1
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Bailey MA, Martyr JG, Hargrove AE, Fitzgerald MC. Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Anal Chem 2024:10.1021/acs.analchem.3c04978. [PMID: 38341805 PMCID: PMC11316846 DOI: 10.1021/acs.analchem.3c04978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.
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Affiliation(s)
- Morgan A Bailey
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Justin G Martyr
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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2
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Wang W, Luo Q, Zhao Y, Geng S, Xu T, Sun Y. Genomic organization, evolution and functional characterization of embryonic lethal abnormal vision like protein 1 (ELAVL1) in miiuy croaker (Miichthys miiuy). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 142:104659. [PMID: 36764421 DOI: 10.1016/j.dci.2023.104659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/06/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Embryonic lethal vision-like protein 1 (ELAVL1), an AU-rich elements (AREs) binding protein involved in the regulation of inflammatory transcript stability, which has not been reported in fish. In this study, we identified the ELAVL1 gene in Miichthys miiuy (mmiELAVL1), and then analyzed its structure and evolution, furthermore described its expression pattern in miiuy croaker. The results showed that mmiELAVL1 and other vertebrate ELAVL1 genes all have three highly conserved RNA recognition motif (RRM) protein domains, and the structure and protein structure are evolutionarily conserved, indicating that their functions may also conservative. In healthy miiuy croaker, mmiELAVL1 was commonly expressed in the tested tissues, and mmiELAVL1 is mainly localized in the nucleus of kidney cells. In addition, mmiELAVL1 responds to poly(I:C) and SCRV stimulation and promotes antiviral genes, indicating its active role in immune process. In summary, this study will facilitate future studies on the role and underlying mechanisms of ELAVL1 in fish immune responses.
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Affiliation(s)
- Wansu Wang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qiang Luo
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yan Zhao
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shang Geng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China.
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3
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Bertoldo JB, Müller S, Hüttelmaier S. RNA-binding proteins in cancer drug discovery. Drug Discov Today 2023; 28:103580. [PMID: 37031812 DOI: 10.1016/j.drudis.2023.103580] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
RNA-binding proteins (RBPs) are crucial players in tumorigenesis and, hence, promising targets in cancer drug discovery. However, they are largely regarded as 'undruggable', because of the often noncatalytic and complex interactions between protein and RNA, which limit the discovery of specific inhibitors. Nonetheless, over the past 10 years, drug discovery efforts have uncovered RBP inhibitors with clinical relevance, highlighting the disruption of RNA-protein networks as a promising avenue for cancer therapeutics. In this review, we discuss the role of structurally distinct RBPs in cancer, and the mechanisms of RBP-directed small-molecule inhibitors (SMOIs) focusing on drug-protein interactions, binding surfaces, potency, and translational potential. Additionally, we underline the limitations of RBP-targeting drug discovery assays and comment on future trends in the field.
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Affiliation(s)
- Jean B Bertoldo
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Simon Müller
- Institute for Molecular Medicine, Faculty of Medicine, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany; New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Stefan Hüttelmaier
- Institute for Molecular Medicine, Faculty of Medicine, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany.
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4
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Abstract
Androgens are essential sex steroid hormones for both sexes. Testosterone (T) is the predominant androgen in males, while in adult females, T concentrations are about 15-fold lower and androgen precursors are converted to estrogens. T is produced primarily in testicular Leydig cells in men, while in women precursors are biosynthesised in the adrenal cortex and ovaries and converted into T in the periphery. The biosynthesis of T occurs via a series of enzymatic reactions in steroidogenic organs. Notably, the more potent androgen, dihydrotestosterone, may be synthesized from T in the classic pathway, however, alternate metabolic pathways also exist. The classic action of androgens on target organs is mediated through the androgen receptor, which regulates nuclear receptor gene transcription. However, the androgen-androgen receptor complex may also interact directly with membrane proteins or signaling molecules to exert more rapid effects. This review summarizes the current knowledge of androgen biosynthesis, mechanisms of action and endocrine effects in human biology, and relates these effects to respective human congenital and acquired disorders.
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Affiliation(s)
- Rawda Naamneh Elzenaty
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Bern University Hospital, University of Bern, Switzerland; Department of Biomedical Research, University of Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Switzerland.
| | - Therina du Toit
- Department of Biomedical Research, University of Bern, Switzerland.
| | - Christa E Flück
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, Bern University Hospital, University of Bern, Switzerland; Department of Biomedical Research, University of Bern, Switzerland.
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5
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Wang Y, Chen D, Xie H, Jia M, Sun X, Peng F, Guo F, Tang D. AUF1 protects against ferroptosis to alleviate sepsis-induced acute lung injury by regulating NRF2 and ATF3. Cell Mol Life Sci 2022; 79:228. [PMID: 35391558 PMCID: PMC11072094 DOI: 10.1007/s00018-022-04248-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND The AU-rich element (ARE)-binding factor 1 (AUF1) acts as a switch for septic shock, although its underlying mechanisms remain largely unknown. In this study, we examined the biological significance and potential molecular mechanism of AUF1 in regulating ferroptosis in sepsis-induced acute lung injury (ALI). METHODS Alveolar epithelial cells (AECs) challenged with ferroptosis-inducing compounds and cecum ligation and puncture (CLP)-induced ALI were used as the in vitro and in vivo model, respectively. The stability of AUF1 and its degradation by ubiquitin-proteasome pathway were examined by cycloheximide chase analysis and co-immunoprecipitation assay. The regulation of AUF1 on nuclear factor E2-related factor 2 (NRF2) and activation transcription factor 3 (ATF3) was explored by RNA immunoprecipitation (RIP), RNA pull-down, and mRNA stability assays. Functionally, the effects of altering AUF1, NRF2 or ATF3 on ferroptosis in AECs or ALI mice were evaluated by measuring cell viability, lipid peroxidation, iron accumulation, and total glutathione level. RESULTS AUF1 was down-regulated in AECs challenged with ferroptosis-inducing compounds, both on mRNA and protein levels. The E3 ubiquitin ligase FBXW7 was responsible for protein degradation of AUF1 during ferroptosis. By up-regulating NRF2 and down-regulating ATF3, AUF1 antagonized ferroptosis in AECs in vitro. In the CLP-induced ALI model, the survival rate of AUF1 knockout mice was significantly reduced and the lung injuries were aggravated, which were related to the enhancement of lung ferroptosis. CONCLUSIONS FBXW7 mediates the ubiquitination and degradation of AUF1 in ferroptosis. AUF1 antagonizes ferroptosis by regulating NRF2 and ATF3 oppositely. Activating AUF1 pathway may be beneficial to the treatment of sepsis-induced ALI.
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Affiliation(s)
- Yichun Wang
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, No.63, Duobao Road, Liwan District, Guangdong, 510150, Guangzhou, People's Republic of China.
| | - Diyu Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangdong, 510150, Guangzhou, People's Republic of China
| | - Han Xie
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangdong, 510150, Guangzhou, People's Republic of China
| | - Mingwang Jia
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, No.63, Duobao Road, Liwan District, Guangdong, 510150, Guangzhou, People's Republic of China
| | - Xiaofang Sun
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangdong, 510150, Guangzhou, People's Republic of China
| | - Fang Peng
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, No.63, Duobao Road, Liwan District, Guangdong, 510150, Guangzhou, People's Republic of China
| | - Feifei Guo
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, No.63, Duobao Road, Liwan District, Guangdong, 510150, Guangzhou, People's Republic of China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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6
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Wu M, Wen L, Zhou Y, Wu W. Role of lncRNA AGAP2-AS1 in Breast Cancer Cell Resistance to Apoptosis by the Regulation of MTA1 Promoter Activity. Technol Cancer Res Treat 2022; 21:15330338221085361. [PMID: 35369814 PMCID: PMC8984859 DOI: 10.1177/15330338221085361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 01/06/2023] Open
Abstract
Introduction Breast cancer (BC) is a common malignant tumor affecting women across the world. LncRNAs are frequently implicated in the course of BC. The current study set out to determine the specific effect of lncRNA AGAP2-AS1 on BC cell resistance to apoptosis. Methods AGAP2-AS1 expression patterns in BC tissues and cells were evaluated. si-AGAP2-AS1 was transfected into MCF-7 cells, followed by the assessment of cell proliferation and apoptosis. In addition to detection of MTA1 expression patterns, the binding relation between AGAP2-AS1 and HuR was verified using RNA pull-down and RNA immunoprecipitation. Next, the regulation enrichment of AGAP2-AS1- and HuR to H3K27ac recruitment in the MTA1 promoter was analyzed. MCF-7 cell resistance to apoptosis was observed after the combined experiment of histone deacetylase inhibitor M344 and si-AGAP2-AS1. Lastly, xenografts tumors were established to detect tumor weight and volume, tumor apoptosis and growth as well as expression of AGAP2-AS1 and MTA1. Results AGAP2-AS1 was overexpressed in BC tissues and cells, and AGAP2-AS1 silencing inhibited cell proliferation but facilitated apoptosis. Physiologically, AGAP2-AS1 bound to HuR to stabilize its own expression, and AGAP2-AS1-HuR complex upregulated H3K27ac levels in the MTA1 promoter region to elevate MTA1 promoter activity and MTA1 expression. H3K27ac upregulation partially-annulled the promotive effect of si-AGAP2-AS1 on BC apoptosis by upregulating MTA1. si-AGAP2-AS1 in vivo inhibited MTA1 expression to enhance apoptosis and suppress tumor growth. Conclusion Collectively, our findings indicated that AGAP2-AS1 bound to HuR to stabilize its own expression, and AGAP2-AS1-HuR complex enhanced H3K27ac levels in the MTA1 promoter region to improve MTA1 promoter activity and MTA1 expression in BC cells, so as to augment BC cell resistance to apoptosis.
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Affiliation(s)
- Minhua Wu
- Department of thyroid and breast surgery, Ningbo medical center Lihuili
Hospital, Ningbo city, 315040, Zhejiang province, People’s Republic of
China
| | - Limu Wen
- Department of thyroid and breast surgery, Ningbo medical center Lihuili
Hospital, Ningbo city, 315040, Zhejiang province, People’s Republic of
China
| | - Yuxin Zhou
- School of Medicine, Ningbo
University, Ningbo city, 315040, Zhejiang province, People’s Republic of
China
| | - Weizhu Wu
- Department of thyroid and breast surgery, Ningbo medical center Lihuili
Hospital, Ningbo city, 315040, Zhejiang province, People’s Republic of
China
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7
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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8
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ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network. JOURNAL OF ONCOLOGY 2021; 2021:4279039. [PMID: 34659409 PMCID: PMC8516523 DOI: 10.1155/2021/4279039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs have been shown with powerful ability in post-transcriptional regulation, enabling intertwined RNA crosstalk and global molecular interaction in a large amount of dysfunctional conditions including cancer. Competing endogenous RNAs (ceRNAs) are those competitively binding with shared microRNAs (miRNAs), freeing their counterparts from miRNA-induced degradation, thus actively influencing and connecting with each other. Constantly updated analytical approaches boost outstanding advancement achieved in this burgeoning hotspot in multilayered intracellular communication, providing new insights into pathogenesis and clinical treatment. Here, we summarize the mechanisms and correlated factors under this RNA interplay and deregulated transcription profile in neoplasm and tumor progression, underscoring the great significance of ceRNAs for diagnostic values, monitoring biomarkers, and prognosis evaluation in cancer.
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9
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Pseudogenes: Four Decades of Discovery. Methods Mol Biol 2021. [PMID: 34165705 DOI: 10.1007/978-1-0716-1503-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
A pseudogene is defined as a genomic DNA sequence that looks like a mutated or truncated version of a known functional gene. Nearly four decades since their first discovery it has been estimated that between ~12,000 and ~20,000 pseudogenes exist in the human genome. Early efforts to characterize functions for pseudogenes were unsuccessful, thus they were considered functionless relics of evolutionary selection, junk DNA or genetic fossils. Remarkably, an increasing number of pseudogenes have been reported to be expressed as RNA transcripts above and beyond levels considered accidental or spurious transcription. There is emerging evidence that some expressed pseudogene transcripts have biological functions and should be defined as a subclass of functional long noncoding RNAs (lncRNA). In this introductory chapter, I briefly summarize the history and the current knowledge of pseudogenes, and highlight the emerging functions of some pseudogenes in human biology and disease. This second iteration of Pseudogenes in Methods in Molecular Biology highlights new methodological approaches to investigate this intriguing family of lncRNAs and the extent of their biological function.
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10
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Liu Y, Pan C, Kong D, Luo J, Zhang Z. A Survey of Regulatory Interactions Among RNA Binding Proteins and MicroRNAs in Cancer. Front Genet 2020; 11:515094. [PMID: 33101370 PMCID: PMC7506142 DOI: 10.3389/fgene.2020.515094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/14/2020] [Indexed: 12/20/2022] Open
Abstract
Recent advances in genomics and proteomics generated a large amount of trans regulatory data such as those mediated by RNA binding proteins (RBPs) and microRNAs. Since many trans regulators target 3′ UTR of mRNA transcripts, it is likely that there would be interactions, i.e., competitive or cooperative effect, among these trans factors. We compiled the available RBP and microRNA binding sites, mapped them to the mRNA transcripts, and correlated the binding data with mRNA expression data generated by The Cancer Genome Atlas (TCGA). We separated pairs of RBPs and microRNAs into three scenarios: those that have overlapping target sites on the same mRNA transcript (overlapping), those that have target sites on the same mRNA transcript but non-overlapping (neighboring), and those that do not target the same mRNA transcript (independent). Through a regression analysis on expression profiles, we indeed observed interaction effect between RBPs and microRNAs in the majority of the cancer expression data sets. We further discussed implication of such widespread interactions in the context of cancer and diseases.
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Affiliation(s)
- Ying Liu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Chu Pan
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Dehan Kong
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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11
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Chen T, Dai X, Dai J, Ding C, Zhang Z, Lin Z, Hu J, Lu M, Wang Z, Qi Y, Zhang L, Pan R, Zhao Z, Lu L, Liao W, Lu X. AFP promotes HCC progression by suppressing the HuR-mediated Fas/FADD apoptotic pathway. Cell Death Dis 2020; 11:822. [PMID: 33009373 PMCID: PMC7532541 DOI: 10.1038/s41419-020-03030-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a major leading cause of cancer-related death worldwide. Alpha fetoprotein (AFP) is reactivated in a majority of hepatocellular carcinoma (HCC) and associated with poor patient outcomes. Although increasing evidence has shown that AFP can regulate HCC cell growth, the precise functions of AFP in hepatocarcinogenesis and the associated underlying mechanism remain incompletely understood. In this study, we demostrated that depleting AFP significantly suppressed diethylnitrosamine (DEN)-induced liver tumor progression in an AFP gene-deficient mouse model. Similarly, knocking down AFP expression inhibited human HCC cell proliferation and tumor growth by inducing apoptosis. AFP expression level was inversely associated with the apoptotic rate in mouse and human HCC specimens. Investigation of potential cross-talk between AFP and apoptotic signaling revealed that AFP exerted its growth-promoting effect by suppressing the Fas/FADD-mediated extrinsic apoptotic pathway. Mechanistically, AFP bound to the RNA-binding protein HuR, increasing the accumulation of HuR in the cytoplasm and subsequent inhibition of Fas mRNA translation. In addition, we found that inhibiting AFP enhanced the cytotoxicity of therapeutics to AFP-positive HCC cells by activating HuR-mediated Fas/FADD apoptotic signaling. Conclusion: Our study defined the pro-oncogenic role of AFP in HCC progression and uncovered a novel antiapoptotic mechanism connecting AFP to HuR-mediated Fas translation. Our findings suggest that AFP is involved in the pathogenesis and chemosensitivity of HCC and that blockade of AFP may be a promising strategy to treat advanced HCC.
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Affiliation(s)
- Tianke Chen
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Xiaowei Dai
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Juji Dai
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Chaodong Ding
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Zheng Zhang
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Ziqi Lin
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Jin Hu
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Mei Lu
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Zhanyu Wang
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Yalei Qi
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Li Zhang
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Rulu Pan
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Zhu Zhao
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Liting Lu
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Wanqin Liao
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China
| | - Xincheng Lu
- School of Basic Medical Sciences, Wenzhou Medical University, 325035, Wenzhou, China.
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12
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Grønning AGB, Doktor TK, Larsen SJ, Petersen USS, Holm LL, Bruun GH, Hansen MB, Hartung AM, Baumbach J, Andresen BS. DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning. Nucleic Acids Res 2020; 48:7099-7118. [PMID: 32558887 PMCID: PMC7367176 DOI: 10.1093/nar/gkaa530] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 05/11/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling of protein-RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to RNA nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods for modeling RNA-protein binding. Importantly, we demonstrate that DeepCLIP predictions correlate with the functional outcomes of nucleotide variants in independent wet lab experiments. Furthermore, we show how DeepCLIP binding profiles can be used in the design of therapeutically relevant antisense oligonucleotides, and to uncover possible position-dependent regulation in a tissue-specific manner. DeepCLIP is freely available as a stand-alone application and as a webtool at http://deepclip.compbio.sdu.dk.
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Affiliation(s)
- Alexander Gulliver Bjørnholt Grønning
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark.,Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Simon Jonas Larsen
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael Birkerod Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Anne-Mette Hartung
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark.,Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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13
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Dong R, Chen P, Polireddy K, Wu X, Wang T, Ramesh R, Dixon DA, Xu L, Aubé J, Chen Q. An RNA-Binding Protein, Hu-antigen R, in Pancreatic Cancer Epithelial to Mesenchymal Transition, Metastasis, and Cancer Stem Cells. Mol Cancer Ther 2020; 19:2267-2277. [PMID: 32879054 DOI: 10.1158/1535-7163.mct-19-0822] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 04/17/2020] [Accepted: 08/21/2020] [Indexed: 01/04/2023]
Abstract
Pancreatic cancer has poor prognosis and treatment outcomes due to its highly metastatic nature and resistance to current treatments. The RNA-binding protein (RBP) Hu-antigen R (HuR) is a central player in posttranscriptional regulation of cancer-related gene expression, and contributes to tumorigenesis, tumor growth, metastasis, and drug resistance. HuR has been suggested to regulate pancreatic cancer epithelial-to-mesenchymal transition (EMT), but the mechanism was not well understood. Here, we further elucidated the role HuR plays in pancreatic cancer cell EMT, and developed a novel inhibitor specifically interrupting HuR-RNA binding. The data showed that HuR binds to the 3'-UTR of the mRNA of the transcription factor Snail, resulting in stabilization of Snail mRNA and enhanced Snail protein expression, thus promoted EMT, metastasis, and formation of stem-like cancer cells (CSC) in pancreatic cancer cells. siRNA silencing or CRISPR/Cas9 gene deletion of HuR inhibited pancreatic cancer cell EMT, migration, invasion, and inhibited CSCs. HuR knockout cells had dampened tumorigenicity in immunocompromised mice. A novel compound KH-3 interrupted HuR-RNA binding, and KH-3 inhibited pancreatic cancer cell viability, EMT, migration/invasion in vitro KH-3 showed HuR-dependent activity and inhibited HuR-positive tumor growth and metastasis in vivo.
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Affiliation(s)
- Ruochen Dong
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Ping Chen
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Kishore Polireddy
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Xiaoqing Wu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Tao Wang
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Remya Ramesh
- Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina, Chapel Hill, North Carolina
| | - Dan A Dixon
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Liang Xu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Jeffrey Aubé
- Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina, Chapel Hill, North Carolina
| | - Qi Chen
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas.
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14
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Woo HH, Chambers SK. The alternative spliced 3'-UTR mediated differential secretion of macrophage colony stimulating factor in breast cancer cells. Biochem Biophys Res Commun 2020; 525:1004-1010. [PMID: 32178869 DOI: 10.1016/j.bbrc.2020.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
CSF-1 mRNA 3'UTR variants (var) are generated from alternative splicing. CSF-1 protein encoded by var-1 mRNA with long 3'UTR derived from exon-10 is rapidly secreted compared to the CSF-1 protein encoded by var-4 mRNA with short 3'UTR derived from exon-9. Secretion kinetics indicates that HuR, which binds the CSF-1 var-1 mRNA, but not var-4 mRNA, accelerates the secretion of CSF-1 protein. HuR overexpression increases the secretion rate of CSF-1 protein. In contrast, silencing of HuR does not have such an effect, suggesting other compensatory mechanisms. Effect of the CSF-1 mRNA variant 3'UTRs on cellular phenotype shows both CSF-1 var-1 or -4 mRNA is involved in the enhanced rates of migration and invasion observed by both in vitro in breast cancer cells. Our study indicates that the alternative splicing of CSF-1 mRNA 3'UTR can regulate differential secretion of CSF-1 protein.
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Affiliation(s)
- Ho-Hyung Woo
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, 85724, USA.
| | - Setsuko K Chambers
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, 85724, USA; Department of Obstetrics and Gynecology, University of Arizona, Tucson, AZ, 85724, USA
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15
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Targeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasis. Commun Biol 2020; 3:193. [PMID: 32332873 PMCID: PMC7181695 DOI: 10.1038/s42003-020-0933-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/07/2020] [Indexed: 01/02/2023] Open
Abstract
Patients diagnosed with metastatic breast cancer have a dismal 5-year survival rate of only 24%. The RNA-binding protein Hu antigen R (HuR) is upregulated in breast cancer, and elevated cytoplasmic HuR correlates with high-grade tumors and poor clinical outcome of breast cancer. HuR promotes tumorigenesis by regulating numerous proto-oncogenes, growth factors, and cytokines that support major tumor hallmarks including invasion and metastasis. Here, we report a HuR inhibitor KH-3, which potently suppresses breast cancer cell growth and invasion. Furthermore, KH-3 inhibits breast cancer experimental lung metastasis, improves mouse survival, and reduces orthotopic tumor growth. Mechanistically, we identify FOXQ1 as a direct target of HuR. KH-3 disrupts HuR–FOXQ1 mRNA interaction, leading to inhibition of breast cancer invasion. Our study suggests that inhibiting HuR is a promising therapeutic strategy for lethal metastatic breast cancer. Wu et al. identify an inhibitor to the RNA-binding protein HuR, KH-3, that disrupts the interaction between HuR and target RNAs and inhibits human cancer growth and metastasis in mouse xenograft assays. This study suggests the therapeutic potential of targeting HuR in breast cancer with HuR overexpression.
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16
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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17
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Poganik JR, Long MJC, Disare MT, Liu X, Chang SH, Hla T, Aye Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1. FASEB J 2019; 33:14636-14652. [PMID: 31665914 DOI: 10.1096/fj.201901930r] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2) signaling axis is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of Nrf2 regulation has been focused at the protein level. Here we report a post-transcriptional modality to directly regulate Nrf2-mRNA. Our initial studies focused on the effects of the key mRNA-binding protein (mRBP) HuR on global transcriptomic changes incurred upon oxidant or electrophile stimulation. These RNA-sequencing data and subsequent mechanistic analyses led us to discover a novel role of HuR in regulating Nrf2 activity, and in the process, we further identified the related mRBP AUF1 as an additional novel Nrf2 regulator. Both mRBPs regulate Nrf2 activity by direct interaction with the Nrf2 transcript. Our data showed that HuR enhances Nrf2-mRNA maturation and promotes its nuclear export, whereas AUF1 stabilizes Nrf2-mRNA. Both mRBPs target the 3'-UTR of Nrf2-mRNA. Using a Nrf2 activity-reporter zebrafish strain, we document that this post-transcriptional control of Nrf2 activity is conserved at the whole-vertebrate level.-Poganik, J. R., Long, M. J. C., Disare, M. T., Liu, X., Chang, S.-H., Hla, T., Aye, Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Marcus J C Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Michael T Disare
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Xuyu Liu
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sung-Hee Chang
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Timothy Hla
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA; and.,Vascular Biology Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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18
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Allegri L, Baldan F, Roy S, Aubé J, Russo D, Filetti S, Damante G. The HuR CMLD-2 inhibitor exhibits antitumor effects via MAD2 downregulation in thyroid cancer cells. Sci Rep 2019; 9:7374. [PMID: 31089242 PMCID: PMC6517587 DOI: 10.1038/s41598-019-43894-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023] Open
Abstract
Hu antigen R (HuR) is indeed one of the most studied RNA-binding protein (RBP) since its fundamental role both in tumorigenesis and cancer progression. For this reason, downregulation in HuR protein levels or inhibition of HuR biological function are, nowadays, attractive goals in cancer research. Here, we examined the antitumor effects of CMLD-2 in four thyroid cancer cell lines (SW1736, 8505 C, BCPAP and K1). Indeed, CMLD-2 competitively binds HuR protein disrupting its interaction with RNA-targets. 35 μM CLMD-2 produced a significant downregulation in thyroid cancer cell viability, coupled to an increase in apoptosis. Moreover, CMLD-2 treatment hindered both migration and colony formation ability. MAD2 is a microtubules-associated protein known to be greatly overexpressed in cancer and correlating with tumor aggressiveness. Furthermore, MAD2 is known to be a HuR target. CMLD-2 treatment induced a strong MAD2 downregulation and rescue experiments depicted it as a key effector in HuR-mediated in cancer. Altogether, these data contributed to foster HuR inhibition as valid antineoplastic treatment in thyroid cancer, highlighting MAD2 as a novel therapeutic target.
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Affiliation(s)
- Lorenzo Allegri
- Department of Medical Area, University of Udine, 33100, Udine, Italy
| | - Federica Baldan
- Department of Translational and Precision Medicine, University of Roma 'Sapienza', 06100, Roma, Italy.
| | - Sudeshna Roy
- Department of BioMelecular Sciences, School of Pharmacy, University of Mississippi, 413 Faser Hall, Mississippi, 38677-1848, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medical Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina, 27599-7363, USA
| | - Diego Russo
- Department of Health Sciences, University of Catanzaro "Magna Graecia", 88100, Catanzaro, Italy
| | - Sebastiano Filetti
- Department of Translational and Precision Medicine, University of Roma 'Sapienza', 06100, Roma, Italy
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100, Udine, Italy
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19
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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20
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Gong Q, Stump MR, Zhou Z. Regulation of Kv11.1 potassium channel C-terminal isoform expression by the RNA-binding proteins HuR and HuD. J Biol Chem 2018; 293:19624-19632. [PMID: 30377250 DOI: 10.1074/jbc.ra118.003720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
The potassium voltage-gated channel subfamily H member 2 (KCNH2) gene encodes the Kv11.1 potassium channel, which conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation and forms a functional, full-length Kv11.1a isoform if exon 15 is polyadenylated or a nonfunctional, C-terminally truncated Kv11.1a-USO isoform if intron 9 is polyadenylated. The molecular mechanisms that regulate Kv11.1 isoform expression are poorly understood. In this study, using HEK293 cells and reporter gene expression, pulldown assays, and RNase protection assays, we identified the RNA-binding proteins Hu antigen R (HuR) and Hu antigen D (HuD) as regulators of Kv11.1 isoform expression. We show that HuR and HuD inhibit activity at the intron 9 polyadenylation site. When co-expressed with the KCNH2 gene, HuR and HuD increased levels of the Kv11.1a isoform and decreased the Kv11.1a-USO isoform in the RNase protection assays and immunoblot analyses. In patch clamp experiments, HuR and HuD significantly increased the Kv11.1 current. siRNA-mediated knockdown of HuR protein decreased levels of the Kv11.1a isoform and increased those of the Kv11.1a-USO isoform. Our findings suggest that the relative expression levels of Kv11.1 C-terminal isoforms are regulated by the RNA-binding HuR and HuD proteins.
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Affiliation(s)
- Qiuming Gong
- From the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon 97239 and
| | - Matthew R Stump
- Department of Biology, George Fox University, Newberg, Oregon 97132
| | - Zhengfeng Zhou
- From the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon 97239 and
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21
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Díaz-Muñoz MD, Turner M. Uncovering the Role of RNA-Binding Proteins in Gene Expression in the Immune System. Front Immunol 2018; 9:1094. [PMID: 29875770 PMCID: PMC5974052 DOI: 10.3389/fimmu.2018.01094] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 12/29/2022] Open
Abstract
Fighting external pathogens requires an ever-changing immune system that relies on tight regulation of gene expression. Transcriptional control is the first step to build efficient responses while preventing immunodeficiencies and autoimmunity. Post-transcriptional regulation of RNA editing, location, stability, and translation are the other key steps for final gene expression, and they are all controlled by RNA-binding proteins (RBPs). Nowadays we have a deep understanding of how transcription factors control the immune system but recent evidences suggest that post-transcriptional regulation by RBPs is equally important for both development and activation of immune responses. Here, we review current knowledge about how post-transcriptional control by RBPs shapes our immune system and discuss the perspective of RBPs being the key players of a hidden immune cell epitranscriptome.
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Affiliation(s)
- Manuel D Díaz-Muñoz
- Centre de Physiopathologie Toulouse-Purpan, INSERM UMR1043/CNRS U5282, Toulouse, France
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
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22
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The AU-rich element landscape across human transcriptome reveals a large proportion in introns and regulation by ELAVL1/HuR. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:167-177. [PMID: 29413897 DOI: 10.1016/j.bbagrm.2017.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 01/19/2023]
Abstract
Adenylate-uridylate (AU)-rich elements (AREs) are sequence instability elements that are known to be located in the 3' untranslated regions (UTR) in thousands of human transcripts. AREs regulate the expression of many genes at the post-transcriptional level, and they are essential for many normal cellular functions. We conducted a transcriptome-wide screen for AREs and found that they are most abundant in introns, with up to 25% of introns containing AREs corresponding to 58% of human genes. Clustering studies of ARE size, complexity, and distribution revealed that, in introns, longer AREs with two or more overlapping repeats are more abundant than in the 3'UTR, and only introns can contain very long AREs with 6-14 overlapping AUUUA pentamers. We found that intronic sites of the ARE binding proteins HuR/ELAVL1, ZFP36/TTP, AUF1, and BRF1/ZFP36L1 overlap with the intronic AREs with HuR being most abundant. Accordingly, RNA-IP experiments demonstrated a specific association of HuR with reporter and endogenous pre-mRNAs that contain intronic AREs. Moreover, HuR knockdown led to a significant general reduction in the mRNA levels of genes that contain intronic AREs and to a specific reduction in the expression of ARE-intronic reporters. The data represent bioinformatics analysis for key RNA-binding proteins interactions with intronic AREs and provide experimental evidence for HuR binding to AREs. The widespread distribution of intronic AREs and their particular association with HuR and HuR binding sites indicates that more than half of human genes can be regulated post-transcriptionally by AREs.
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23
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Lema I, Amazit L, Lamribet K, Fagart J, Blanchard A, Lombès M, Cherradi N, Viengchareun S. RNA-binding protein HuR enhances mineralocorticoid signaling in renal KC3AC1 cells under hypotonicity. Cell Mol Life Sci 2017; 74:4587-4597. [PMID: 28744670 PMCID: PMC11107542 DOI: 10.1007/s00018-017-2594-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 02/03/2023]
Abstract
Mineralocorticoid receptor (MR) mediates the sodium-retaining action of aldosterone in the distal nephron. Herein, we decipher mechanisms by which hypotonicity increases MR expression in renal principal cells. We identify HuR (human antigen R), an mRNA-stabilizing protein, as an important posttranscriptional regulator of MR expression. Hypotonicity triggers a rapid and reversible nuclear export of HuR in renal KC3AC1 cells, as quantified by high-throughput microscopy. We also identify a key hairpin motif in the 3'-untranslated region of MR transcript, pivotal for the interaction with HuR and its stabilizing function. Next, we show that hypotonicity increases MR recruitment onto Sgk1 promoter, a well-known MR target gene, thereby enhancing aldosterone responsiveness. Our data shed new light on the crucial role of HuR as a stabilizing factor for the MR transcript and provide evidence for a short autoregulatory loop in which expression of a nuclear receptor transcriptionally regulating water and sodium balance is controlled by osmotic tone.
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Affiliation(s)
- Ingrid Lema
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
| | - Larbi Amazit
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
- UMS 32, 94276, Le Kremlin-Bicêtre, France
| | - Khadija Lamribet
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
| | - Jérôme Fagart
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France
| | - Anne Blanchard
- Inserm, Centre d'Investigations Cliniques 9201, 75015, Paris, France
| | - Marc Lombès
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France.
- Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service d'Endocrinologie et des Maladies de la Reproduction, 94275, Le Kremlin-Bicêtre, France.
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale, Inserm U1036, 38000, Grenoble, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biosciences et Biotechnologies de Grenoble, Laboratoire Biologie du Cancer et de l'Infection, 38000, Grenoble, France.
- Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000, Grenoble, France.
| | - Say Viengchareun
- Inserm U1185, Faculté de Médecine Paris-Sud, Université Paris-Saclay, 63 rue Gabriel Peri, 94276, Le Kremlin-Bicêtre, France.
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24
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Nasti R, Rossi D, Amadio M, Pascale A, Unver MY, Hirsch AKH, Collina S. Compounds Interfering with Embryonic Lethal Abnormal Vision (ELAV) Protein–RNA Complexes: An Avenue for Discovering New Drugs. J Med Chem 2017; 60:8257-8267. [DOI: 10.1021/acs.jmedchem.6b01871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rita Nasti
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Marialaura Amadio
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - Alessia Pascale
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - M. Yagiz Unver
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Simona Collina
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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25
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Pyrin-only protein 2 limits inflammation but improves protection against bacteria. Nat Commun 2017; 8:15564. [PMID: 28580947 PMCID: PMC5512670 DOI: 10.1038/ncomms15564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/07/2017] [Indexed: 12/13/2022] Open
Abstract
Pyrin domain-only proteins (POPs) are recently evolved, primate-specific proteins demonstrated in vitro as negative regulators of inflammatory responses. However, their in vivo function is not understood. Of the four known POPs, only POP2 is reported to regulate NF-κB-dependent transcription and multiple inflammasomes. Here we use a transgenic mouse-expressing POP2 controlled by its endogenous human promotor to study the immunological functions of POP2. Despite having significantly reduced inflammatory cytokine responses to LPS and bacterial infection, POP2 transgenic mice are more resistant to bacterial infection than wild-type mice. In a pulmonary tularaemia model, POP2 enhances IFN-γ production, modulates neutrophil numbers, improves macrophage functions, increases bacterial control and diminishes lung pathology. Thus, unlike other POPs thought to diminish innate protection, POP2 reduces detrimental inflammation while preserving and enhancing protective immunity. Our findings suggest that POP2 acts as a high-order regulator balancing cellular function and inflammation with broad implications for inflammation-associated diseases and therapeutic intervention. Pyrin-only proteins (POPs) are primate-specific negative regulators of inflammasome activation. Here the authors generate transgenic mice expressing POP2 under the control of the human promoter, and show that POP2 is important for balancing antibacterial inflammatory responses in vivo.
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26
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O. Temajo N, Howard N. The divergence between the virus and cellular oxidative stress as separate environmental agents that trigger autoimmunity originates from their different procedural mechanisms of activating the same molecular entity: the transcription factor NF-kappa B. AIMS ALLERGY AND IMMUNOLOGY 2017. [DOI: 10.3934/allergy.2017.2.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Hwang CK, Wagley Y, Law PY, Wei LN, Loh HH. Phosphorylation of poly(rC) binding protein 1 (PCBP1) contributes to stabilization of mu opioid receptor (MOR) mRNA via interaction with AU-rich element RNA-binding protein 1 (AUF1) and poly A binding protein (PABP). Gene 2016; 598:113-130. [PMID: 27836661 DOI: 10.1016/j.gene.2016.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 11/30/2022]
Abstract
Gene regulation at the post-transcriptional level is frequently based on cis- and trans-acting factors on target mRNAs. We found a C-rich element (CRE) in mu-opioid receptor (MOR) 3'-untranslated region (UTR) to which poly (rC) binding protein 1 (PCBP1) binds, resulting in MOR mRNA stabilization. RNA immunoprecipitation and RNA EMSA revealed the formation of PCBP1-RNA complexes at the element. Knockdown of PCBP1 decreased MOR mRNA half-life and protein expression. Stimulation by forskolin increased cytoplasmic localization of PCBP1 and PCBP1/MOR 3'-UTR interactions via increased serine phosphorylation that was blocked by protein kinase A (PKA) or (phosphatidyl inositol-3) PI3-kinase inhibitors. The forskolin treatment also enhanced serine- and tyrosine-phosphorylation of AU-rich element binding protein (AUF1), concurrent with its increased binding to the CRE, and led to an increased interaction of poly A binding protein (PABP) with the CRE and poly(A) sites. AUF1 phosphorylation also led to an increased interaction with PCBP1. These findings suggest that a single co-regulator, PCBP1, plays a crucial role in stabilizing MOR mRNA, and is induced by PKA signaling by conforming to AUF1 and PABP.
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Affiliation(s)
- Cheol Kyu Hwang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Yadav Wagley
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
| | - Ping-Yee Law
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Li-Na Wei
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Horace H Loh
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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28
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Gao Y, Wang W, Cao J, Wang F, Geng Y, Cao J, Xu X, Zhou J, Liu P, Zhang S. Upregulation of AUF1 is involved in the proliferation of esophageal squamous cell carcinoma through GCH1. Int J Oncol 2016; 49:2001-2010. [PMID: 27826622 DOI: 10.3892/ijo.2016.3713] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/23/2016] [Indexed: 02/04/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) has one of the highest mortality rates worldwide. AU-rich element RNA-binding factor 1 (AUF1) is an established RNA-binding protein. AUF1 influences the process of development, apoptosis and tumorigenesis via interacting with adenylate-uridylate rich elements (AREs) bearing mRNAs. However, the clinical relevance of AUF1 and its biological function in ESCC progression have not been reported. In the present study, we first investigated the expression of AUF1 in the ESCC tissue samles and normal samples. We found a significantly higher expression of AUF1 in ESCC tissues than that in normal tissues and tumor adjacent tissues. The expression of AUF1 correlated with ESCC stage (P=0.011) and marginally correlated with lymph node metastasis (P=0.055) of ESCC patients. Silencing of AUF1 by an siRNA inhibited the proliferation and enhanced the apoptosis of ESCC cells. mRNA profiling by microarray analysis revealed that AUF1 knockdown affected 285 genes (fold change ≥2) that function in multiple pathways. GTP cyclohydrolase I (GCH1), the rate limiting enzyme for BH4 synthesis, was found to be downregulated. One of the AU-rich elements in the 3'UTR of GCH1 was found to be responsive to AUF1 expression by luciferase assay. Knockdown of GCH1 suppressed cell proliferation and colony formation of ESCC cells. The expression of AUF1 significantly correlated with that of GCH1 in ESCC tissues. Taken together, we demonstrated the overexpression of AUF1 in esophageal carcinoma and identified GCH1 as AUF1's effector for the proliferation of ESCC cells.
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Affiliation(s)
- Yi Gao
- Department of Gastroenterology, The Jiangyin Clinical College of Xuzhou Medical University, Jiangyin, Jiangsu 214400, P.R. China
| | - Wenjie Wang
- School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Jinming Cao
- School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Fangjun Wang
- Department of Gastroenterology, The Jiangyin Clinical College of Xuzhou Medical University, Jiangyin, Jiangsu 214400, P.R. China
| | - Yangyang Geng
- School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Jianping Cao
- School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiaohui Xu
- Department of General Surgery, The First People's Hospital of Taicang, Soochow University, Taicang, Jiangsu 215400, P.R. China
| | - Jundong Zhou
- The Core Laboratory of Suzhou Cancer Center and Department of Radiotherapy of Suzhou Municipal Hospital, Suzhou, Jiangsu 215001, P.R. China
| | - Pengfei Liu
- Department of Gastroenterology, The Jiangyin Clinical College of Xuzhou Medical University, Jiangyin, Jiangsu 214400, P.R. China
| | - Shuyu Zhang
- School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
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White EJF, Matsangos AE, Wilson GM. AUF1 regulation of coding and noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27620010 DOI: 10.1002/wrna.1393] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 01/12/2023]
Abstract
AUF1 is a family of four RNA-binding proteins (RBPs) generated by alternative pre-messenger RNA (pre-mRNA) splicing, with canonical roles in controlling the stability and/or translation of mRNA targets based on recognition of AU-rich sequences within mRNA 3' untranslated regions. However, recent studies identifying AUF1 target sites across the transcriptome have revealed that these canonical functions are but a subset of its roles in posttranscriptional regulation of gene expression. In this review, we describe recent developments in our understanding of the RNA-binding properties of AUF1 together with their biochemical implications and roles in directing mRNA decay and translation. This is then followed by a survey of newly discovered activities for AUF1 proteins in control of miRNA synthesis and function, including miRNA assembly into microRNA (miRNA)-loaded RNA-induced silencing complexes (miRISCs), miRISC targeting to mRNA substrates, interplay with an expanding network of other cellular RBPs, and reciprocal regulatory relationships between miRNA and AUF1 synthesis. Finally, we discuss recently reported relationships between AUF1 and long noncoding RNAs and regulatory roles on viral RNA substrates. Cumulatively, these findings have significantly expanded our appreciation of the scope and diversity of AUF1 functions in the cell, and are prompting an exciting array of new questions moving forward. WIREs RNA 2017, 8:e1393. doi: 10.1002/wrna.1393 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Elizabeth J F White
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aerielle E Matsangos
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
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30
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Shikama Y, Cao M, Ono T, Feng X, Noji H, Kimura H, Ogawa K, Suzuki Y, Ikeda K, Takeishi Y, Kimura J. Reduction of c-Fos via Overexpression of miR-34a Results in Enhancement of TNF- Production by LPS in Neutrophils from Myelodysplastic Syndrome Patients. PLoS One 2016; 11:e0158527. [PMID: 27513856 PMCID: PMC4981319 DOI: 10.1371/journal.pone.0158527] [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: 01/04/2016] [Accepted: 06/16/2016] [Indexed: 02/07/2023] Open
Abstract
Although increased TNF-α has been considered to cause ineffective hematopoiesis in myelodysplastic syndromes (MDS), the mechanisms of TNF-α elevation are not known. We recently found that c-Fos mRNA stabilization under translation-inhibiting stimuli was impaired in MDS-derived neutrophilic granulocytes. In the current study, we identified overexpression of c-Fos-targeting miR-34a and miR-155 as the cause of impairment. Expression levels of miR-34a but not miR-155 inversely correlated with ratios of c-Fos-positive cells in MDS-derived CD16+ neutrophils (r = -0.618, P<0.05), which were analyzed by flow cytometry. Among the seventeen patients, c-Fos was detectable in less than 60% of CD16+ cells in eight patients (Group A), while five (Group B) expressed c-Fos in more than 80% of CD16+ cells, which was consistent with the controls (88.6 ± 7.8%). Group A-derived granulocytes secreted more TNF-α in response to 1 μM LPS for 3 hours (735.4 ± 237.5 pg/mL) than Group B (143.5 ± 65.7 pg/mL, P<0.05) and healthy controls (150.8 ± 91.5 pg/mL, P<0.05). Knockdown of c-Fos in neutrophil-like differentiated HL60 increased the binding of NF-κB p65 to the promoter region of TNF-α DNA. Thus, c-Fos reduction via overexpression of miR-34a contributes to TNF-α overproduction under inflammatory stimuli in MDS.
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Affiliation(s)
- Yayoi Shikama
- Department of Pharmacology, Fukushima Medical University, Fukushima, Japan
- * E-mail:
| | - Meiwan Cao
- Department of Pharmacology, Fukushima Medical University, Fukushima, Japan
| | - Tomoyuki Ono
- Department of Pharmacology, Fukushima Medical University, Fukushima, Japan
| | - Xiaomin Feng
- Department of Pharmacology, Fukushima Medical University, Fukushima, Japan
| | - Hideyoshi Noji
- Department of Cardiology and Hematology, Fukushima Medical University, Fukushima, Japan
| | - Hideo Kimura
- Department of Hematology, Kita Fukushima Medical Center, Date, Japan
| | - Kazuei Ogawa
- Department of Cardiology and Hematology, Fukushima Medical University, Fukushima, Japan
| | - Yuko Suzuki
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University, Fukushima, Japan
| | - Kazuhiko Ikeda
- Department of Cardiology and Hematology, Fukushima Medical University, Fukushima, Japan
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University, Fukushima, Japan
| | - Yasuchika Takeishi
- Department of Cardiology and Hematology, Fukushima Medical University, Fukushima, Japan
| | - Junko Kimura
- Department of Pharmacology, Fukushima Medical University, Fukushima, Japan
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31
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Grammatikakis I, Abdelmohsen K, Gorospe M. Posttranslational control of HuR function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27307117 DOI: 10.1002/wrna.1372] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/28/2022]
Abstract
The RNA-binding protein HuR (human antigen R) associates with numerous transcripts, coding and noncoding, and controls their splicing, localization, stability, and translation. Through its regulation of target transcripts, HuR has been implicated in cellular events including proliferation, senescence, differentiation, apoptosis, and the stress and immune responses. In turn, HuR influences processes such as cancer and inflammation. HuR function is primarily regulated through posttranslational modifications that alter its subcellular localization and its ability to bind target RNAs; such modifications include phosphorylation, methylation, ubiquitination, NEDDylation, and proteolytic cleavage. In this review, we describe the modifications that impact upon HuR function on gene expression programs and disease states. WIREs RNA 2017, 8:e1372. doi: 10.1002/wrna.1372 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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32
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Bose S, Tholanikunnel TE, Reuben A, Tholanikunnel BG, Spicer EK. Regulation of nucleolin expression by miR-194, miR-206, and HuR. Mol Cell Biochem 2016; 417:141-53. [PMID: 27221739 DOI: 10.1007/s11010-016-2721-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 05/13/2016] [Indexed: 11/29/2022]
Abstract
Nucleolin is a proliferation-associated protein that is overexpressed in multiple types of cancer. The mechanisms leading to overexpression of nucleolin in specific cancers are not fully understood. This study found that nucleolin is notably elevated in breast cancer cell lines MCF-7 and MDA-231 compared to nonmalignant breast epithelial MCF-10A cells. In silico analyses revealed the presence of putative binding sites for microRNAs miR-194 and miR-206 in the 3'-untranslated region (3'-UTR) of Ncl mRNA. Transfection of the three cell lines with pre-miR-194 or pre-miR-206 specifically decreased the Ncl mRNA and protein expression. Treatments of the cells with antagomiR-194 or antagomiR-206 upregulated nucleolin expression ~2- to 3-fold. Co-transfection of cells with a reporter vector containing the Ncl 3'-UTR downstream from the Renilla luciferase gene and pre-miR-194 or pre-miR-206 led to a ~3-fold decrease in Renilla/firefly luciferase activity. Cytoplasmic levels of the RNA-binding protein HuR were higher in MCF-7 and MDA-231 cells than those in MCF-10A cells. RNA immunoprecipitation assays demonstrated that HuR binds to Ncl mRNA in all the three cell types. ShRNA-mediated knock-down of HuR induced a decrease in nucleolin expression, while exogenous expression of HuR led to upregulation of nucleolin expression. Analysis of the polysome-monosome distribution of Ncl mRNA in HuR knock-down cells demonstrated that HuR enhances the translation efficiency of Ncl mRNA. These findings demonstrate that nucleolin expression is down-regulated by miR-194 and miR-206 and upregulated by HuR.
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Affiliation(s)
- Sudeep Bose
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, P. O. Box 250509, Charleston, SC, 29425, USA
- Amity Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Gautam Buddha Nagar Sec-125, Noida, 201301, India
| | - Tracy E Tholanikunnel
- College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Adrian Reuben
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Baby G Tholanikunnel
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, P. O. Box 250509, Charleston, SC, 29425, USA.
| | - Eleanor K Spicer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, P. O. Box 250509, Charleston, SC, 29425, USA
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33
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Cascajo MV, Abdelmohsen K, Noh JH, Fernández-Ayala DJM, Willers IM, Brea G, López-Lluch G, Valenzuela-Villatoro M, Cuezva JM, Gorospe M, Siendones E, Navas P. RNA-binding proteins regulate cell respiration and coenzyme Q biosynthesis by post-transcriptional regulation of COQ7. RNA Biol 2015; 13:622-34. [PMID: 26690054 PMCID: PMC7609068 DOI: 10.1080/15476286.2015.1119366] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Coenzyme Q (CoQ) is a key component of the mitochondrial respiratory chain carrying electrons from complexes I and II to complex III and it is an intrinsic component of the respirasome. CoQ concentration is highly regulated in cells in order to adapt the metabolism of the cell to challenges of nutrient availability and stress stimuli. At least 10 proteins have been shown to be required for CoQ biosynthesis in a multi-peptide complex and COQ7 is a central regulatory factor of this pathway. We found that the first 765 bp of the 3′-untranslated region (UTR) of COQ7 mRNA contains cis-acting elements of interaction with RNA-binding proteins (RBPs) HuR and hnRNP C1/C2. Binding of hnRNP C1/C2 to COQ7 mRNA was found to require the presence of HuR, and hnRNP C1/C2 silencing appeared to stabilize COQ7 mRNA modestly. By contrast, lowering HuR levels by silencing or depriving cells of serum destabilized and reduced the half-life of COQ7 mRNA, thereby reducing COQ7 protein and CoQ biosynthesis rate. Accordingly, HuR knockdown decreased oxygen consumption rate and mitochondrial production of ATP, and increased lactate levels. Taken together, our results indicate that a reduction in COQ7 mRNA levels by HuR depletion causes mitochondrial dysfunction and a switch toward an enhanced aerobic glycolysis, the characteristic phenotype exhibited by primary deficiency of CoQ10. Thus HuR contributes to efficient oxidative phosphorylation by regulating of CoQ10 biosynthesis.
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Affiliation(s)
- María V Cascajo
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Kotb Abdelmohsen
- b Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH , Baltimore , Maryland , USA
| | - Ji Heon Noh
- b Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH , Baltimore , Maryland , USA
| | - Daniel J M Fernández-Ayala
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Imke M Willers
- c Departamento de Biología Molecular , Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM) and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Madrid , Spain
| | - Gloria Brea
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Guillermo López-Lluch
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Marina Valenzuela-Villatoro
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - José M Cuezva
- c Departamento de Biología Molecular , Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM) and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Madrid , Spain
| | - Myriam Gorospe
- b Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH , Baltimore , Maryland , USA
| | - Emilio Siendones
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Plácido Navas
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
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Scheiba RM, de Opakua AI, Díaz-Quintana A, Cruz-Gallardo I, Martínez-Cruz LA, Martínez-Chantar ML, Blanco FJ, Díaz-Moreno I. The C-terminal RNA binding motif of HuR is a multi-functional domain leading to HuR oligomerization and binding to U-rich RNA targets. RNA Biol 2015; 11:1250-61. [PMID: 25584704 DOI: 10.1080/15476286.2014.996069] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human antigen R (HuR) is a 32 kDa protein with 3 RNA Recognition Motifs (RRMs), which bind to Adenylate and uridylate Rich Elements (AREs) of mRNAs. Whereas the N-terminal and central domains (RRM1 and RRM2) are essential for AREs recognition, little is known on the C-terminal RRM3 beyond its implication in HuR oligomerization and apoptotic signaling. We have developed a detergent-based strategy to produce soluble RRM3 for structural studies. We have found that it adopts the typical RRM fold, does not interact with the RRM1 and RRM2 modules, and forms dimers in solution. Our NMR measurements, combined with Molecular Dynamics simulations and Analytical Ultracentrifugation experiments, show that the protein dimerizes through a helical region that contains the conserved W261 residue. We found that HuR RRM3 binds to 5'-mer U-rich RNA stretches through the solvent exposed side of its β-sheet, located opposite to the dimerization site. Upon mimicking phosphorylation by the S318D replacement, RRM3 mutant shows less ability to recognize RNA due to an electrostatic repulsion effect with the phosphate groups. Our study brings new insights of HuR RRM3 as a domain involved in protein oligomerization and RNA interaction, both functions regulated by 2 surfaces on opposite sides of the RRM domain.
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Key Words
- AREs, Adenylate and uridylate Rich Elements
- AU, Analytical Ultracentrifugation
- CARM1, Coactivator associated Arginine Methyltransferase 1
- CD, Circular Dichroism
- Cdk1, Cyclin-dependent kinase 1
- Chk2, Checkpoint kinase 2
- ELAV1, Embryonic Lethal Abnormal Vision system human homolog 1
- EMSA, Electrophoretic Mobility Shift Assay
- FIR, FBP-Interacting Repressor
- FL, Full-Length, HNS, HuR Nucleocytoplasmic Shuttling Sequence
- HSQC, Heteronuclear Single-Quantum Correlation
- HuR, Human antigen R
- Human antigen R (HuR)
- MD, Molecular Dynamics
- NMR, Nuclear Magnetic Resonance
- NOE, Nuclear Overhauser Effect
- Nuclear Magnetic Resonance (NMR)
- PCA, Principal Component Analysis
- PKCα, Protein Kinase C α
- PKCδ, Protein Kinase C δ
- PMSF, PhenylMethylSulfonyl Fluoride
- PTB, Polypyrimidine Tract Binding protein
- RBPs, RNA Binding Proteins
- RNA binding
- RNA binding protein (RBP)
- RNA recognition motif (RRM)
- RRMs, RNA Recognition Motifs
- SPR, Surface Plasmon Resonance
- Serine Phosphorylation
- WT, Wild-Type
- dimerization
- hnRNP1, heterogeneous nuclear RiboNucleoprotein C protein
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Affiliation(s)
- Rafael M Scheiba
- a Instituto de Bioquímica Vegetal y Fotosíntesis; cicCartuja ; Sevilla , Spain
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35
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Kumar M, Matta A, Masui O, Srivastava G, Kaur J, Thakar A, Shukla NK, RoyChoudhury A, Sharma M, Walfish PG, Michael Siu KW, Chauhan SS, Ralhan R. Nuclear heterogeneous nuclear ribonucleoprotein D is associated with poor prognosis and interactome analysis reveals its novel binding partners in oral cancer. J Transl Med 2015; 13:285. [PMID: 26318153 PMCID: PMC4553214 DOI: 10.1186/s12967-015-0637-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/13/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Post-transcriptional regulation by heterogeneous ribonucleoproteins (hnRNPs) is an important regulatory paradigm in cancer development. Our proteomic analysis revealed hnRNPD overexpression in oral dysplasia as compared with normal mucosa; its role in oral carcinogenesis remains unknown. Here in we determined the hnRNPD associated protein networks and its clinical significance in oral squamous cell carcinoma (OSCC). METHODS Immunoprecipitation (IP) followed by tandem mass spectrometry was used to identify the binding partners of hnRNPD in oral cancer cell lines. Ingenuity pathway analysis (IPA) was carried out to unravel the protein interaction networks associated with hnRNPD and key interactions were confirmed by co-IP-western blotting. hnRNPD expression was analyzed in 183 OSCCs, 44 oral dysplasia and 106 normal tissues using immunohistochemistry (IHC) and correlated with clinico-pathological parameters and follow up data over a period of 91 months. Kaplan-Meier survival and Cox-multivariate-regression analyses were used to evaluate the prognostic significance of hnRNPD in OSCC. RESULTS We identified 345 binding partners of hnRNPD in oral cancer cells. IPA unraveled novel protein-protein interaction networks associated with hnRNPD and suggested its involvement in multiple cellular processes: DNA repair, replication, chromatin remodeling, cellular proliferation, RNA splicing and stability, thereby directing the fate of oral cancer cells. Protein-protein interactions of hnRNPD with 14-3-3ζ, hnRNPK and S100A9 were confirmed using co-IP-western blotting. IHC analysis showed significant overexpression of nuclear hnRNPD in oral dysplasia [p = 0.001, Odds ratio (OR) = 5.1, 95% CI = 2.1-11.1) and OSCCs (p = 0.001, OR = 8.1, 95% CI = 4.5-14.4) in comparison with normal mucosa. OSCC patients showing nuclear hnRNPD overexpression had significantly reduced recurrence free survival [p = 0.026, Hazard ratio = 1.95, 95% CI = 1.0-3.5] by Kaplan-Meier survival and Cox-multivariate-regression analyses and has potential to define a high-risk subgroup among OSCC patients with nodal negative disease. CONCLUSIONS Our findings suggest novel functions of hnRNPD in cellular proliferation and survival, besides RNA splicing and stability in oral cancer. Association of nuclear hnRNPD with poor prognosis in OSCC patients taken together with its associated protein networks in oral cancer warrant future studies designed to explore its potential as a plausible novel target for molecular therapeutics.
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Affiliation(s)
- Manish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Room No. 3009, New Delhi, 110029, India.
| | - Ajay Matta
- Alex and Simona Shnaider Laboratory of Molecular Oncology, Mount Sinai Hospital, 6-500, Toronto, ON, M5G 1X5, Canada.
| | - Olena Masui
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, ON, Canada.
| | - Gunjan Srivastava
- Alex and Simona Shnaider Laboratory of Molecular Oncology, Mount Sinai Hospital, 6-500, Toronto, ON, M5G 1X5, Canada.
| | - Jatinder Kaur
- Department of Biochemistry, All India Institute of Medical Sciences, Room No. 3009, New Delhi, 110029, India.
| | - Alok Thakar
- Department of Otorhinolaryngology, All India Institute of Medical Sciences, New Delhi, India.
| | - Nootan Kumar Shukla
- Department of Surgery, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India.
| | - Ajoy RoyChoudhury
- Department of Dental Surgery, All India Institute of Medical Sciences, New Delhi, India.
| | - Meherchand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India.
| | - Paul G Walfish
- Alex and Simona Shnaider Laboratory of Molecular Oncology, Mount Sinai Hospital, 6-500, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology-Head and Neck Surgery, Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Mount Sinai Hospital, Toronto, ON, Canada. .,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph & Wolf Lebovic Health Complex, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Toronto, ON, Canada. .,Department of Medicine, Endocrine Division, Mount Sinai Hospital and University of Toronto, Toronto, ON, Canada.
| | - K W Michael Siu
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, ON, Canada. .,Department of Chemistry, University of Windsor, Windsor, ON, Canada.
| | - Shyam Singh Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, Room No. 3009, New Delhi, 110029, India.
| | - Ranju Ralhan
- Alex and Simona Shnaider Laboratory of Molecular Oncology, Mount Sinai Hospital, 6-500, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology-Head and Neck Surgery, Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Mount Sinai Hospital, Toronto, ON, Canada. .,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph & Wolf Lebovic Health Complex, Toronto, ON, M5G 1X5, Canada. .,Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Toronto, ON, Canada.
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Wu X, Lan L, Wilson DM, Marquez RT, Tsao WC, Gao P, Roy A, Turner BA, McDonald P, Tunge JA, Rogers SA, Dixon DA, Aubé J, Xu L. Identification and validation of novel small molecule disruptors of HuR-mRNA interaction. ACS Chem Biol 2015; 10:1476-84. [PMID: 25750985 DOI: 10.1021/cb500851u] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HuR, an RNA binding protein, binds to adenine- and uridine-rich elements (ARE) in the 3'-untranslated region (UTR) of target mRNAs, regulating their stability and translation. HuR is highly abundant in many types of cancer, and it promotes tumorigenesis by interacting with cancer-associated mRNAs, which encode proteins that are implicated in different tumor processes including cell proliferation, cell survival, angiogenesis, invasion, and metastasis. Drugs that disrupt the stabilizing effect of HuR upon mRNA targets could have dramatic effects on inhibiting cancer growth and persistence. In order to identify small molecules that directly disrupt the HuR-ARE interaction, we established a fluorescence polarization (FP) assay optimized for high throughput screening (HTS) using HuR protein and an ARE oligo from Musashi RNA-binding protein 1 (Msi1) mRNA, a HuR target. Following the performance of an HTS of ∼6000 compounds, we discovered a cluster of potential disruptors, which were then validated by AlphaLISA (Amplified Luminescent Proximity Homogeneous Assay), surface plasmon resonance (SPR), ribonucleoprotein immunoprecipitation (RNP IP) assay, and luciferase reporter functional studies. These compounds disrupted HuR-ARE interactions at the nanomolar level and blocked HuR function by competitive binding to HuR. These results support future studies toward chemical probes for a HuR function study and possibly a novel therapy for HuR-overexpressing cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Dan A. Dixon
- Department
of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
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PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nat Commun 2014; 5:5248. [PMID: 25366541 DOI: 10.1038/ncomms6248] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022] Open
Abstract
Post-transcriptional gene regulation is robustly regulated by RNA-binding proteins (RBPs). Here we describe the collection of RNAs regulated by AUF1 (AU-binding factor 1), an RBP linked to cancer, inflammation and aging. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis reveals that AUF1 primarily recognizes U-/GU-rich sequences in mRNAs and noncoding RNAs and influences target transcript fate in three main directions. First, AUF1 lowers the steady-state levels of numerous target RNAs, including long noncoding RNA NEAT1, in turn affecting the organization of nuclear paraspeckles. Second, AUF1 does not change the abundance of many target RNAs, but ribosome profiling reveals that AUF1 promotes the translation of numerous mRNAs in this group. Third, AUF1 unexpectedly enhances the steady-state levels of several target mRNAs encoding DNA-maintenance proteins. Through its actions on target RNAs, AUF1 preserves genomic integrity, in agreement with the AUF1-elicited prevention of premature cellular senescence.
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38
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A single element in the 3'UTR of the apical sodium-dependent bile acid transporter controls both stabilization and destabilization of mRNA. Biochem J 2014; 462:547-53. [PMID: 24946903 DOI: 10.1042/bj20140070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
mRNA stability appears to play a key role in the ontogenic regulation of the apical sodium-dependent bile acid transporter (ASBT). The RNA-binding proteins Hu antigen R (HuR) and tristetraprolin (TTP) stabilize and destabilize ASBT mRNA, respectively. Potential HuR-binding sites were assessed by sequence analysis in the context of prior in vitro functional analyses of the rat ASBT 3'UTR. Wild-type and mutant-binding sites were investigated by gel-shift analysis using IEC-6 cell extracts. The functional consequences of binding site mutations were assessed using two different hybrid reporter constructs linking the 3'UTR element to either a luciferase or a β-globin coding mRNA sequence. A specific metastasis-associated gene 1 (MTA1) cis-element was identified in the ASBT 3'UTR that became associated with proteins in IEC-6 cell extracts and could be supershifted by anti-HuR or anti-TTP antibodies. Mutation of this cis-element abrogated the gel shift of IEC-6 proteins. Furthermore, hybrid constructs containing a mutant MTA1 element had reduced responses to modulation of HuR or TTP. For the first time, we have identified a single specific sequence element in the 3'UTR of the rat ASBT mRNA that mediates counter-regulatory changes in mRNA abundance in response to both HuR and TTP.
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39
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Kafasla P, Skliris A, Kontoyiannis DL. Post-transcriptional coordination of immunological responses by RNA-binding proteins. Nat Immunol 2014; 15:492-502. [PMID: 24840980 DOI: 10.1038/ni.2884] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/01/2014] [Indexed: 12/22/2022]
Abstract
Immunological reactions are propelled by ever-changing signals that alter the translational ability of the RNA in the cells involved. Such alterations are considered to be consequential modifications in the transcriptomic decoding of the genetic blueprint. The identification of RNA-binding protein (RBP) assemblies engaged in the coordinative regulation of state-specific RNAs indicates alternative and exclusive means for determining the activation, plasticity and tolerance of cells of the immune system. Here we review current knowledge about RBP-regulated post-transcriptional events involved in the reactivity of cells of the immune system and the importance of their alteration during chronic inflammatory pathology and autoimmunity.
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Affiliation(s)
- Panagiota Kafasla
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Antonis Skliris
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Dimitris L Kontoyiannis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
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40
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Adjibade P, Mazroui R. Control of mRNA turnover: implication of cytoplasmic RNA granules. Semin Cell Dev Biol 2014; 34:15-23. [PMID: 24946962 DOI: 10.1016/j.semcdb.2014.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/21/2014] [Indexed: 12/15/2022]
Abstract
The control of mRNA turnover is essential for the cell to rationalize its mRNA content both under physiological conditions and upon stress. Several mechanisms involved in the control of mRNA turnover have been elucidated. These include surveillance mechanisms such as nonsense-mediated decay, non-stop mediated decay and non-go-mediated decay that eliminate aberrant mRNAs, and regulatory mechanisms including AU-mediated decay, GU-mediated decay, and CDE-mediated decay that ensure mRNA plasticity. In general, the mechanisms of RNA decay rely on interactions between specific cis-acting RNA elements and selected RNA-binding proteins that either prevent the degradation of mRNA targets or induce the recruitment of decaying effectors leading to mRNA degradation. Formation of cytoplasmic RNA granules including processing bodies, stress granules, UV granules, and exosome granules have recently emerged as an additional mechanism that control mRNA turnover of selected mRNAs. Here we will review briefly review the main mechanisms that control mRNA decay and highlight possible implication of RNA granules in such mechanisms.
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Affiliation(s)
- Pauline Adjibade
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada.
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41
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Singh AB, Kan CFK, Shende V, Dong B, Liu J. A novel posttranscriptional mechanism for dietary cholesterol-mediated suppression of liver LDL receptor expression. J Lipid Res 2014; 55:1397-407. [PMID: 24792925 DOI: 10.1194/jlr.m049429] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 12/21/2022] Open
Abstract
It is well-established that over-accumulation of dietary cholesterol in the liver inhibits sterol-regulatory element binding protein (SREBP)-mediated LDL receptor (LDLR) gene transcription leading to a reduced hepatic LDLR mRNA level in hypercholesterolemic animals. However, it is unknown whether elevated cholesterol levels can elicit a cellular response to increase LDLR mRNA turnover to further repress LDLR expression in liver tissue. In the current study, we examined the effect of a high cholesterol diet on the hepatic expression of LDLR mRNA binding proteins in three different animal models and in cultured hepatic cells. Our results demonstrate that high cholesterol feeding specifically elevates the hepatic expression of LDLR mRNA decay promoting factor heterogeneous nuclear ribonucleoprotein (HNRNP)D without affecting expressions of other LDLR mRNA binding proteins in vivo and in vitro. Employing the approach of adenovirus-mediated gene knockdown, we further show that depletion of HNRNPD in the liver results in a marked reduction of serum LDL-cholesterol and a substantial increase in liver LDLR expression in hyperlipidemic mice. Additional studies of gene knockdown in albumin-luciferase-untranslated region (UTR) transgenic mice provide strong evidence supporting the essential role of 3'UTR in HNRNPD-mediated LDLR mRNA degradation in liver tissue. Altogether, this work identifies a novel posttranscriptional regulatory mechanism by which dietary cholesterol inhibits liver LDLR expression via inducing HNRNPD to accelerate LDLR mRNA degradation.
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Affiliation(s)
- Amar Bahadur Singh
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304 Department of Medicine, Stanford University, Stanford, CA 94305
| | | | - Vikram Shende
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304 Department of Medicine, Stanford University, Stanford, CA 94305
| | - Bin Dong
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304
| | - Jingwen Liu
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304
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42
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Karreth FA, Tay Y, Pandolfi PP. Target competition: transcription factors enter the limelight. Genome Biol 2014; 15:114. [PMID: 25001290 PMCID: PMC4052382 DOI: 10.1186/gb4174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcription factor binding sites compete for a limited pool of bioavailable transcription factor molecules to fine tune gene expression.
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43
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Chalupnikova K, Solc P, Sulimenko V, Sedlacek R, Svoboda P. An oocyte-specific ELAVL2 isoform is a translational repressor ablated from meiotically competent antral oocytes. Cell Cycle 2014; 13:1187-200. [PMID: 24553115 PMCID: PMC4013169 DOI: 10.4161/cc.28107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
At the end of the growth phase, mouse antral follicle oocytes acquire full developmental competence. In the mouse, this event is marked by the transition from the so-called non-surrounded nucleolus (NSN) chromatin configuration into the transcriptionally quiescent surrounded nucleolus (SN) configuration, which is named after a prominent perinucleolar condensed chromatin ring. However, the SN chromatin configuration alone is not sufficient for determining the developmental competence of the SN oocyte. There are additional nuclear and cytoplamic factors involved, while a little is known about the changes occurring in the cytoplasm during the NSN/SN transition. Here, we report functional analysis of maternal ELAVL2 an AU-rich element binding protein. Elavl2 gene encodes an oocyte-specific protein isoform (denoted ELAVL2°), which acts as a translational repressor. ELAVL2° is abundant in fully grown NSN oocytes, is ablated during the NSN/SN transition and remains low during the oocyte-to-embryo transition (OET). ELAVL2° overexpression during meiotic maturation causes errors in chromosome segregation, indicating the significance of naturally reduced ELAVL2° levels in SN oocytes. On the other hand, during oocyte growth, prematurely reduced Elavl2 expression results in lower yields of fully grown and meiotically matured oocytes, suggesting that Elavl2 is necessary for proper oocyte maturation. Moreover, Elavl2 knockdown showed stimulating effects on translation in fully grown oocytes. We propose that ELAVL2 has an ambivalent role in oocytes: it functions as a pleiotropic translational repressor in efficient production of fully grown oocytes, while its disposal during the NSN/SN transition contributes to the acquisition of full developmental competence.
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Affiliation(s)
| | - Petr Solc
- Institute of Animal Physiology and Genetics AS CR; Libechov, Czech Republic
| | - Vadym Sulimenko
- Institute of Molecular Genetics AS CR; Prague, Czech Republic
| | | | - Petr Svoboda
- Institute of Molecular Genetics AS CR; Prague, Czech Republic
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44
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Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature 2014; 505:344-52. [PMID: 24429633 DOI: 10.1038/nature12986] [Citation(s) in RCA: 2888] [Impact Index Per Article: 288.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 11/06/2013] [Indexed: 12/11/2022]
Abstract
Recent reports have described an intricate interplay among diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs. These RNA transcripts act as competing endogenous RNAs (ceRNAs) or natural microRNA sponges - they communicate with and co-regulate each other by competing for binding to shared microRNAs, a family of small non-coding RNAs that are important post-transcriptional regulators of gene expression. Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.
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Affiliation(s)
- Yvonne Tay
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - John Rinn
- 1] Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA. [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. [3] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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45
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Frank SB, Miranti CK. Disruption of prostate epithelial differentiation pathways and prostate cancer development. Front Oncol 2013; 3:273. [PMID: 24199173 PMCID: PMC3813973 DOI: 10.3389/fonc.2013.00273] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/18/2013] [Indexed: 12/14/2022] Open
Abstract
One of the foremost problems in the prostate cancer (PCa) field is the inability to distinguish aggressive from indolent disease, which leads to difficult prognoses and thousands of unnecessary surgeries. This limitation stems from the fact that the mechanisms of tumorigenesis in the prostate are poorly understood. Some genetic alterations are commonly reported in prostate tumors, including upregulation of Myc, fusion of Ets genes to androgen-regulated promoters, and loss of Pten. However, the specific roles of these aberrations in tumor initiation and progression are poorly understood. Likewise, the cell of origin for PCa remains controversial and may be linked to the aggressive potential of the tumor. One important clue is that prostate tumors co-express basal and luminal protein markers that are restricted to their distinct cell types in normal tissue. Prostate epithelium contains layer-specific stem cells as well as rare bipotent cells, which can differentiate into basal or luminal cells. We hypothesize that the primary oncogenic cell of origin is a transient-differentiating bipotent cell. Such a cell must maintain tight temporal and spatial control of differentiation pathways, thus increasing its susceptibility for oncogenic disruption. In support of this hypothesis, many of the pathways known to be involved in prostate differentiation can be linked to genes commonly altered in PCa. In this article, we review what is known about important differentiation pathways (Myc, p38MAPK, Notch, PI3K/Pten) in the prostate and how their misregulation could lead to oncogenesis. Better understanding of normal differentiation will offer new insights into tumor initiation and may help explain the functional significance of common genetic alterations seen in PCa. Additionally, this understanding could lead to new methods for classifying prostate tumors based on their differentiation status and may aid in identifying more aggressive tumors.
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Affiliation(s)
- Sander B Frank
- Laboratory of Integrin Signaling and Tumorigenesis, Van Andel Research Institute , Grand Rapids, MI , USA ; Genetics Graduate Program, Michigan State University , East Lansing, MI , USA
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46
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Singh AB, Li H, Kan CFK, Dong B, Nicolls MR, Liu J. The critical role of mRNA destabilizing protein heterogeneous nuclear ribonucleoprotein d in 3' untranslated region-mediated decay of low-density lipoprotein receptor mRNA in liver tissue. Arterioscler Thromb Vasc Biol 2013; 34:8-16. [PMID: 24158514 DOI: 10.1161/atvbaha.112.301131] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Previous studies showed that low-density lipoprotein receptor (LDLR) mRNA 3' untranslated region (UTR) contains regulatory elements responsible for rapid mRNA turnover in hepatic cells and mediates the mRNA stabilization induced by berberine (BBR). Here, we elucidate the underlying mechanism of BBR's action by characterizing mRNA-binding proteins that modulate LDLR mRNA decay via 3'UTR in liver tissue in vivo. APPROACH AND RESULTS We generated a transgenic mouse model (Alb-Luc-UTR) that expresses Luc-LDLR3'UTR reporter gene driven by the albumin promoter to study 3'UTR function in mediating LDLR mRNA decay in liver tissue. We show that treating Alb-Luc-UTR mice with BBR led to significant increases in hepatic bioluminescence signals, Luc-UTR mRNA, and LDLR mRNA levels as compared with control mice. These effects were accompanied by specific reductions of mRNA decay-promoting factor heterogeneous nuclear ribonucleoprotein D (hnRNP D) in liver of BBR-treated mice. Knockdown and overexpression studies further demonstrated that hnRNP D p37 isoform plays a major role in promoting hepatic LDLR mRNA degradation. In addition, we examined LDLR mRNA half-life, Luc-UTR reporter activity, and hnRNP D expression levels in cell lines derived from extrahepatic tissues. We demonstrated that strengths of 3'UTR in promoting mRNA degradation correlate with hnRNP D cellular abundances in nonhepatic cell lines, thereby suggesting its involvement in LDLR mRNA degradation beyond liver tissue. CONCLUSIONS hnRNP D is critically involved in LDLR mRNA degradation in liver tissue in vivo. The inverse relationship of hnRNP D abundance with LDLR mRNA levels after BBR treatment suggests the potential of hnRNP D of being a novel therapeutic target for LDL cholesterol lowering.
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Affiliation(s)
- Amar Bahadur Singh
- From the Veterans Affairs Palo Alto Health Care System, CA (A.B.S., H.L., C.F.K.K., B.D., M.R.N., J.L.); and Department of Medicine, Stanford University, CA (A.B.S., H.L., B.D., M.R.N.)
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Schulz S, Doller A, Pendini NR, Wilce JA, Pfeilschifter J, Eberhardt W. Domain-specific phosphomimetic mutation allows dissection of different protein kinase C (PKC) isotype-triggered activities of the RNA binding protein HuR. Cell Signal 2013; 25:2485-95. [PMID: 23978401 DOI: 10.1016/j.cellsig.2013.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/06/2013] [Accepted: 08/15/2013] [Indexed: 01/21/2023]
Abstract
The ubiquitous mRNA binding protein human antigen R (HuR) participates in the post-transcriptional regulation of many AU-rich element (ARE)-bearing mRNAs. Previously, by using in vitro kinase assay, we have identified serines (Ser) 158, 221 and 318 as targets of protein kinase C (PKC)-triggered phosphorylation. In this study, we tested whether GFP- or GST-tagged HuR constructs bearing a phosphomimetic Ser (S)-to-Asp (D) substitution at the different PKC target sites, would affect different HuR functions including HuR nucleo-cytoplasmic redistribution and binding to different types of ARE-containing mRNAs. The phosphomimetic GFP-tagged HuR protein bearing a phosphomimetic substitution in the hinge region of HuR (HuR-S221D) showed an increased cytoplasmic abundance when compared to wild-type HuR. Conversely, data from in vitro kinase assay and electrophoretic mobility shift assay (EMSA), implicates that phosphorylation at Ser 221 is not relevant for mRNA binding of HuR. Quantification of in vitro binding affinities of GST-tagged wild-type HuR and corresponding HuR proteins bearing a phosphomimetic substitution in either RRM2 (HuR-S158D) or in RRM3 (HuR-S318D) by microscale thermophoresis (MST) indicates a specific binding of wild-type HuR to type I, II or type III-ARE-oligonucleotides in the high nanomolar range. Interestingly, phosphomimetic mutation at position 158 or 318 had a negative influence on HuR binding to type I- and type II-ARE-mRNAs whereas it significantly enhanced HuR affinity to a type III-ARE substrate. Our data suggest that differential phosphorylation of HuR by PKCs at different HuR domains coordinates subcellular HuR distribution and leads to a preferential binding to U-rich bearing target mRNA.
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Affiliation(s)
- Sebastian Schulz
- pharmazentrum frankfurt/ZAFES, Klinikum der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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48
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Impairment of FOS mRNA stabilization following translation arrest in granulocytes from myelodysplastic syndrome patients. PLoS One 2013; 8:e61107. [PMID: 23593403 PMCID: PMC3625160 DOI: 10.1371/journal.pone.0061107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/05/2013] [Indexed: 02/06/2023] Open
Abstract
Although quantitative and qualitative granulocyte defects have been described in myelodysplastic syndromes (MDS), the underlying molecular basis of granulocyte dysfunction in MDS is largely unknown. We recently found that FOS mRNA elevation under translation-inhibiting stimuli was significantly smaller in granulocytes from MDS patients than in healthy individuals. The aim of this study is to clarify the cause of the impaired FOS induction in MDS. We first examined the mechanisms of FOS mRNA elevation using granulocytes from healthy donors cultured with the translation inhibitor emetine. Emetine increased both transcription and mRNA stability of FOS. p38 MAPK inhibition abolished the emetine-induced increase of FOS transcription but did not affect FOS mRNA stabilization. The binding of an AU-rich element (ARE)-binding protein HuR to FOS mRNA containing an ARE in 3'UTR was increased by emetine, and the knockdown of HuR reduced the FOS mRNA stabilizing effect of emetine. We next compared the emetine-induced transcription and mRNA stabilization of FOS between MDS patients and healthy controls. Increased rates of FOS transcription by emetine were similar in MDS and controls. In the absence of emetine, FOS mRNA decayed to nearly 17% of initial levels in 45 min in both groups. In the presence of emetine, however, 76.7±19.8% of FOS mRNA remained after 45 min in healthy controls, versus 37.9±25.5% in MDS (P<0.01). To our knowledge, this is the first report demonstrating attenuation of stress-induced FOS mRNA stabilization in MDS granulocytes.
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49
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Mino T, Takeuchi O. Post-transcriptional regulation of cytokine mRNA controls the initiation and resolution of inflammation. Biotechnol Genet Eng Rev 2013; 29:49-60. [DOI: 10.1080/02648725.2013.801236] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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50
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Hinman MN, Zhou HL, Sharma A, Lou H. All three RNA recognition motifs and the hinge region of HuC play distinct roles in the regulation of alternative splicing. Nucleic Acids Res 2013; 41:5049-61. [PMID: 23525460 PMCID: PMC3643579 DOI: 10.1093/nar/gkt166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins contains a divergent N-terminus, three highly conserved RNA recognition motifs (RRM1, RRM2 and RRM3) and a hinge region separating RRM2 and RRM3. The roles of each domain in splicing regulation are not well understood. Here, we investigate how HuC, a relatively poorly characterized family member, regulates three target pre-mRNAs: neurofibromatosis type I, Fas and HuD. We find that the HuC N-terminus is dispensable for splicing regulation, and the three RRMs are required for splicing regulation of each target, whereas the hinge region contributes to regulation of only some targets. Interestingly, the regions of the hinge and RRM3 required for regulating different targets only partially overlap, implying substrate-specific mechanisms of HuC-mediated splicing regulation. We show that RRM1 and RRM2 are required for binding to target pre-mRNAs, whereas the hinge and RRM3 are required for HuC–HuC self-interaction. Finally, we find that the portions of RRM3 required for HuC–HuC interaction overlap with those required for splicing regulation of all three targets, suggesting a role of HuC–HuC interaction in splicing regulation.
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Affiliation(s)
- Melissa N Hinman
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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