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Kikuchi M, Viet J, Nagata K, Sato M, David G, Audic Y, Silverman MA, Yamamoto M, Akatsu H, Hashizume Y, Takeda S, Akamine S, Miyamoto T, Uozumi R, Gotoh S, Mori K, Ikeda M, Paillard L, Morihara T. Gene-gene functional relationships in Alzheimer's disease: CELF1 regulates KLC1 alternative splicing. Biochem Biophys Res Commun 2024; 721:150025. [PMID: 38768546 DOI: 10.1016/j.bbrc.2024.150025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/16/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024]
Abstract
The causes of Alzheimer's disease (AD) are poorly understood, although many genes are known to be involved in this pathology. To gain insights into the underlying molecular mechanisms, it is essential to identify the relationships between individual AD genes. Previous work has shown that the splice variant E of KLC1 (KLC1_vE) promotes AD, and that the CELF1 gene, which encodes an RNA-binding protein involved in splicing regulation, is at a risk locus for AD. Here, we identified a functional link between CELF1 and KLC1 in AD pathogenesis. Transcriptomic data from human samples from different ethnic groups revealed that CELF1 mRNA levels are low in AD brains, and the splicing pattern of KLC1 is strongly correlated with CELF1 expression levels. Specifically, KLC1_vE is negatively correlated with CELF1. Depletion and overexpression experiments in cultured cells demonstrated that the CELF1 protein down-regulates KLC1_vE. In a cross-linking and immunoprecipitation sequencing (CLIP-seq) database, CELF1 directly binds to KLC1 RNA, following which it likely modulates terminal exon usage, hence KLC1_vE formation. These findings reveal a new pathogenic pathway where a risk allele of CELF1 is associated with reduced CELF1 expression, which up-regulates KLC1_vE to promote AD.
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Affiliation(s)
- Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Justine Viet
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Kenichi Nagata
- Department of Functional Anatomy and Neuroscience, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Masahiro Sato
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Geraldine David
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Yann Audic
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Michael A Silverman
- Department of Biological Sciences, Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Mitsuko Yamamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hiroyasu Akatsu
- Department of Community-based Medical Education, Graduate School of Medicine, Nagoya City University, Nagoya, Japan; Choju Medical/Neuropathological Institute, Fukushimura Hospital, Toyohashi, Japan
| | | | - Shuko Takeda
- Department of Clinical Gene Therapy, Graduate School of Medicine, Osaka University, Suita, Japan; Osaka Psychiatric Medical Center, Osaka Psychiatric Research Center, Hirakata, Japan
| | - Shoshin Akamine
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tesshin Miyamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Ryota Uozumi
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shiho Gotoh
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kohji Mori
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Manabu Ikeda
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Luc Paillard
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France.
| | - Takashi Morihara
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan; Toyonaka Municipal Hospital, Toyonaka, Japan.
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Sudhakaran M, Navarrete TG, Mejía-Guerra K, Mukundi E, Eubank TD, Grotewold E, Arango D, Doseff AI. Transcriptome reprogramming through alternative splicing triggered by apigenin drives cell death in triple-negative breast cancer. Cell Death Dis 2023; 14:824. [PMID: 38092740 PMCID: PMC10719380 DOI: 10.1038/s41419-023-06342-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized by its aggressiveness and resistance to cancer-specific transcriptome alterations. Alternative splicing (AS) is a major contributor to the diversification of cancer-specific transcriptomes. The TNBC transcriptome landscape is characterized by aberrantly spliced isoforms that promote tumor growth and resistance, underscoring the need to identify approaches that reprogram AS circuitry towards transcriptomes, favoring a delay in tumorigenesis or responsiveness to therapy. We have previously shown that flavonoid apigenin is associated with splicing factors, including heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2). Here, we showed that apigenin reprograms TNBC-associated AS transcriptome-wide. The AS events affected by apigenin were statistically enriched in hnRNPA2 substrates. Comparative transcriptomic analyses of human TNBC tumors and non-tumor tissues showed that apigenin can switch cancer-associated alternative spliced isoforms (ASI) to those found in non-tumor tissues. Apigenin preferentially affects the splicing of anti-apoptotic and proliferation factors, which are uniquely observed in cancer cells, but not in non-tumor cells. Apigenin switches cancer-associated aberrant ASI in vivo in TNBC xenograft mice by diminishing proliferation and increasing pro-apoptotic ASI. In accordance with these findings, apigenin increased apoptosis and reduced tumor proliferation, thereby halting TNBC growth in vivo. Our results revealed that apigenin reprograms transcriptome-wide TNBC-specific AS, thereby inducing apoptosis and hindering tumor growth. These findings underscore the impactful effects of nutraceuticals in altering cancer transcriptomes, offering new options to influence outcomes in TNBC treatments.
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Affiliation(s)
- Meenakshi Sudhakaran
- Molecular, Cellular, and Integrative Physiology Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Eric Mukundi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Timothy D Eubank
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Daniel Arango
- Department of Pharmacology and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Andrea I Doseff
- Department of Physiology and Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA.
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3
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Siddam AD, Duot M, Coomson SY, Anand D, Aryal S, Weatherbee BAT, Audic Y, Paillard L, Lachke SA. High-Throughput Transcriptomics of Celf1 Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology. Cells 2023; 12:1070. [PMID: 37048143 PMCID: PMC10093462 DOI: 10.3390/cells12071070] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Defects in the development of the ocular lens can cause congenital cataracts. To understand the various etiologies of congenital cataracts, it is important to characterize the genes linked to this developmental defect and to define their downstream pathways that are relevant to lens biology and pathology. Deficiency or alteration of several RNA-binding proteins, including the conserved RBP Celf1 (CUGBP Elav-like family member 1), has been described to cause lens defects and early onset cataracts in animal models and/or humans. Celf1 is involved in various aspects of post-transcriptional gene expression control, including regulation of mRNA stability/decay, alternative splicing and translation. Celf1 germline knockout mice and lens conditional knockout (Celf1cKO) mice develop fully penetrant cataracts in early postnatal stages. To define the genome-level changes in RNA transcripts that result from Celf1 deficiency, we performed high-throughput RNA-sequencing of Celf1cKO mouse lenses at postnatal day (P) 0. Celf1cKO lenses exhibit 987 differentially expressed genes (DEGs) at cut-offs of >1.0 log2 counts per million (CPM), ≥±0.58 log2 fold-change and <0.05 false discovery rate (FDR). Of these, 327 RNAs were reduced while 660 were elevated in Celf1cKO lenses. The DEGs were subjected to various downstream analyses including iSyTE lens enriched-expression, presence in Cat-map, and gene ontology (GO) and representation of regulatory pathways. Further, a comparative analysis was done with previously generated microarray datasets on Celf1cKO lenses P0 and P6. Together, these analyses validated and prioritized several key genes mis-expressed in Celf1cKO lenses that are relevant to lens biology, including known cataract-linked genes (e.g., Cryab, Cryba2, Cryba4, Crybb1, Crybb2, Cryga, Crygb, Crygc, Crygd, Cryge, Crygf, Dnase2b, Bfsp1, Gja3, Pxdn, Sparc, Tdrd7, etc.) as well as novel candidates (e.g., Ell2 and Prdm16). Together, these data have defined the alterations in lens transcriptome caused by Celf1 deficiency, in turn uncovering downstream genes and pathways (e.g., structural constituents of eye lenses, lens fiber cell differentiation, etc.) associated with lens development and early-onset cataracts.
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Affiliation(s)
- Archana D. Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Matthieu Duot
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- CNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, France
| | - Sarah Y. Coomson
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | | | - Yann Audic
- CNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, France
| | - Luc Paillard
- CNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, France
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
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David G, Reboutier D, Deschamps S, Méreau A, Taylor W, Padilla-Parra S, Tramier M, Audic Y, Paillard L. The RNA-binding proteins CELF1 and ELAVL1 cooperatively control the alternative splicing of CD44. Biochem Biophys Res Commun 2022; 626:79-84. [DOI: 10.1016/j.bbrc.2022.07.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022]
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Xiao J, Tian X, Jin S, He Y, Song M, Zou H. CELF1 promotes matrix metalloproteinases gene expression at transcriptional level in lens epithelial cells. BMC Ophthalmol 2022; 22:122. [PMID: 35287612 PMCID: PMC8922852 DOI: 10.1186/s12886-022-02344-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background RNA binding proteins (RBPs)-mediated regulation plays important roles in many eye diseases, including the canonical RBP CELF1 in cataract. While the definite molecular regulatory mechanisms of CELF1 on cataract still remain elusive. Methods In this study, we overexpressed CELF1 in human cultured lens epithelial SRA01/04 cells and applied whole transcriptome sequencing (RNA-seq) method to analyze the global differences mediated by CELF1. We then analyzed public RNA-seq and CELF1-RNA interactome data to decipher the underlying mechanisms. Results The results showed that transcriptome profile was globally changed by CELF1 overexpression (CELF1-OE). Functional analysis revealed CELF1 specifically increased the expression of genes in extracellular matrix disassembly, extracellular matrix organization, and proteolysis, which could be classified into matrix metalloproteinases (MMPs) family. This finding was also validated by RT-qPCR and public mouse early embryonic lens data. Integrating analysis with public CELF1-RNA interactome data revealed that no obvious CELF1-binding peak was found on the transcripts of these genes, indicating an indirectly regulatory role of CELF1 in lens epithelial cells. Conclusions Our study demonstrated that CELF1-OE promotes transcriptional level of MMP genes; and this regulation may be completed by other ways except for binding to RNA targets. These results suggest that CELF1-OE is implicated in the development of lens, which is associated with cataract and expands our understanding of CELF1 regulatory roles as an RNA binding protein. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-022-02344-8.
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Affiliation(s)
- Jun Xiao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun city, Jilin province, China
| | - Xin Tian
- Department of Pediatrics, The Second Hospital of Jilin University, Changchun city, Jilin province, China
| | - Siyan Jin
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun city, Jilin province, China
| | - Yanhui He
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun city, Jilin province, China
| | - Meijiao Song
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun city, Jilin province, China
| | - He Zou
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun city, Jilin province, China.
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The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13246261. [PMID: 34944881 PMCID: PMC8699117 DOI: 10.3390/cancers13246261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.
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DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity. Nat Commun 2021; 12:6648. [PMID: 34789764 PMCID: PMC8599867 DOI: 10.1038/s41467-021-26932-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 10/22/2021] [Indexed: 11/29/2022] Open
Abstract
The U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2'-O-methylation being most common. However, how U6 2'-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2'-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2'-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator.
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8
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Nasiri-Aghdam M, Garcia-Garduño TC, Jave-Suárez LF. CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis. Int J Mol Sci 2021; 22:11056. [PMID: 34681716 PMCID: PMC8537729 DOI: 10.3390/ijms222011056] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional modifications to coding and non-coding RNAs are unquestionably a pivotal way in which human mRNA and protein diversity can influence the different phases of a transcript's life cycle. CELF (CUGBP Elav-like family) proteins are RBPs (RNA-binding proteins) with pleiotropic capabilities in RNA processing. Their responsibilities extend from alternative splicing and transcript editing in the nucleus to mRNA stability, and translation into the cytoplasm. In this way, CELF family members have been connected to global alterations in cancer proliferation and invasion, leading to their identification as potential tumor suppressors or even oncogenes. Notably, genetic variants, alternative splicing, phosphorylation, acetylation, subcellular distribution, competition with other RBPs, and ultimately lncRNAs, miRNAs, and circRNAs all impact CELF regulation. Discoveries have emerged about the control of CELF functions, particularly via noncoding RNAs, and CELF proteins have been identified as competing, antagonizing, and regulating agents of noncoding RNA biogenesis. On the other hand, CELFs are an intriguing example through which to broaden our understanding of the RBP/noncoding RNA regulatory axis. Balancing these complex pathways in cancer is undeniably pivotal and deserves further research. This review outlines some mechanisms of CELF protein regulation and their functional consequences in cancer physiology.
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Affiliation(s)
- Maryam Nasiri-Aghdam
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Texali C. Garcia-Garduño
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
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9
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Aryal S, Viet J, Weatherbee BAT, Siddam AD, Hernandez FG, Gautier-Courteille C, Paillard L, Lachke SA. The cataract-linked RNA-binding protein Celf1 post-transcriptionally controls the spatiotemporal expression of the key homeodomain transcription factors Pax6 and Prox1 in lens development. Hum Genet 2020; 139:1541-1554. [PMID: 32594240 DOI: 10.1007/s00439-020-02195-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022]
Abstract
The homeodomain transcription factors (TFs) Pax6 (OMIM: 607108) and Prox1 (OMIM: 601546) critically regulate gene expression in lens development. While PAX6 mutations in humans can cause cataract, aniridia, microphthalmia, and anophthalmia, among other defects, Prox1 deletion in mice causes severe lens abnormalities, in addition to other organ defects. Furthermore, the optimal dosage/spatiotemporal expression of these key TFs is essential for development. In lens development, Pax6 expression is elevated in cells of the anterior epithelium compared to fiber cells, while Prox1 exhibits the opposite pattern. Whether post-transcriptional regulatory mechanisms control these precise TF expression patterns is unknown. Here, we report the unprecedented finding that the cataract-linked RNA-binding protein (RBP), Celf1 (OMIM: 601074), post-transcriptionally regulates Pax6 and Prox1 protein expression in lens development. Immunostaining shows that Celf1 lens-specific conditional knockout (Celf1cKO) mice exhibit abnormal elevation of Pax6 protein in fiber cells and abnormal Prox1 protein levels in epithelial cells-directly opposite to their normal expression patterns in development. Furthermore, RT-qPCR shows no change in Pax6 and Prox1 transcript levels in Celf1cKO lenses, suggesting that Celf1 regulates these TFs on the translational level. Indeed, RNA-immunoprecipitation assays using Celf1 antibody indicate that Celf1 protein binds to Pax6 and Prox1 transcripts. Furthermore, reporter assays in Celf1 knockdown and Celf1-overexpression cells demonstrate that Celf1 negatively controls Pax6 and Prox1 translation via their 3' UTRs. These data define a new mechanism of RBP-based post-transcriptional regulation that enables precise control over spatiotemporal expression of Pax6 and Prox1 in lens development, thereby uncovering a new etiological mechanism for Celf1 deficiency-based cataract.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Justine Viet
- Institut de Génétique et Développement de Rennes, Univ Rennes, CNRS, IGDR-UMR 6290, 35000, Rennes, France
| | | | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | | | - Carole Gautier-Courteille
- Institut de Génétique et Développement de Rennes, Univ Rennes, CNRS, IGDR-UMR 6290, 35000, Rennes, France
| | - Luc Paillard
- Institut de Génétique et Développement de Rennes, Univ Rennes, CNRS, IGDR-UMR 6290, 35000, Rennes, France.
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA. .,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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10
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Popovitchenko T, Park Y, Page NF, Luo X, Krsnik Z, Liu Y, Salamon I, Stephenson JD, Kraushar ML, Volk NL, Patel SM, Wijeratne HRS, Li D, Suthar KS, Wach A, Sun M, Arnold SJ, Akamatsu W, Okano H, Paillard L, Zhang H, Buyske S, Kostovic I, De Rubeis S, Hart RP, Rasin MR. Translational derepression of Elavl4 isoforms at their alternative 5' UTRs determines neuronal development. Nat Commun 2020; 11:1674. [PMID: 32245946 PMCID: PMC7125149 DOI: 10.1038/s41467-020-15412-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Neurodevelopment requires precise regulation of gene expression, including post-transcriptional regulatory events such as alternative splicing and mRNA translation. However, translational regulation of specific isoforms during neurodevelopment and the mechanisms behind it remain unknown. Using RNA-seq analysis of mouse neocortical polysomes, here we report translationally repressed and derepressed mRNA isoforms during neocortical neurogenesis whose orthologs include risk genes for neurodevelopmental disorders. We demonstrate that the translation of distinct mRNA isoforms of the RNA binding protein (RBP), Elavl4, in radial glia progenitors and early neurons depends on its alternative 5' UTRs. Furthermore, 5' UTR-driven Elavl4 isoform-specific translation depends on upstream control by another RBP, Celf1. Celf1 regulation of Elavl4 translation dictates development of glutamatergic neurons. Our findings reveal a dynamic interplay between distinct RBPs and alternative 5' UTRs in neuronal development and underscore the risk of post-transcriptional dysregulation in co-occurring neurodevelopmental disorders.
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Affiliation(s)
- Tatiana Popovitchenko
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Graduate Program in Neurosciences, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yongkyu Park
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Nicholas F Page
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - Xiaobing Luo
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Zeljka Krsnik
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Yuan Liu
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Graduate Program in Neurosciences, Rutgers University, Piscataway, NJ, 08854, USA
| | - Iva Salamon
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Graduate Program in Neurosciences, Rutgers University, Piscataway, NJ, 08854, USA
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Jessica D Stephenson
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Matthew L Kraushar
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Graduate Program in Neurosciences, Rutgers University, Piscataway, NJ, 08854, USA
| | - Nicole L Volk
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Sejal M Patel
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - H R Sagara Wijeratne
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Diana Li
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Kandarp S Suthar
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Aaron Wach
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Miao Sun
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, D-79104, Germany
| | - Wado Akamatsu
- Department of Physiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Luc Paillard
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)-UMR 6290, F-35000, Rennes, France
| | - Huaye Zhang
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ivica Kostovic
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Silvia De Rubeis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Seaver Autism Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
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11
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Groenendyk J, Fan X, Peng Z, Kurgan L, Michalak M. Endoplasmic reticulum and the microRNA environment in the cardiovascular system 1. Can J Physiol Pharmacol 2019; 97:515-527. [PMID: 31063413 DOI: 10.1139/cjpp-2018-0720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Stress responses are important to human physiology and pathology, and the inability to adapt to cellular stress leads to cell death. To mitigate cellular stress and re-establish homeostasis, cells, including those in the cardiovascular system, activate stress coping response mechanisms. The endoplasmic reticulum, a component of the cellular reticular network in cardiac cells, mobilizes so-called endoplasmic reticulum stress coping responses, such as the unfolded protein response. MicroRNAs play an important part in the maintenance of cellular and tissue homeostasis, perform a central role in the biology of the cardiac myocyte, and are involved in pathological cardiac function and remodeling. In this paper, we review a link between endoplasmic reticulum homeostasis and microRNA with an emphasis on the impact on stress responses in the cardiovascular system.
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Affiliation(s)
- Jody Groenendyk
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2S7, Canada
| | - Xiao Fan
- b Irving Medical Center, Columbia University, New York, NY 10032, USA
| | - Zhenling Peng
- c Center for Applied Mathematics, Tianjin University, Tianjin 300072, China
| | - Lukasz Kurgan
- d Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA.,e Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada
| | - Marek Michalak
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2S7, Canada
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12
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Chatterji P, Rustgi AK. RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. Trends Mol Med 2018; 24:490-506. [PMID: 29627433 DOI: 10.1016/j.molmed.2018.03.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022]
Abstract
The intestinal epithelium is highly proliferative and consists of crypt invaginations that house stem cells and villus projections with differentiated cells. There exists a dynamic equilibrium between proliferation, migration, differentiation, and senescence that is regulated by several factors. Among these are RNA binding proteins (RBPs) that bind their targets in a both context dependent and independent manner. RBP-RNA complexes act as rheostats by regulating expression of RNAs both co- and post-transcriptionally. This is important, especially in response to intestinal injury, to fuel regeneration. The manner in which these RBPs function in the intestine and their interactions with other pivotal pathways in colorectal cancer may provide a framework for new insights and potential therapeutic applications.
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Affiliation(s)
- Priya Chatterji
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA.
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13
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Siddam AD, Gautier-Courteille C, Perez-Campos L, Anand D, Kakrana A, Dang CA, Legagneux V, Méreau A, Viet J, Gross JM, Paillard L, Lachke SA. The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development. PLoS Genet 2018; 14:e1007278. [PMID: 29565969 PMCID: PMC5889275 DOI: 10.1371/journal.pgen.1007278] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 04/06/2018] [Accepted: 02/26/2018] [Indexed: 11/18/2022] Open
Abstract
Opacification of the ocular lens, termed cataract, is a common cause of blindness. To become transparent, lens fiber cells undergo degradation of their organelles, including their nuclei, presenting a fundamental question: does signaling/transcription sufficiently explain differentiation of cells progressing toward compromised transcriptional potential? We report that a conserved RNA-binding protein Celf1 post-transcriptionally controls key genes to regulate lens fiber cell differentiation. Celf1-targeted knockout mice and celf1-knockdown zebrafish and Xenopus morphants have severe eye defects/cataract. Celf1 spatiotemporally down-regulates the cyclin-dependent kinase (Cdk) inhibitor p27Kip1 by interacting with its 5' UTR and mediating translation inhibition. Celf1 deficiency causes ectopic up-regulation of p21Cip1. Further, Celf1 directly binds to the mRNA of the nuclease Dnase2b to maintain its high levels. Together these events are necessary for Cdk1-mediated lamin A/C phosphorylation to initiate nuclear envelope breakdown and DNA degradation in fiber cells. Moreover, Celf1 controls alternative splicing of the membrane-organization factor beta-spectrin and regulates F-actin-crosslinking factor Actn2 mRNA levels, thereby controlling fiber cell morphology. Thus, we illustrate new Celf1-regulated molecular mechanisms in lens development, suggesting that post-transcriptional regulatory RNA-binding proteins have evolved conserved functions to control vertebrate oculogenesis.
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Affiliation(s)
- Archana D. Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
| | - Carole Gautier-Courteille
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Linette Perez-Campos
- Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
| | - Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Christine A. Dang
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
| | - Vincent Legagneux
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Agnès Méreau
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Justine Viet
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Jeffrey M. Gross
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Luc Paillard
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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14
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Guo L, Louis IVS, Bohjanen PR. Post-transcriptional regulation of cytokine expression and signaling. CURRENT TRENDS IN IMMUNOLOGY 2018; 19:33-40. [PMID: 30568341 PMCID: PMC6296478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cytokines and cytokine signaling pathways are crucial for regulating cellular functions, including cell growth, proliferation, differentiation, and cell death. Cytokines regulate physiological processes such as immune responses and maintain immune homeostasis, and they also mediate pathological conditions such as autoimmune diseases and cancer. Hence, the precise control of the expression of cytokines and the transduction of cytokine signals is tightly regulated at transcriptional and post-transcriptional levels. In particular, post-transcriptional regulation at the level of mRNA stability is critical for coordinating cytokine expression and cytokine signaling. Numerous cytokine transcripts contain AU-rich elements (AREs), whereas transcripts encoding numerous components of cytokine signaling pathways contain GU-rich elements (GREs). AREs and GREs are mRNA decay elements that mediate rapid mRNA degradation. Through ARE- and GRE-mediated decay mechanisms, immune cells selectively and specifically regulate cytokine networks during immune responses. Aberrant expression and stability of ARE- or GRE-containing transcripts that encode cytokines or components of cytokine signaling pathways are observed in disease states, including cancer. In this review, we focus on the role of AREs and GREs in regulating cytokine expression and signal transduction at the level of mRNA stability.
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Affiliation(s)
- Liang Guo
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Irina Vlasova-St. Louis
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul R. Bohjanen
- Department of Medicine, Division of Infectious Diseases and International Medicine, Program in Infection and Immunity, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Comparative and Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
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15
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Cifdaloz M, Osterloh L, Graña O, Riveiro-Falkenbach E, Ximénez-Embún P, Muñoz J, Tejedo C, Calvo TG, Karras P, Olmeda D, Miñana B, Gómez-López G, Cañon E, Eyras E, Guo H, Kappes F, Ortiz-Romero PL, Rodríguez-Peralto JL, Megías D, Valcárcel J, Soengas MS. Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1. Nat Commun 2017; 8:2249. [PMID: 29269732 PMCID: PMC5740069 DOI: 10.1038/s41467-017-02353-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 11/23/2017] [Indexed: 12/19/2022] Open
Abstract
Melanomas are well-known for their altered mRNA expression profiles. Yet, the specific contribution of mRNA binding proteins (mRBPs) to melanoma development remains unclear. Here we identify a cluster of melanoma-enriched genes under the control of CUGBP Elav-like family member 1 (CELF1). CELF1 was discovered with a distinct prognostic value in melanoma after mining the genomic landscape of the 692 known mRBPs across different cancer types. Genome-wide transcriptomic, proteomic, and RNA-immunoprecipitation studies, together with loss-of-function analyses in cell lines, and histopathological evaluation in clinical biopsies, revealed an intricate repertoire of CELF1-RNA interactors with minimal overlap with other malignancies. This systems approach uncovered the oncogene DEK as an unexpected target and downstream effector of CELF1. Importantly, CELF1 and DEK were found to represent early-induced melanoma genes and adverse indicators of overall patient survival. These results underscore novel roles of CELF1 in melanoma, illustrating tumor type-restricted functions of RBPs in cancer.
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Affiliation(s)
- Metehan Cifdaloz
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Lisa Osterloh
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | | | - Erica Riveiro-Falkenbach
- Instituto de Investigación i+12, Hospital 12 de Octubre Medical School, Universidad Complutense, 28041, Madrid, Spain
| | | | | | - Cristina Tejedo
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Tonantzin G Calvo
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Panagiotis Karras
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - David Olmeda
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Belén Miñana
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | | | - Estela Cañon
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Eduardo Eyras
- Department of Experimental and Health Sciences, Universidad Pompeu Fabra, Barcelona, 08002, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
| | - Haihong Guo
- Institute of Biochemistry and Molecular Biology; Medical School, RWTH Aachen University, Aachen, 52074, Germany
| | - Ferdinand Kappes
- Institute of Biochemistry and Molecular Biology; Medical School, RWTH Aachen University, Aachen, 52074, Germany
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, No. 111, Ren Ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park (SIP), Suzhou, 215123, China
| | - Pablo L Ortiz-Romero
- Instituto de Investigación i+12, Hospital 12 de Octubre Medical School, Universidad Complutense, 28041, Madrid, Spain
| | - Jose L Rodríguez-Peralto
- Instituto de Investigación i+12, Hospital 12 de Octubre Medical School, Universidad Complutense, 28041, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, (CNIO), Madrid, 28029, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
| | - María S Soengas
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain.
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16
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Xia H, Chen D, Wu Q, Wu G, Zhou Y, Zhang Y, Zhang L. CELF1 preferentially binds to exon-intron boundary and regulates alternative splicing in HeLa cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:911-921. [DOI: 10.1016/j.bbagrm.2017.07.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022]
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17
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Russo J, Lee JE, López CM, Anderson J, Nguyen TMP, Heck AM, Wilusz J, Wilusz CJ. The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS One 2017; 12:e0170680. [PMID: 28129347 PMCID: PMC5271678 DOI: 10.1371/journal.pone.0170680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jerome E. Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carolina M. López
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - John Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Thuy-mi P. Nguyen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Adam M. Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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18
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Vlasova-St Louis I, Bohjanen PR. Post-transcriptional regulation of cytokine and growth factor signaling in cancer. Cytokine Growth Factor Rev 2016; 33:83-93. [PMID: 27956133 DOI: 10.1016/j.cytogfr.2016.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 12/11/2022]
Abstract
Cytokines and growth factors regulate cell proliferation, differentiation, migration and apoptosis, and play important roles in coordinating growth signal responses during development. The expression of cytokine genes and the signals transmitted through cytokine receptors are tightly regulated at several levels, including transcriptional and post-transcriptional levels. A majority of cytokine mRNAs, including growth factor transcripts, contain AU-rich elements (AREs) in their 3' untranslated regions that control gene expression by regulating mRNA degradation and changing translational rates. In addition, numerous proteins involved in transmitting signals downstream of cytokine receptors are regulated at the level of mRNA degradation by GU-rich elements (GREs) found in their 3' untranslated regions. Abnormal stabilization and overexpression of ARE or GRE-containing transcripts had been observed in many malignancies, which is a consequence of the malfunction of RNA-binding proteins. In this review, we briefly summarize the role of AREs and GREs in regulating mRNA turnover to coordinate cytokine and growth factor expression, and we describe how dysregulation of mRNA degradation mechanisms contributes to the development and progression of cancer.
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Affiliation(s)
| | - Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
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