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Bailey LR, Bugg D, Reichardt IM, Ortaç CD, Nagle A, Gunaje J, Martinson A, Johnson R, MacCoss MJ, Sakamoto T, Kelly DP, Regnier M, Davis JM. MBNL1 Regulates Programmed Postnatal Switching Between Regenerative and Differentiated Cardiac States. Circulation 2024; 149:1812-1829. [PMID: 38426339 PMCID: PMC11147738 DOI: 10.1161/circulationaha.123.066860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Discovering determinants of cardiomyocyte maturity is critical for deeply understanding the maintenance of differentiated states and potentially reawakening endogenous regenerative programs in adult mammalian hearts as a therapeutic strategy. Forced dedifferentiation paired with oncogene expression is sufficient to drive cardiac regeneration, but elucidation of endogenous developmental regulators of the switch between regenerative and mature cardiomyocyte cell states is necessary for optimal design of regenerative approaches for heart disease. MBNL1 (muscleblind-like 1) regulates fibroblast, thymocyte, and erythroid differentiation and proliferation. Hence, we examined whether MBNL1 promotes and maintains mature cardiomyocyte states while antagonizing cardiomyocyte proliferation. METHODS MBNL1 gain- and loss-of-function mouse models were studied at several developmental time points and in surgical models of heart regeneration. Multi-omics approaches were combined with biochemical, histological, and in vitro assays to determine the mechanisms through which MBNL1 exerts its effects. RESULTS MBNL1 is coexpressed with a maturation-association genetic program in the heart and is regulated by the MEIS1/calcineurin signaling axis. Targeted MBNL1 overexpression early in development prematurely transitioned cardiomyocytes to hypertrophic growth, hypoplasia, and dysfunction, whereas loss of MBNL1 function increased cardiomyocyte cell cycle entry and proliferation through altered cell cycle inhibitor transcript stability. Moreover, MBNL1-dependent stabilization of estrogen-related receptor signaling was essential for maintaining cardiomyocyte maturity in adult myocytes. In accordance with these data, modulating MBNL1 dose tuned the temporal window of neonatal cardiac regeneration, where increased MBNL1 expression arrested myocyte proliferation and regeneration and MBNL1 deletion promoted regenerative states with prolonged myocyte proliferation. However, MBNL1 deficiency was insufficient to promote regeneration in the adult heart because of cell cycle checkpoint activation. CONCLUSIONS Here, MBNL1 was identified as an essential regulator of cardiomyocyte differentiated states, their developmental switch from hyperplastic to hypertrophic growth, and their regenerative potential through controlling an entire maturation program by stabilizing adult myocyte mRNAs during postnatal development and throughout adulthood. Targeting loss of cardiomyocyte maturity and downregulation of cell cycle inhibitors through MBNL1 deletion was not sufficient to promote adult regeneration.
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Affiliation(s)
- Logan R.J. Bailey
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Molecular and Cellular Biology, University of Washington, Seattle, WA
- Medical Scientist Training Program, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Darrian Bugg
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Isabella M. Reichardt
- Bioengineering, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - C. Dessirée Ortaç
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Abigail Nagle
- Bioengineering, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Jagadambika Gunaje
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Amy Martinson
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | | | | | - Tomoya Sakamoto
- Cardiovascular Institute, Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel P. Kelly
- Cardiovascular Institute, Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael Regnier
- Bioengineering, University of Washington, Seattle, WA
- Center for Translational Muscle Research, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Jennifer M. Davis
- Lab Medicine and Pathology, University of Washington, Seattle, WA
- Bioengineering, University of Washington, Seattle, WA
- Center for Translational Muscle Research, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
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Bailey LRJ, Bugg D, Reichardt IM, Ortaç CD, Gunaje J, Johnson R, MacCoss MJ, Sakamoto T, Kelly DP, Regnier M, Davis JM. MBNL1 regulates programmed postnatal switching between regenerative and differentiated cardiac states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532974. [PMID: 36993225 PMCID: PMC10055038 DOI: 10.1101/2023.03.16.532974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Discovering determinants of cardiomyocyte maturity and the maintenance of differentiated states is critical to both understanding development and potentially reawakening endogenous regenerative programs in adult mammalian hearts as a therapeutic strategy. Here, the RNA binding protein Muscleblind-like 1 (MBNL1) was identified as a critical regulator of cardiomyocyte differentiated states and their regenerative potential through transcriptome-wide control of RNA stability. Targeted MBNL1 overexpression early in development prematurely transitioned cardiomyocytes to hypertrophic growth, hypoplasia, and dysfunction, whereas loss of MBNL1 function increased cardiomyocyte cell cycle entry and proliferation through altered cell cycle inhibitor transcript stability. Moreover, MBNL1-dependent stabilization of the estrogen-related receptor signaling axis was essential for maintaining cardiomyocyte maturity. In accordance with these data, modulating MBNL1 dose tuned the temporal window of cardiac regeneration, where enhanced MBNL1 activity arrested myocyte proliferation, and MBNL1 deletion promoted regenerative states with prolonged myocyte proliferation. Collectively these data suggest MBNL1 acts as a transcriptome-wide switch between regenerative and mature myocyte states postnatally and throughout adulthood.
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Haskell D, Zinovyeva A. KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development. G3-GENES GENOMES GENETICS 2021; 11:6114466. [PMID: 33585875 PMCID: PMC8022929 DOI: 10.1093/g3journal/jkab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022]
Abstract
MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate their activities and the precise mechanisms of this coordination are not well understood. RBPs often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs during Caenorhabditis elegans development, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonaute alg-1. Interestingly, two KH domain genes, predicted splicing factors sfa-1 and asd-2, genetically interacted with all of the miRNA mutants tested, whereas other KH domain genes showed genetic interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of the C. elegans KH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that many C. elegans KH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.
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Affiliation(s)
- Dustin Haskell
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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Bretherton R, Bugg D, Olszewski E, Davis J. Regulators of cardiac fibroblast cell state. Matrix Biol 2020; 91-92:117-135. [PMID: 32416242 PMCID: PMC7789291 DOI: 10.1016/j.matbio.2020.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/13/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Fibroblasts are the primary regulator of cardiac extracellular matrix (ECM). In response to disease stimuli cardiac fibroblasts undergo cell state transitions to a myofibroblast phenotype, which underlies the fibrotic response in the heart and other organs. Identifying regulators of fibroblast state transitions would inform which pathways could be therapeutically modulated to tactically control maladaptive extracellular matrix remodeling. Indeed, a deeper understanding of fibroblast cell state and plasticity is necessary for controlling its fate for therapeutic benefit. p38 mitogen activated protein kinase (MAPK), which is part of the noncanonical transforming growth factor β (TGFβ) pathway, is a central regulator of fibroblast to myofibroblast cell state transitions that is activated by chemical and mechanical stress signals. Fibroblast intrinsic signaling, local and global cardiac mechanics, and multicellular interactions individually and synergistically impact these state transitions and hence the ECM, which will be reviewed here in the context of cardiac fibrosis.
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Affiliation(s)
- Ross Bretherton
- Department of Bioengineering, University of Washington, Seattle, WA 98105, United States
| | - Darrian Bugg
- Department of Pathology, University of Washington, 850 Republican, #343, Seattle, WA 98109, United States
| | - Emily Olszewski
- Department of Bioengineering, University of Washington, Seattle, WA 98105, United States
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA 98105, United States; Department of Pathology, University of Washington, 850 Republican, #343, Seattle, WA 98109, United States; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, United States; Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, United States.
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Vemuri S, Srivastava R, Mir Q, Hashemikhabir S, Dong XC, Janga SC. SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome. Methods 2020; 178:104-113. [PMID: 31494246 PMCID: PMC7056568 DOI: 10.1016/j.ymeth.2019.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/25/2019] [Accepted: 09/01/2019] [Indexed: 12/26/2022] Open
Abstract
Several protein-RNA cross linking protocols have been established in recent years to delineate the molecular interaction of an RNA Binding Protein (RBP) and its target RNAs. However, functional dissection of the role of the RBP binding sites in modulating the post-transcriptional fate of the target RNA remains challenging. CRISPR/Cas9 genome editing system is being commonly employed to perturb both coding and noncoding regions in the genome. With the advancements in genome-scale CRISPR/Cas9 screens, it is now possible to not only perturb specific binding sites but also probe the global impact of protein-RNA interaction sites across cell types. Here, we present SliceIt (http://sliceit.soic.iupui.edu/), a database of in silico sgRNA (single guide RNA) library to facilitate conducting such high throughput screens. SliceIt comprises of ~4.8 million unique sgRNAs with an estimated range of 2-8 sgRNAs designed per RBP binding site, for eCLIP experiments of >100 RBPs in HepG2 and K562 cell lines from the ENCODE project. SliceIt provides a user friendly environment, developed using advanced search engine framework, Elasticsearch. It is available in both table and genome browser views facilitating the easy navigation of RBP binding sites, designed sgRNAs, exon expression levels across 53 human tissues along with prevalence of SNPs and GWAS hits on binding sites. Exon expression profiles enable examination of locus specific changes proximal to the binding sites. Users can also upload custom tracks of various file formats directly onto genome browser, to navigate additional genomic features in the genome and compare with other types of omics profiles. All the binding site-centric information is dynamically accessible via "search by gene", "search by coordinates" and "search by RBP" options and readily available to download. Validation of the sgRNA library in SliceIt was performed by selecting RBP binding sites in Lipt1 gene and designing sgRNAs. Effect of CRISPR/Cas9 perturbations on the selected binding sites in HepG2 cell line, was confirmed based on altered proximal exon expression levels using qPCR, further supporting the utility of the resource to design experiments for perturbing protein-RNA interaction networks. Thus, SliceIt provides a one-stop repertoire of guide RNA library to perturb RBP binding sites, along with several layers of functional information to design both low and high throughput CRISPR/Cas9 screens, for studying the phenotypes and diseases associated with RBP binding sites.
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Affiliation(s)
- Sasank Vemuri
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Seyedsasan Hashemikhabir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - X Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States; Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States.
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Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, Nakshatri H, Janga SC. Mutational landscape of RNA-binding proteins in human cancers. RNA Biol 2017; 15:115-129. [PMID: 29023197 PMCID: PMC5786023 DOI: 10.1080/15476286.2017.1391436] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations. Functional analysis of these RBPs revealed the enrichment of pathways associated with apoptosis, splicing and translation. Using the OncodriveFM framework, we also identified more than 200 candidate driver RBPs that were found to accumulate functionally impactful mutations in at least one cancer. Expression levels of 15% of these driver RBPs exhibited significant difference, when transcriptome groups with and without deleterious mutations were compared. Functional interaction network of the driver RBPs revealed the enrichment of spliceosomal machinery, suggesting a plausible mechanism for tumorogenesis while network analysis of the protein interactions between RBPs unambiguously revealed the higher degree, betweenness and closeness centrality for driver RBPs compared to non-drivers. Analysis to reveal cancer-specific Ribonucleoprotein (RNP) mutational hotspots showed extensive rewiring even among common drivers between cancer types. Knockdown experiments on pan-cancer drivers such as SF3B1 and PRPF8 in breast cancer cell lines, revealed cancer subtype specific functions like selective stem cell features, indicating a plausible means for RBPs to mediate cancer-specific phenotypes. Hence, this study would form a foundation to uncover the contribution of the mutational spectrum of RBPs in dysregulating the post-transcriptional regulatory networks in different cancer types.
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Affiliation(s)
- Yaseswini Neelamraju
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA
| | - Abel Gonzalez-Perez
- b Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences , Universitat Pompeu Fabra , Barcelona , Spain
| | - Poornima Bhat-Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA
| | - Harikrishna Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA.,d Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana , USA.,e VA Roudebush Medical Center , Indianapolis , Indiana , USA
| | - Sarath Chandra Janga
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA.,f Centre for Computational Biology and Bioinformatics , Indiana University School of Medicine , 5021 Health Information and Translational Sciences (HITS), Indianapolis , Indiana , USA.,g Department of Medical and Molecular Genetics , Indiana University School of Medicine , Medical Research and Library Building, Indianapolis , Indiana , USA
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Budak G, Srivastava R, Janga SC. Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles. RNA (NEW YORK, N.Y.) 2017; 23:836-846. [PMID: 28336542 PMCID: PMC5435856 DOI: 10.1261/rna.059089.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/21/2017] [Indexed: 06/06/2023]
Abstract
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single-nucleotide resolution in a cell, currently there are very few tools that can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps. Here, we present Seten, a web-based and command line tool, which can identify and compare processes, phenotypes, and diseases associated with RBPs from condition-specific CLIP-seq profiles. Seten uses BED files resulting from most peak calling algorithms, which include scores reflecting the extent of binding of an RBP on the target transcript, to provide both traditional functional enrichment as well as gene set enrichment results for a number of gene set collections including BioCarta, KEGG, Reactome, Gene Ontology (GO), Human Phenotype Ontology (HPO), and MalaCards Disease Ontology for several organisms including fruit fly, human, mouse, rat, worm, and yeast. It also provides an option to dynamically compare the associated gene sets across data sets as bubble charts, to facilitate comparative analysis. Benchmarking of Seten using eCLIP data for IGF2BP1, SRSF7, and PTBP1 against their corresponding CRISPR RNA-seq in K562 cells as well as randomized negative controls, demonstrated that its gene set enrichment method outperforms functional enrichment, with scores significantly contributing to the discovery of true annotations. Comparative performance analysis using these CRISPR control data sets revealed significantly higher precision and comparable recall to that observed using ChIP-Enrich. Seten's web interface currently provides precomputed results for about 200 CLIP-seq data sets and both command line as well as web interfaces can be used to analyze CLIP-seq data sets. We highlight several examples to show the utility of Seten for rapid profiling of various CLIP-seq data sets. Seten is available on http://www.iupui.edu/∼sysbio/seten/.
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Affiliation(s)
- Gungor Budak
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202, USA
| | - Rajneesh Srivastava
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. Sci Rep 2016; 6:25711. [PMID: 27161996 PMCID: PMC4861959 DOI: 10.1038/srep25711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.
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Anji A, Kumari M. Guardian of Genetic Messenger-RNA-Binding Proteins. Biomolecules 2016; 6:4. [PMID: 26751491 PMCID: PMC4808798 DOI: 10.3390/biom6010004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 12/18/2022] Open
Abstract
RNA in cells is always associated with RNA-binding proteins that regulate all aspects of RNA metabolism including RNA splicing, export from the nucleus, RNA localization, mRNA turn-over as well as translation. Given their diverse functions, cells express a variety of RNA-binding proteins, which play important roles in the pathologies of a number of diseases. In this review we focus on the effect of alcohol on different RNA-binding proteins and their possible contribution to alcohol-related disorders, and discuss the role of these proteins in the development of neurological diseases and cancer. We further discuss the conventional methods and newer techniques that are employed to identify RNA-binding proteins.
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Affiliation(s)
- Antje Anji
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Meena Kumari
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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Hashemikhabir S, Neelamraju Y, Janga SC. Database of RNA binding protein expression and disease dynamics (READ DB). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015. [PMID: 26210853 PMCID: PMC4515031 DOI: 10.1093/database/bav072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB) is a non-redundant, curated database of human RBPs. RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks.
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Affiliation(s)
- Seyedsasan Hashemikhabir
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA
| | - Yaseswini Neelamraju
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, USA
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Agostini F, Cirillo D, Ponti RD, Tartaglia GG. SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences. BMC Genomics 2014; 15:925. [PMID: 25341390 PMCID: PMC4223730 DOI: 10.1186/1471-2164-15-925] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/16/2014] [Indexed: 01/06/2023] Open
Abstract
Background The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. Results Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment) algorithm for discovery of regulatory regions in nucleic acid sequences. SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern occurrences and (iii) an easy-to-use web-server interface. We applied our method to recently published data including 351 chromatin immunoprecipitation (ChIP) and 13 crosslinking immunoprecipitation (CLIP) experiments and compared our results with those of other well-established motif discovery tools. SeAMotE shows an average accuracy of 80% in finding discriminative motifs and outperforms other methods available in literature. Conclusions SeAMotE is a fast, accurate and flexible algorithm for the identification of sequence patterns involved in protein-DNA and protein-RNA recognition. The server can be freely accessed at http://s.tartaglialab.com/new_submission/seamote. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-925) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Gian Gaetano Tartaglia
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), C/ Dr, Aiguader 88, 08003 Barcelona, Spain.
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Faoro C, Ataide SF. Ribonomic approaches to study the RNA-binding proteome. FEBS Lett 2014; 588:3649-64. [PMID: 25150170 DOI: 10.1016/j.febslet.2014.07.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 01/23/2023]
Abstract
Gene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).
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Affiliation(s)
- Camilla Faoro
- School of Molecular Biosciences, University of Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Molecular Biosciences, University of Sydney, NSW, Australia.
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13
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Kechavarzi B, Janga SC. Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol 2014; 15:R14. [PMID: 24410894 PMCID: PMC4053825 DOI: 10.1186/gb-2014-15-1-r14] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/10/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA-binding proteins (RBPs) play important roles in cellular homeostasis by controlling gene expression at the post-transcriptional level. RESULTS We explore the expression of more than 800 RBPs in sixteen healthy human tissues and their patterns of dysregulation in cancer genomes from The Cancer Genome Atlas project. We show that genes encoding RBPs are consistently and significantly highly expressed compared with other classes of genes, including those encoding regulatory components such as transcription factors, miRNAs and long non-coding RNAs. We also demonstrate that a set of RBPs, numbering approximately 30, are strongly upregulated (SUR) across at least two-thirds of the nine cancers profiled in this study. Analysis of the protein-protein interaction network properties for the SUR and non-SUR groups of RBPs suggests that path length distributions between SUR RBPs is significantly lower than those observed for non-SUR RBPs. We further find that the mean path lengths between SUR RBPs increases in proportion to their contribution to prognostic impact. We also note that RBPs exhibiting higher variability in the extent of dysregulation across breast cancer patients have a higher number of protein-protein interactions. We propose that fluctuating RBP levels might result in an increase in non-specific protein interactions, potentially leading to changes in the functional consequences of RBP binding. Finally, we show that the expression variation of a gene within a patient group is inversely correlated with prognostic impact. CONCLUSIONS Overall, our results provide a roadmap for understanding the impact of RBPs on cancer pathogenesis.
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Affiliation(s)
- Bobak Kechavarzi
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University – Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University – Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, USA
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Abstract
Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy-referring to the multiple pathways that a system recruits to achieve functional plasticity-is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability.
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