discoveries.
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241
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Hsiao HC, Gonzalez KL, Catanese DJ, Jordy KE, Matthews KS, Bondos SE. The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PLoS One 2014; 9:e108217. [PMID: 25286318 PMCID: PMC4186791 DOI: 10.1371/journal.pone.0108217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/27/2014] [Indexed: 02/05/2023] Open
Abstract
Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues.
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Affiliation(s)
- Hao-Ching Hsiao
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Kim L. Gonzalez
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Daniel J. Catanese
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Kristopher E. Jordy
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Kathleen S. Matthews
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Sarah E. Bondos
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
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242
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Abstract
Sequence-specific RNA-binding proteins (RBPs) bind to pre-mRNA to control alternative splicing, but it is not yet possible to read the 'splicing code' that dictates splicing regulation on the basis of genome sequence. Each alternative splicing event is controlled by multiple RBPs, the combined action of which creates a distribution of alternatively spliced products in a given cell type. As each cell type expresses a distinct array of RBPs, the interpretation of regulatory information on a given RNA target is exceedingly dependent on the cell type. RBPs also control each other's functions at many levels, including by mutual modulation of their binding activities on specific regulatory RNA elements. In this Review, we describe some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation.
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Affiliation(s)
- Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic, Medicine, University of California San Diego, La Jolla, California 92093–0651, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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243
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A global regulatory mechanism for activating an exon network required for neurogenesis. Mol Cell 2014; 56:90-103. [PMID: 25219497 DOI: 10.1016/j.molcel.2014.08.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/27/2014] [Accepted: 08/07/2014] [Indexed: 12/15/2022]
Abstract
The vertebrate and neural-specific Ser/Arg (SR)-related protein nSR100/SRRM4 regulates an extensive program of alternative splicing with critical roles in nervous system development. However, the mechanism by which nSR100 controls its target exons is poorly understood. We demonstrate that nSR100-dependent neural exons are associated with a unique configuration of intronic cis-elements that promote rapid switch-like regulation during neurogenesis. A key feature of this configuration is the insertion of specialized intronic enhancers between polypyrimidine tracts and acceptor sites that bind nSR100 to potently activate exon inclusion in neural cells while weakening 3' splice site recognition and contributing to exon skipping in nonneural cells. nSR100 further operates by forming multiple interactions with early spliceosome components bound proximal to 3' splice sites. These multifaceted interactions achieve dominance over neural exon silencing mediated by the splicing regulator PTBP1. The results thus illuminate a widespread mechanism by which a critical neural exon network is activated during neurogenesis.
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244
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Sinha A, Nagarajaram HA. Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics 2014; 14:2242-8. [PMID: 25092398 DOI: 10.1002/pmic.201400249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/04/2014] [Accepted: 08/01/2014] [Indexed: 12/22/2022]
Abstract
The functional repertoire of genes in the eukaryotic organisms is enhanced by the phenomenon of alternative splicing. Hence, a node in a tissue specific protein-protein interaction (TS PPIN) network can be thought of as an ensemble of various spliced protein products of the corresponding gene expressed in that tissue. Here we demonstrate that the nodes that occupy topologically central positions characterized by high degree, betweenness, closeness, and eigenvector centrality values in TS PPINs of Homo sapiens are associated with high number of splice variants. We also show that the high "centrality" of these genes/nodes could in part be explained by the presence of a large number of promiscuous domains.
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Affiliation(s)
- Anupam Sinha
- Laboratory of Computational Biology, Centre for DNA Fingerprinting & Diagnostics (CDFD), Hyderabad, Telangana, India
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245
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Solomon O, Bazak L, Levanon EY, Amariglio N, Unger R, Rechavi G, Eyal E. Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives. Proteins 2014; 82:3117-31. [DOI: 10.1002/prot.24672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/28/2014] [Accepted: 08/11/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Oz Solomon
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Lily Bazak
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Erez Y. Levanon
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Ninette Amariglio
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
| | - Ron Unger
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Gideon Rechavi
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
- Sackler School of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Eran Eyal
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
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246
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Structured and disordered facets of the GPCR fold. Curr Opin Struct Biol 2014; 27:129-37. [PMID: 25198166 DOI: 10.1016/j.sbi.2014.08.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 07/28/2014] [Accepted: 08/05/2014] [Indexed: 01/14/2023]
Abstract
The seven-transmembrane (7TM) helix fold of G-protein coupled receptors (GPCRs) has been adapted for a wide variety of physiologically important signaling functions. Here, we discuss the diversity in the structured and disordered regions of GPCRs based on the recently published crystal structures and sequence analysis of all human GPCRs. A comparison of the structures of rhodopsin-like receptors (class A), secretin-like receptors (class B), metabotropic receptors (class C) and frizzled receptors (class F) shows that the relative arrangement of the transmembrane helices is conserved across all four GPCR classes although individual receptors can be activated by ligand binding at varying positions within and around the transmembrane helical bundle. A systematic analysis of GPCR sequences reveals the presence of disordered segments in the cytoplasmic side, abundant post-translational modification sites, evidence for alternative splicing and several putative linear peptide motifs that have the potential to mediate interactions with cytosolic proteins. While the structured regions permit the receptor to bind diverse ligands, the disordered regions appear to have an underappreciated role in modulating downstream signaling in response to the cellular state. An integrated paradigm combining the knowledge of structured and disordered regions is imperative for gaining a holistic understanding of the GPCR (un)structure-function relationship.
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247
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Intracellular clusterin interacts with brain isoforms of the bridging integrator 1 and with the microtubule-associated protein Tau in Alzheimer's disease. PLoS One 2014; 9:e103187. [PMID: 25051234 PMCID: PMC4106906 DOI: 10.1371/journal.pone.0103187] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/26/2014] [Indexed: 12/11/2022] Open
Abstract
Sporadic or late-onset Alzheimer's disease (AD) is expected to affect 50% of individuals reaching 85 years of age. The most significant genetic risk factor for late-onset AD is the e4 allele of APOE gene encoding apolipoprotein E, a lipid carrier shown to modulate brain amyloid burden. Recent genome-wide association studies have uncovered additional single nucleotide polymorphisms (SNPs) linked to AD susceptibility, including those in the CLU and BIN1 genes encoding for clusterin (CLU) and the bridging integrator 1 (BIN1) proteins, respectively. Because CLU has been implicated in brain amyloid-β (Aβ) clearance in mouse models of amyloid deposition, we sought to investigate whether an AD-linked SNP in the CLU gene altered Aβ42 biomarker levels in the cerebrospinal fluid (CSF). Instead, we found that the CLU rs11136000 SNP modified CSF levels of the microtubule-associated protein Tau in AD patients. We also found that an intracellular form of CLU (iCLU) was upregulated in the brain of Tau overexpressing Tg4510 mice, but not in Tg2576 amyloid mouse model. By overexpressing iCLU and Tau in cell culture systems we discovered that iCLU was a Tau-interacting protein and that iCLU associated with brain-specific isoforms of BIN1, also recently identified as a Tau-binding protein. Through expression analysis of CLU and BIN1 variants, we found that CLU and BIN1 interacted via their coiled-coil motifs. In co-immunoprecipitation studies using human brain tissue, we showed that iCLU and the major BIN1 isoform expressed in neurons were associated with modified Tau species found in AD. Finally, we showed that expression of certain coding CLU variants linked to AD risk led to increased levels of iCLU. Together, our findings suggest that iCLU and BIN1 interaction might impact Tau function in neurons and uncover potential new mechanisms underlying the etiology of Tau pathology in AD.
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248
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van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright P, Babu MM. Classification of intrinsically disordered regions and proteins. Chem Rev 2014; 114:6589-631. [PMID: 24773235 PMCID: PMC4095912 DOI: 10.1021/cr400525m] [Citation(s) in RCA: 1569] [Impact Index Per Article: 142.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Robin van der Lee
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Centre
for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The
Netherlands
| | - Marija Buljan
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Benjamin Lang
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gary W. Daughdrill
- Department
of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 3720 Spectrum Boulevard, Suite 321, Tampa, Florida 33612, United States
| | - A. Keith Dunker
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, H-4032 Debrecen, Nagyerdei krt 98, Hungary
| | - Julian Gough
- Department
of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, United Kingdom
| | - Joerg Gsponer
- Department
of Biochemistry and Molecular Biology, Centre for High-Throughput
Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - David
T. Jones
- Bioinformatics
Group, Department of Computer Science, University
College London, London, WC1E 6BT, United Kingdom
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular
Genetics, and Department of Computer Science, University
of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Richard
W. Kriwacki
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
| | - Christopher J. Oldfield
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Rohit V. Pappu
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Peter Tompa
- VIB Department
of Structural Biology, Vrije Universiteit
Brussel, Brussels, Belgium
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vladimir N. Uversky
- Department
of Molecular Medicine and USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation,
Russian Academy of Sciences, Pushchino,
Moscow Region, Russia
| | - Peter
E. Wright
- Department
of Integrative Structural and Computational Biology and Skaggs Institute
of Chemical Biology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Madan Babu
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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249
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Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CXD, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 2014; 15:92-101. [PMID: 24813856 PMCID: PMC4082735 DOI: 10.1016/j.stem.2014.04.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/28/2014] [Accepted: 04/02/2014] [Indexed: 12/20/2022]
Abstract
Alternative RNA splicing (AS) regulates proteome diversity, including isoform-specific expression of several pluripotency genes. Here, we integrated global gene expression and proteomic analyses and identified a molecular signature suggesting a central role for AS in maintaining human pluripotent stem cell (hPSC) self-renewal. We demonstrate that the splicing factor SFRS2 is an OCT4 target gene required for pluripotency. SFRS2 regulates AS of the methyl-CpG binding protein MBD2, whose isoforms play opposing roles in maintenance of and reprogramming to pluripotency. Although both MDB2a and MBD2c are enriched at the OCT4 and NANOG promoters, MBD2a preferentially interacts with repressive NuRD chromatin remodeling factors and promotes hPSC differentiation, whereas overexpression of MBD2c enhances reprogramming of fibroblasts to pluripotency. The miR-301 and miR-302 families provide additional regulation by targeting SFRS2 and MDB2a. These data suggest that OCT4, SFRS2, and MBD2 participate in a positive feedback loop, regulating proteome diversity in support of hPSC self-renewal and reprogramming.
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Affiliation(s)
- Yu Lu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yuin-Han Loh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Pediatric Hematology Oncology, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA; A(∗)STAR Institute of Molecular and Cell Biology and Department of Biological Sciences, National University of Singapore, Singapore 138673, Singapore
| | - Hu Li
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcella Cesana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Pediatric Hematology Oncology, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jignesh R Parikh
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Bioinformatics Program, Boston University, Boston, MA 02115, USA
| | - Nathan Salomonis
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Cheng-Xu Delon Toh
- A(∗)STAR Institute of Molecular and Cell Biology and Department of Biological Sciences, National University of Singapore, Singapore 138673, Singapore
| | - Stelios T Andreadis
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - C John Luckey
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James J Collins
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George Q Daley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Pediatric Hematology Oncology, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA.
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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250
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Li HD, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014; 30:340-7. [PMID: 24951248 DOI: 10.1016/j.tig.2014.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
Abstract
The vast majority of multi-exon genes in humans undergo alternative splicing, which greatly increases the functional diversity of protein species. Predicting functions at the isoform level is essential to further our understanding of developmental abnormalities and cancers, which frequently exhibit aberrant splicing and dysregulation of isoform expression. However, determination of isoform function is very difficult, and efforts to predict isoform function have been limited in the functional genomics field. Deep sequencing of RNA now provides an unprecedented amount of expression data at the transcript level. We describe here emerging computational approaches that integrate such large-scale whole-transcriptome sequencing (RNA-seq) data for predicting the functions of alternatively spliced isoforms, and we discuss their applications in developmental and cancer biology. We outline future directions for isoform function prediction, emphasizing the need for heterogeneous genomic data integration and tissue-specific, dynamic isoform-level network modeling, which will allow the field to realize its full potential.
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Affiliation(s)
- Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA; Department of Electrical Engineering and Computer Science, Ann Arbor, MI, USA.
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