1
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An Evolutionarily Conserved AU-Rich Element in the 3' Untranslated Region of a Transcript Misannotated as a Long Noncoding RNA Regulates RNA Stability. Mol Cell Biol 2022; 42:e0050521. [PMID: 35274990 DOI: 10.1128/mcb.00505-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the primary mechanisms of post-transcriptional gene regulation is the modulation of RNA stability. We recently discovered that LINC00675, a transcript annotated as a long noncoding RNA (lncRNA), is transcriptionally regulated by FOXA1 and encodes a highly conserved small protein that localizes to the endoplasmic reticulum, hence renamed as FORCP (FOXA1-regulated conserved small protein). Here, we show that the endogenous FORCP transcript is rapidly degraded and rendered unstable as a result of 3'UTR-mediated degradation. Surprisingly, although the FORCP transcript is a canonical nonsense-mediated decay (NMD) and microRNA (miRNA) target, we found that it is not degraded by NMD or miRNAs. Targeted deletion of an evolutionarily conserved region in the FORCP 3'UTR using CRISPR/Cas9 significantly increased the stability of the FORCP transcript. Interestingly, this region requires the presence of an immediate downstream 55-nt-long sequence for transcript stability regulation. Functionally, colorectal cancer cells lacking this conserved region expressed from the endogenous FORCP locus displayed decreased proliferation and clonogenicity. These data demonstrate that the FORCP transcript is destabilized via conserved elements within its 3'UTR and emphasize the need to interrogate the function of a given 3'UTR in its native context.
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2
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Bonnet-Magnaval F, DesGroseillers L. The Staufen1-dependent cell cycle regulon or how a misregulated RNA-binding protein leads to cancer. Biol Rev Camb Philos Soc 2021; 96:2192-2208. [PMID: 34018319 DOI: 10.1111/brv.12749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
In recent years, an increasing number of reports have linked the RNA-binding protein Staufen1 (STAU1) to the control of cell decision making. In non-transformed cells, STAU1 balances the expression of messenger RNA (mRNA) regulons that regulate differentiation and well-ordered cell division. Misregulation of STAU1 expression and/or functions changes the fragile balance in the expression of pro- and anti-proliferative and apoptotic genes and favours a novel equilibrium that supports cell proliferation and cancer development. The misregulation of STAU1 functions causes multiple coordinated modest effects in the post-transcriptional regulation of many RNA targets that code for cell cycle regulators, leading to dramatic consequences at the cellular level. The new tumorigenic equilibrium in STAU1-mediated gene regulation observed in cancer cells can be further altered by a slight increase in STAU1 expression that favours expression of pro-apoptotic genes and cell death. The STAU1-dependent cell cycle regulon is a good model to study how abnormal expression of an RNA-binding protein promotes cell growth and provides an advantageous selection of malignant cells in the first step of cancer development.
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Affiliation(s)
- Florence Bonnet-Magnaval
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Luc DesGroseillers
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC, H3T 1J4, Canada
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3
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Sun X, Zhang K, Gu J, Yang J, Huang Q, Yan R, Qin S, Hou C, Zhang G, Wang S, Li M. The biological characters of Bmelav-like genes in the development of Bombyx mori. INSECT MOLECULAR BIOLOGY 2021; 30:9-17. [PMID: 32940384 DOI: 10.1111/imb.12668] [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: 06/22/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
The ELAV/Hu family is a conserved multigene family of pan-neuronal RNA-binding protein involved in post-transcriptional regulation in metazoans. In Drosophila, three members of this family, ELAV, RBP9 and FNE, are involved in neuronal differentiation, gene expression regulation and so on. This family is less well characterized in Bombyx mori. Two orthologs BmELAV-like-1 (BmEL-1) and BmELAV-like-2 (BmEL-2) share 55%-71% and 47%-62% identity with that of in Drosophila and humans, respectively. Bmel-1 is ubiquitously expressed while Bmel-2 is expressed in the head and ovaries specifically. Proteins encoded by both genes are localized in nuclear and cytoplasm. The weight of body, cocoon, pupae and cocoon shell are differently affected in Bmel-1- /-2- mutants created using CRISPR/Cas9 technology. Mutations of both genes increase the expression of four silk protein genes, Fib-L, Fib-H, P25 and Ser-1. In addition, the oviposition ability of Bmel-2- females is decreased. This study not only provides valuable insights into the functional roles of Bmelav-like genes in the growth, cocoon characters and regulation of silk protein genes expression, but also provides useful information for silkworm variety breeding.
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Affiliation(s)
- X Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - K Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - J Gu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - J Yang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Q Huang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - R Yan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - S Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - C Hou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - G Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - S Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - M Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
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4
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Just PA, Charawi S, Denis RGP, Savall M, Traore M, Foretz M, Bastu S, Magassa S, Senni N, Sohier P, Wursmer M, Vasseur-Cognet M, Schmitt A, Le Gall M, Leduc M, Guillonneau F, De Bandt JP, Mayeux P, Romagnolo B, Luquet S, Bossard P, Perret C. Lkb1 suppresses amino acid-driven gluconeogenesis in the liver. Nat Commun 2020; 11:6127. [PMID: 33257663 PMCID: PMC7705018 DOI: 10.1038/s41467-020-19490-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
Excessive glucose production by the liver is a key factor in the hyperglycemia observed in type 2 diabetes mellitus (T2DM). Here, we highlight a novel role of liver kinase B1 (Lkb1) in this regulation. We show that mice with a hepatocyte-specific deletion of Lkb1 have higher levels of hepatic amino acid catabolism, driving gluconeogenesis. This effect is observed during both fasting and the postprandial period, identifying Lkb1 as a critical suppressor of postprandial hepatic gluconeogenesis. Hepatic Lkb1 deletion is associated with major changes in whole-body metabolism, leading to a lower lean body mass and, in the longer term, sarcopenia and cachexia, as a consequence of the diversion of amino acids to liver metabolism at the expense of muscle. Using genetic, proteomic and pharmacological approaches, we identify the aminotransferases and specifically Agxt as effectors of the suppressor function of Lkb1 in amino acid-driven gluconeogenesis. Excessive glucose production by the liver contributes to poor blood glucose control in type 2 diabetes. Here the authors report that the liver kinase B1 (Lkb1) suppresses amino acid driven postprandial glucose production in the liver through the aminotransferase Agxt.
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Affiliation(s)
- Pierre-Alexandre Just
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.,APHP, Centre-Université de Paris, Paris, France
| | - Sara Charawi
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Raphaël G P Denis
- Unité de Biologie Fonctionnelle et Adaptative, Centre National la Recherche Scientifique, Unité Mixte de Recherche 8251, Université Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | - Mathilde Savall
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Massiré Traore
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Marc Foretz
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Sultan Bastu
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | | | - Nadia Senni
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Pierre Sohier
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Maud Wursmer
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Mireille Vasseur-Cognet
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRA 1392, Sorbonne Universités Paris and Institut d'Ecologie et des Sciences de l'Environnement de Paris, Bondy, France
| | - Alain Schmitt
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.,Electron Miscroscopy Facility, Institut Cochin, F75014, Paris, France
| | - Morgane Le Gall
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.,3P5 proteom'IC Facility, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | - Marjorie Leduc
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.,3P5 proteom'IC Facility, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | - François Guillonneau
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.,3P5 proteom'IC Facility, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | | | - Patrick Mayeux
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.,3P5 proteom'IC Facility, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | - Béatrice Romagnolo
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Serge Luquet
- Unité de Biologie Fonctionnelle et Adaptative, Centre National la Recherche Scientifique, Unité Mixte de Recherche 8251, Université Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | - Pascale Bossard
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France
| | - Christine Perret
- Université de Paris, Institut Cochin, INSERM, CNRS, F75014, Paris, France.
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5
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SMN protein promotes membrane compartmentalization of ribosomal protein S6 transcript in human fibroblasts. Sci Rep 2020; 10:19000. [PMID: 33149163 PMCID: PMC7643083 DOI: 10.1038/s41598-020-76174-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Alterations of RNA homeostasis can lead to severe pathological conditions. The Survival of Motor Neuron (SMN) protein, which is reduced in Spinal Muscular Atrophy, impacts critical aspects of the RNA life cycle, such as splicing, trafficking, and translation. Increasing evidence points to a potential role of SMN in ribosome biogenesis. Our previous study revealed that SMN promotes membrane-bound ribosomal proteins (RPs), sustaining activity-dependent local translation. Here, we suggest that plasma membrane domains could be a docking site not only for RPs but also for their encoding transcripts. We have shown that SMN knockdown perturbs subcellular localization as well as translation efficiency of RPS6 mRNA. We have also shown that plasma membrane-enriched fractions from human fibroblasts retain RPS6 transcripts in an SMN-dependent manner. Furthermore, we revealed that SMN traffics with RPS6 mRNA promoting its association with caveolin-1, a key component of membrane dynamics. Overall, these findings further support the SMN-mediated crosstalk between plasma membrane dynamics and translation machinery. Importantly, our study points to a potential role of SMN in the ribosome assembly pathway by selective RPs synthesis/localization in both space and time.
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6
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Nakazawa K, Shichino Y, Iwasaki S, Shiina N. Implications of RNG140 (caprin2)-mediated translational regulation in eye lens differentiation. J Biol Chem 2020; 295:15029-15044. [PMID: 32839273 DOI: 10.1074/jbc.ra120.012715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 08/07/2020] [Indexed: 01/02/2023] Open
Abstract
Regulation of gene expression at the translational level is key to determining cell fate and function. An RNA-binding protein, RNG140 (caprin2), plays a role in eye lens differentiation and has been reported to function in translational regulation. However, the mechanism and its role in eyes has remained unclear. Here, we show that RNG140 binds to the translation initiation factor eukaryotic initiation factor 3 (eIF3) and suppresses translation through mechanisms involving suppression of eIF3-dependent translation initiation. Comprehensive ribosome profiling revealed that overexpression of RNG140 in cultured Chinese hamster ovary cells reduces translation of long mRNAs, including those associated with cell proliferation. RNG140-mediated translational regulation also operates in the mouse eye, where RNG140 knockout increased the translation of long mRNAs. mRNAs involved in lens differentiation, such as crystallin mRNAs, are short and can escape translational inhibition by RNG140 and be translated in differentiating lenses. Thus, this study provides insights into the mechanistic basis of lens cell transition from proliferation to differentiation via RNG140-mediated translational regulation.
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Affiliation(s)
- Kaori Nakazawa
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan; Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan; Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Aichi, Japan.
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7
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Abstract
Parathyroid hormone is an essential regulator of extracellular calcium and phosphate. PTH enhances calcium reabsorption while inhibiting phosphate reabsorption in the kidneys, increases the synthesis of 1,25-dihydroxyvitamin D, which then increases gastrointestinal absorption of calcium, and increases bone resorption to increase calcium and phosphate. Parathyroid disease can be an isolated endocrine disorder or part of a complex syndrome. Genetic mutations can account for diseases of parathyroid gland formulation, dysregulation of parathyroid hormone synthesis or secretion, and destruction of the parathyroid glands. Over the years, a number of different options are available for the treatment of different types of parathyroid disease. Therapeutic options include surgical removal of hypersecreting parathyroid tissue, administration of parathyroid hormone, vitamin D, activated vitamin D, calcium, phosphate binders, calcium-sensing receptor, and vitamin D receptor activators to name a few. The accurate assessment of parathyroid hormone also provides essential biochemical information to properly diagnose parathyroid disease. Currently available immunoassays may overestimate or underestimate bioactive parathyroid hormone because of interferences from truncated parathyroid hormone fragments, phosphorylation of parathyroid hormone, and oxidation of amino acids of parathyroid hormone.
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Affiliation(s)
- Edward Ki Yun Leung
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, United States.
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8
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Matsuyama T. Recent developments in terminator technology in Saccharomyces cerevisiae. J Biosci Bioeng 2019; 128:655-661. [PMID: 31324384 DOI: 10.1016/j.jbiosc.2019.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022]
Abstract
Metabolically engineered microorganisms that produce useful organic compounds will be helpful for realizing a sustainable society. The budding yeast Saccharomyces cerevisiae has high utility as a metabolic engineering platform because of its high fermentation ability, non-pathogenicity, and ease of handling. When producing yeast strains that produce exogenous compounds, it is a prerequisite to control the expression of exogenous enzyme-encoding genes. Terminator region in a gene expression cassette, as well as promoter region, could be used to improve metabolically engineered yeasts by increasing or decreasing the expression of the target enzyme-encoding genes. The findings on terminators have grown rapidly in the last decade, so an overview of these findings should provide a foothold for new developments.
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9
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Chung HW, Weng JC, King CE, Chuang CF, Chow WY, Chang YC. BDNF elevates the axonal levels of hnRNPs Q and R in cultured rat cortical neurons. Mol Cell Neurosci 2019; 98:97-108. [PMID: 31202892 DOI: 10.1016/j.mcn.2019.06.005] [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: 11/01/2018] [Revised: 05/08/2019] [Accepted: 06/12/2019] [Indexed: 11/17/2022] Open
Abstract
Local translation plays important roles in the maintenance and various functions of axons, and dysfunctions of local translation in axons are implicated in various neurological diseases. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA binding proteins with multiple functions in RNA metabolism. Here, we identified 20 hnRNPs in the axons of cultured rat cortical neurons by interrogating published axon mass spectrometric databases with rat protein databases. Among those identified in axons are highly related hnRNPs Q and R. RT-PCR analysis indicated that axons also contained low levels of hnRNPs Q and R mRNAs. We further found that BDNF treatments raised the levels of hnRNPs Q and R proteins in whole neurons and axons. BDNF also increased the level of poly(A) RNA as well as the proportion of poly(A) RNA granules containing hnRNPs Q and R in the axon. However, following severing the connection between the cell bodies and axons, BDNF did not affect the levels of hnRNPs Q and R, the content of poly(A) RNA, or the colocalization of poly(A) RNA and hnRNPs Q and R in the axon any more, although BDNF still stimulated the local translation in severed axons as it did in intact axons. The results are consistent with that BDNF enhances the axonal transport of RNA granules. The results further suggest that hnRNPs Q and R play a role in the mechanism underlying the enhancement of axonal RNA transport by BDNF.
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Affiliation(s)
- Hui-Wen Chung
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.
| | - Ju-Chen Weng
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-En King
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Fan Chuang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.
| | - Wei-Yuan Chow
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Yen-Chung Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan; Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan.
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10
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Dzakah EE, Waqas A, Wei S, Yu B, Wang X, Fu T, Liu L, Shan G. Loss of miR-83 extends lifespan and affects target gene expression in an age-dependent manner in Caenorhabditis elegans. J Genet Genomics 2018; 45:651-662. [PMID: 30595472 DOI: 10.1016/j.jgg.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/11/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the post-transcriptional regulation of protein-coding genes. miRNAs modulate lifespan and the aging process in a variety of organisms. In this study, we identified a role of miR-83 in regulating lifespan of Caenorhabditis elegans. mir-83 mutants exhibited extended lifespan, and the overexpression of miR-83 was sufficient to decrease the prolonged lifespan of the mutants. We observed upregulation of the expression levels of a set of miR-83 target genes in young mir-83 mutant adults; while different sets of genes were upregulated in older mir-83 mutant adults. In vivo assays showed that miR-83 regulated expression of target genes including din-1, spp-9 and col-178, and we demonstrated that daf-16 and din-1 were required for the extension of lifespan in the mir-83 mutants. The regulation of din-1 by miR-83 during aging resulted in the differential expression of din-1 targets such as gst-4 and gst-10. In daf-2 mutants, the expression level of miR-83 was significantly reduced compared to wild-type animals. We identified a role for miR-83 in modulating lifespan in C. elegans and provided molecular insights into its functional mechanism.
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Affiliation(s)
- Emmanuel Enoch Dzakah
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast 03321, Ghana
| | - Ahmed Waqas
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shuai Wei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Bin Yu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xiaolin Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Tao Fu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Lei Liu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ge Shan
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Centre for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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11
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Lee HC, Jung SH, Hwang HJ, Kang D, De S, Dudekula DB, Martindale JL, Park B, Park SK, Lee EK, Lee JH, Jeong S, Han K, Park HJ, Ko YG, Gorospe M, Lee JS. WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. Nucleic Acids Res 2017; 45:6894-6910. [PMID: 28472401 PMCID: PMC5499809 DOI: 10.1093/nar/gkx307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins (RBPs) are involved in mRNA splicing, maturation, transport, translation, storage and turnover. Here, we identified ACOT7 mRNA as a novel target of human WIG1. ACOT7 mRNA decay was triggered by the microRNA miR-9 in a WIG1-dependent manner via classic recruitment of Argonaute 2 (AGO2). Interestingly, AGO2 was also recruited to ACOT7 mRNA in a WIG1-dependent manner in the absence of miR-9, which indicates an alternative model whereby WIG1 controls AGO2-mediated gene silencing. The WIG1–AGO2 complex attenuated translation initiation via an interaction with translation initiation factor 5B (eIF5B). These results were confirmed using a WIG1 tethering system based on the MS2 bacteriophage coat protein and a reporter construct containing an MS2-binding site, and by immunoprecipitation of WIG1 and detection of WIG1-associated proteins using liquid chromatography-tandem mass spectrometry. We also identified WIG1-binding motifs using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation analyses. Altogether, our data indicate that WIG1 governs the miRNA-dependent and the miRNA-independent recruitment of AGO2 to lower the stability of and suppress the translation of ACOT7 mRNA.
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Affiliation(s)
- Hyung Chul Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Seung Hee Jung
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Hyun Jung Hwang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Donghee Kang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Byungkyu Park
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Seung Kuk Park
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Sunjoo Jeong
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Kyungsook Han
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Heon Joo Park
- Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Department of Microbiology, Inha University College of Medicine, Incheon 22212, Korea
| | - Young-Gyu Ko
- Division of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jae-Seon Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
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12
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An in vitro technique to identify the RNA binding-site sequences for RNA-binding proteins. Biotechniques 2017; 63:28-33. [DOI: 10.2144/000114567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/12/2017] [Indexed: 11/23/2022] Open
Abstract
RNA–protein interactions play a major role in gene regulation. Although many techniques to analyze RNA–protein interactions have been developed, noteworthy challenges such as determining the RNA sequences that bind RNA-binding proteins (RBPs) remain unsolved. Here, we describe a novel technique using a 4-thio-uridine-incorporated RNA pool to identify the RBP-binding consensus sequences for RBPs produced by in vitro transcription and translation. To confirm the fidelity of this approach, we determined the consensus RBP-binding sequence for RBFOX2, UGC(A/U)(A/U)NU, which is very similar to the known RBFOX2-binding sequence, UGCAUG. Using our method, consensus RBP-binding sequences were determined for three RBPs, namely FUS (fused in sarcoma), SFPQ (splicing factor proline and glutamine rich), and SAM68 (Src-Associated substrate in Mitosis 68 kDa). The consensus RBP-binding sequences for these RBPs were confirmed by RNA–protein complex immunoprecipitation–PCR analysis.
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13
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Kloetgen A, Borkhardt A, Hoell JI, McHardy AC. The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ 2016; 4:e2619. [PMID: 27812418 PMCID: PMC5088580 DOI: 10.7717/peerj.2619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/27/2016] [Indexed: 01/13/2023] Open
Abstract
Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, respectively, under the GNU GPLv3 license.
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Affiliation(s)
- Andreas Kloetgen
- Department for Algorithmic Bioinformatics, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf , Düsseldorf , Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine Universität Düsseldorf , Düsseldorf , Germany
| | - Alice C McHardy
- Department for Algorithmic Bioinformatics, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
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14
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Lien PTK, Izumikawa K, Muroi K, Irie K, Suda Y, Irie K. Analysis of the Physiological Activities of Scd6 through Its Interaction with Hmt1. PLoS One 2016; 11:e0164773. [PMID: 27776129 PMCID: PMC5077174 DOI: 10.1371/journal.pone.0164773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/30/2016] [Indexed: 01/26/2023] Open
Abstract
Scd6, a yeast homologue of human RAP55, is a component of messenger ribonucleoproteins (mRNPs) that repress translation by binding to translation initiation factors, and also is a decapping activator along with the binding partners Edc3 and Dhh1. Herein, we report that Scd6 is a substrate of the intrinsic protein arginine methyltransferase, Hmt1, in budding yeast Saccharomyces cerevisiae. Mass spectrometric analysis revealed that several arginine residues within the Scd6 RGG motif, which is important for mRNA binding, were methylated in Hmt1 dependent manner. Under stress conditions such as glucose starvation, Scd6 localized to cytoplasmic processing bodies (P-bodies) wherein translationally repressed mRNPs and untranslated mRNAs accumulate. Localization of Scd6 to P-bodies was impaired in hmt1 deletion mutant and in the presence of methylation-deficient substitution of Scd6. In addition, deletion of scd6 and dhh1 led to severe synthetic growth defect at high temperature. Methylation-deficient mutation of Scd6 suppressed the phenotypic defects of scd6 dhh1 double mutant, whereas methylation-mimic mutation did not, suggesting that the arginine methylation might negatively regulate Scd6 function relating to Dhh1. Therefore, the present data suggest that Hmt1-based arginine methylation is required for Scd6 localization and function.
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Affiliation(s)
- Pham Thi Kim Lien
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiichi Izumikawa
- Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Kei Muroi
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
- * E-mail:
| | - Kenji Irie
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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15
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Fred RG, Mehrabi S, Adams CM, Welsh N. PTB and TIAR binding to insulin mRNA 3'- and 5'UTRs; implications for insulin biosynthesis and messenger stability. Heliyon 2016; 2:e00159. [PMID: 27699280 PMCID: PMC5035359 DOI: 10.1016/j.heliyon.2016.e00159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 09/09/2016] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES Insulin expression is highly controlled on the posttranscriptional level. The RNA binding proteins (RBPs) responsible for this result are still largely unknown. METHODS AND RESULTS To identify RBPs that bind to insulin mRNA we performed mass spectrometry analysis on proteins that bound synthetic oligonucloetides mimicing the 5'- and the 3'-untranslated regions (UTRs) of rat and human insulin mRNA in vitro. We observed that the RBPs heterogeneous nuclear ribonucleoprotein (hnRNP) U, polypyrimidine tract binding protein (PTB), hnRNP L and T-cell restricted intracellular antigen 1-related protein (TIA-1-related protein; TIAR) bind to insulin mRNA sequences, and that the in vitro binding affinity of these RBPs changed when INS-1 cells were exposed to glucose, 3-isobutyl-1-methylxanthine (IBMX) or nitric oxide. High glucose exposure resulted in a modest increase in PTB and TIAR binding to an insulin mRNA sequence. The inducer of nitrosative stress DETAnonoate increased markedly hnRNP U and TIAR mRNA binding. An increased PTB to TIAR binding ratio in vitro correlated with higher insulin mRNA levels and insulin biosynthesis rates in INS-1 cells. To further investigate the importance of RNA-binding proteins for insulin mRNA stability, we decreased INS-1 and EndoC-βH1 cell levels of PTB and TIAR by RNAi. In both cell lines, decreased levels of PTB resulted in lowered insulin mRNA levels while decreased levels of TIAR resulted in increased insulin mRNA levels. Thapsigargin-induced stress granule formation was associated with a redistribution of TIAR from the cytosol to stress granules. CONCLUSIONS These experiments indicate that alterations in insulin mRNA stability and translation correlate with differential RBP binding. We propose that the balance between PTB on one hand and TIAR on the other participates in the control of insulin mRNA stability and utilization for insulin biosynthesis.
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Affiliation(s)
- Rikard G Fred
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Syrina Mehrabi
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Christopher M Adams
- Department of Biological and Medical Mass Spectrometry, Uppsala University, Uppsala, Sweden
| | - Nils Welsh
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
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16
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Kumachi S, Husimi Y, Nemoto N. An RNA Binding Peptide Consisting of Four Types of Amino Acid by in Vitro Selection Using cDNA Display. ACS OMEGA 2016; 1:52-57. [PMID: 30023471 PMCID: PMC6044570 DOI: 10.1021/acsomega.6b00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/17/2016] [Indexed: 05/06/2023]
Abstract
RNA-protein interactions have a central role in the living world. In this article, we examined whether primitive peptides (30 residues) consisting of four types of amino acid (Gly, Ala, Asp, and Val) could interact with tRNA as a model of primitive RNAs in the RNA world. By in vitro selection of binding peptides using the cDNA display method, a characteristic peptide was selected from a random peptide library and assayed by electrophoretic mobility shift and pull-down assays. Interestingly, the selected peptide bound to a single-stranded region including a loop structure of an RNA molecule with some sequence specificity.
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Affiliation(s)
- Shigefumi Kumachi
- Graduate
School of Science and Engineering, Saitama
University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yuzuru Husimi
- SOKENDAI
(The Graduate University for Advanced Studies), Shonan International Village, Hayama, Kanagawa 240-0193, Japan
| | - Naoto Nemoto
- Graduate
School of Science and Engineering, Saitama
University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
- E-mail: . Fax: +81-48-858-3531. Tel: +81-48-858-3531
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17
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Loiselle JJ, Tessier SJ, Sutherland LC. Post-transcriptional regulation of Rbm5 expression in undifferentiated H9c2 myoblasts. In Vitro Cell Dev Biol Anim 2015; 52:327-336. [PMID: 26659391 PMCID: PMC4833810 DOI: 10.1007/s11626-015-9976-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/04/2015] [Indexed: 12/20/2022]
Abstract
We previously examined the expression of Rbm5 during myoblast differentiation and found significantly more protein in the early stages of skeletal myoblast differentiation than during the later stages. We decided to determine if this elevated level was necessary for differentiation. Our hypothesis was that if high levels of Rbm5 protein expression were necessary for the initiation of skeletal myoblast differentiation, then inhibition of expression would prevent differentiation. Our long-term objective is to inhibit Rbm5 expression and examine the effect on H9c2 differentiation. Towards this end, stable knockdown clones and transient knockdown populations were generated. Expression analyses in H9c2 myoblasts demonstrated significant Rbm5 messenger RNA (mRNA) inhibition but, surprisingly, no effect on RBM5 protein levels. Expression of the Rbm5 paralogue Rbm10 was examined in order to (a) ensure no off-target knockdown effect, and (b) investigate any possible compensatory effects. RBM10 protein levels were found to be elevated, in both the clonal and transiently transfected populations. These results suggest that myoblast RBM5 expression is regulated by a process that includes RNA sequestration and/or controlled translation, and that (a) RBM5 function is compensated for by RBM10, and/or (b) RBM5 regulates RBM10 expression. We have developed a model to describe our findings, and suggest further experiments for testing its validity. Since upregulation of Rbm10 might compensate for downregulated Rbm5, and consequently might mask any potential knockdown effect, it could lead to incorrect conclusions regarding the importance of Rbm5 for differentiation. It is therefore imperative to determine how both RBM5 and RBM10 protein expression is regulated.
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Affiliation(s)
- Julie J Loiselle
- Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada. .,AMRIC, Health Sciences North, 41 Ramsey Lake Road, Sudbury, ON, P3E 5J1, Canada.
| | - Sarah J Tessier
- Department of Biology, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | - Leslie C Sutherland
- Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada.,AMRIC, Health Sciences North, 41 Ramsey Lake Road, Sudbury, ON, P3E 5J1, Canada.,Department of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada.,Division of Medical Sciences, Northern Ontario School of Medicine, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada.,Department of Medicine, Division of Medical Oncology, University of Ottawa, Ottawa, ON, Canada
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18
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Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PLoS Biol 2015; 13:e1002307. [PMID: 26587879 PMCID: PMC4654594 DOI: 10.1371/journal.pbio.1002307] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022] Open
Abstract
Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport chain (ETC) complex I as well as hundreds of other mRNAs with nonmitochondrial functions. The many concerted and conserved changes in the RNA targets of Puf proteins strongly support an extensive role of RNA binding proteins in coordinating gene expression, as originally proposed by Keene. Rewiring of Puf-coordinated mRNA targets and transcriptional control of the same genes occurred at different points in evolution, suggesting that there have been distinct adaptations via RNA binding proteins and transcription factors. The changes in Puf targets and in the Puf proteins indicate an integral involvement of RNA binding proteins and their RNA targets in the adaptation, reprogramming, and function of gene expression. A map of the evolutionary history of Puf proteins and their RNA targets shows that reprogramming of global gene expression programs via adaptive mutations that affect protein-RNA interactions is an important source of biological diversity. We set out to trace the evolutionary history of an RNA binding protein and how its interactions with targets change over evolution. Identifying this natural history is a step toward understanding the critical differences between organisms and how gene expression programs are rewired during evolution. Using bioinformatics and experimental approaches, we broadly surveyed the evolution of binding targets of a particular family of RNA binding proteins—the Puf proteins, whose protein sequences and target RNA sequences are relatively well-characterized—across 99 eukaryotic species. We found five groups of species in which targets have been conserved for at least 100 million years and then took advantage of genome sequences from a large number of fungal species to deeply investigate the conservation and changes in Puf proteins and their RNA targets. Our analyses identified multiple and extensive reconfigurations during the natural history of fungi and suggest that RNA binding proteins and their RNA targets are profoundly involved in evolutionary reprogramming of gene expression and help define distinct programs unique to each organism. Continuing to uncover the natural history of RNA binding proteins and their interactions will provide a unique window into the gene expression programs of present day species and point to new ways to engineer gene expression programs.
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Affiliation(s)
- Gregory J. Hogan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (POB); (DH)
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- ChEM-H Institute, Stanford University, Stanford, California, United States of America
- * E-mail: (POB); (DH)
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19
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Kim HH, Lee SJ, Gardiner AS, Perrone-Bizzozero NI, Yoo S. Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1. Nucleic Acids Res 2015; 43:7432-46. [PMID: 26152301 PMCID: PMC4551932 DOI: 10.1093/nar/gkv699] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/29/2015] [Indexed: 11/13/2022] Open
Abstract
Interactions of RNA-binding proteins (RBPs) with their target transcripts are essential for regulating gene expression at the posttranscriptional level including mRNA export/localization, stability, and translation. ZBP1 and HuD are RBPs that play pivotal roles in mRNA transport and local translational control in neuronal processes. While HuD possesses three RNA recognition motifs (RRMs), ZBP1 contains two RRMs and four K homology (KH) domains that either increase target specificity or provide a multi-target binding capability. Here we used isolated cis-element sequences of the target mRNA to examine directly protein-RNA interactions in cell-free systems. We found that both ZBP1 and HuD bind the zipcode element in rat β-actin mRNA's 3' UTR. Differences between HuD and ZBP1 were observed in their binding preference to the element. HuD showed a binding preference for U-rich sequence. In contrast, ZBP1 binding to the zipcode RNA depended more on the structural level, as it required the proper spatial organization of a stem-loop that is mainly determined by the U-rich element juxtaposed to the 3' end of a 5'-ACACCC-3' motif. On the basis of this work, we propose that ZBP1 and HuD bind to overlapping sites in the β-actin zipcode, but they recognize different features of this target sequence.
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Affiliation(s)
- Hak Hee Kim
- Nemours Biomedical Research, Alfred I. duPont Hosp. for Children, Wilmington, DE 19803, USA
| | - Seung Joon Lee
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Amy S Gardiner
- Department of Neuroscience, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Nora I Perrone-Bizzozero
- Department of Neuroscience, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Soonmoon Yoo
- Nemours Biomedical Research, Alfred I. duPont Hosp. for Children, Wilmington, DE 19803, USA
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20
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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21
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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22
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Yan G, Yan X. Ribosomal proteomics: Strategies, approaches, and perspectives. Biochimie 2015; 113:69-77. [PMID: 25869001 DOI: 10.1016/j.biochi.2015.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
Abstract
Over the past few decades, proteomic research has seen unprecedented development due to technological advancement. However, whole-cell proteomics still has limitations with respect to sample complexity and the accuracy of determining protein locations. To deal with these limitations, several subcellular proteomic studies have been initiated. Nevertheless, compared to other subcellular proteomic fields, such as mitochondrial proteomics, ribosomal proteomics has lagged behind due to the long-held idea that the ribosome is just a translation machine. Recently, with the proposed ribosome filter hypothesis and subsequent studies of ribosome-specific regulatory capacity, ribosomal proteomics has become a promising chapter for both proteomic and ribosomal research. In this review, we discuss the current strategies and approaches in ribosomal proteomics and the efficacies as well as disadvantages of individual approaches for further improvement.
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Affiliation(s)
- Guokai Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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23
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Posttranscriptional adaptations of the vascular endothelium to hypoxia. Curr Opin Hematol 2015; 22:243-51. [PMID: 25767954 DOI: 10.1097/moh.0000000000000139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE OF REVIEW Remarkable new advances have been made in the field of posttranscriptional gene regulation over recent years. These include the revelation of noncoding RNAs, such as microRNAs, antisense transcripts and their interactions with RNA-binding proteins (RBPs) in the context of both health and disease settings, such as hypoxia. In particular, these discoveries bear much relevance to the field of vascular biology, which historically has focused upon transcriptional processes. Thus, the contributions of these posttranscriptional gene regulatory mechanisms to vascular and endothelial biology represent a newer concept that warrants discussion. RECENT FINDINGS Recent studies have revealed two emerging themes that are critical to endothelial/vascular biology and function. First is the functional integration between the microRNA pathway and the cellular hypoxic response, which, in addition to specific microRNAs, involves key components of the microRNA biogenesis machinery. A key concept here is the regulation of a master transcriptional programme through posttranscriptional mechanisms. The second major theme involves the dynamic interactions between RBPs, microRNAs and antisense RNAs. The condition-dependent collaborations and competitions between these different classes of posttranscriptional regulators reveal a critical layer of control for gene expression. SUMMARY Taken together, these findings bear significant diagnostic and therapeutic implications for vascular disease.
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Walsh MJ, Cooper-Knock J, Dodd JE, Stopford MJ, Mihaylov SR, Kirby J, Shaw PJ, Hautbergue GM. Invited review: decoding the pathophysiological mechanisms that underlie RNA dysregulation in neurodegenerative disorders: a review of the current state of the art. Neuropathol Appl Neurobiol 2015; 41:109-34. [PMID: 25319671 PMCID: PMC4329338 DOI: 10.1111/nan.12187] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/07/2014] [Indexed: 12/12/2022]
Abstract
Altered RNA metabolism is a key pathophysiological component causing several neurodegenerative diseases. Genetic mutations causing neurodegeneration occur in coding and noncoding regions of seemingly unrelated genes whose products do not always contribute to the gene expression process. Several pathogenic mechanisms may coexist within a single neuronal cell, including RNA/protein toxic gain-of-function and/or protein loss-of-function. Genetic mutations that cause neurodegenerative disorders disrupt healthy gene expression at diverse levels, from chromatin remodelling, transcription, splicing, through to axonal transport and repeat-associated non-ATG (RAN) translation. We address neurodegeneration in repeat expansion disorders [Huntington's disease, spinocerebellar ataxias, C9ORF72-related amyotrophic lateral sclerosis (ALS)] and in diseases caused by deletions or point mutations (spinal muscular atrophy, most subtypes of familial ALS). Some neurodegenerative disorders exhibit broad dysregulation of gene expression with the synthesis of hundreds to thousands of abnormal messenger RNA (mRNA) molecules. However, the number and identity of aberrant mRNAs that are translated into proteins - and how these lead to neurodegeneration - remain unknown. The field of RNA biology research faces the challenge of identifying pathophysiological events of dysregulated gene expression. In conclusion, we discuss current research limitations and future directions to improve our characterization of pathological mechanisms that trigger disease onset and progression.
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Affiliation(s)
- M J Walsh
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - J Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - J E Dodd
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - M J Stopford
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - S R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - J Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - P J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - G M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
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25
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Yao C, Weng L, Shi Y. Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq. Methods Mol Biol 2014; 1126:399-410. [PMID: 24549678 DOI: 10.1007/978-1-62703-980-2_27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Eukaryotic genomes encode a large number of RNA-binding proteins, which play critical roles in many aspects of gene regulation. To functionally characterize these proteins, a key step is to map their interactions with target RNAs. UV crosslinking and immunoprecipitation coupled with high-throughput sequencing has become the standard method for this purpose. Here we describe the detailed procedure that we have used to characterize the protein-RNA interactions of the mRNA 3' processing factors.
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Affiliation(s)
- Chengguo Yao
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
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26
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Faoro C, Ataide SF. Ribonomic approaches to study the RNA-binding proteome. FEBS Lett 2014; 588:3649-64. [PMID: 25150170 DOI: 10.1016/j.febslet.2014.07.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 01/23/2023]
Abstract
Gene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).
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Affiliation(s)
- Camilla Faoro
- School of Molecular Biosciences, University of Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Molecular Biosciences, University of Sydney, NSW, Australia.
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27
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Kloetgen A, Münch PC, Borkhardt A, Hoell JI, McHardy AC. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics 2014; 14:102-14. [PMID: 24951655 PMCID: PMC4471435 DOI: 10.1093/bfgp/elu020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Our understanding of transcriptional gene regulation has dramatically increased over the past decades, and many regulators of gene expression, such as transcription factors, have been analyzed extensively. Additionally, in recent years, deeper insights into the physiological roles of RNA have been obtained. More precisely, splicing, polyadenylation, various modifications, localization and the translation of messenger RNAs (mRNAs) are regulated by their interaction with RNA-binding proteins (RBPs). New technologies now enable the analysis of this regulation at different levels. A technique known as ultraviolet (UV) cross-linking and immunoprecipitation (CLIP) allows us to determine physical protein–RNA interactions on a genome-wide scale. UV cross-linking introduces covalent bonds between interacting RBPs and RNAs. In combination with immunoprecipitation and deep sequencing techniques, tens of millions of short reads (representing bound RNAs by an RBP of interest) are generated and are used to characterize the regulatory network mediated by an RBP. Other methods, such as mass spectrometry, can also be used for characterization of cross-linked RBPs and RNAs instead of CLIP methods. In this review, we discuss experimental and computational methods for the generation and analysis of CLIP data. The computational methods include short-read alignment, annotation and RNA-binding motif discovery. We describe the challenges of analyzing CLIP data and indicate areas where improvements are needed.
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Affiliation(s)
| | | | | | | | - Alice C McHardy
- Corresponding author. Alice C. McHardy, Heinrich-Heine University, Department of Algorithmic Bioinformatics, Universitaetsstrasse 1, 40225 Duesseldorf, Germany. Tel.: +49-211-8110427; Fax: +49-211-8113464; E-mail:
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28
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Chen CYA, Shyu AB. Emerging mechanisms of mRNP remodeling regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:713-22. [PMID: 24923990 DOI: 10.1002/wrna.1241] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/11/2014] [Accepted: 04/17/2014] [Indexed: 12/12/2022]
Abstract
The assembly and remodeling of the components of messenger ribonucleoprotein particles (mRNPs) are important in determining the fate of a messenger RNA (mRNA). A combination of biochemical and cell biology research, recently complemented by genome-wide high-throughput approaches, has led to significant progress on understanding the formation, dynamics, and function of mRNPs. These studies also advanced the challenging process of identifying the evolving constituents of individual mRNPs at various stages during an mRNA's lifetime. While research on mRNP remodeling in general has been gaining momentum, there has been relatively little attention paid to the regulatory aspect of mRNP remodeling. Here, we discuss the results of some new studies and potential mechanisms for regulation of mRNP remodeling.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, The University of Texas, Medical School at Houston, Houston, TX, USA
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29
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Kurisaki I, Takayanagi M, Nagaoka M. Combined mechanism of conformational selection and induced fit in U1A-RNA molecular recognition. Biochemistry 2014; 53:3646-57. [PMID: 24828852 DOI: 10.1021/bi401708q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this study, we demonstrate that U1A-RNA molecular recognition is mediated by a combined mechanism of conformational selection and induced fit. The binding of U1A to RNA has been discussed in the context of induced fit that involves the reorientation of the α-helix in the C-terminal region (Helix-C) of U1A to permit RNA access only when U1A correctly recognizes RNA. However, according to our molecular dynamics simulations, even in the absence of RNA, Helix-C spontaneously reoriented to permit RNA access. Nonetheless, such a conformational change was still incomplete. Helix-C was often partially or even fully unfolded and in an infrequent RNA-accessible conformation, which can be detected using state-of-the-art nuclear magnetic resonance methodology. These results suggest that the formation of an energetically stabilized complex is promoted by specific interactions between U1A and RNA. In conclusion, in the recognition of RNA by U1A protein, we propose a combined mechanism that requires the reorientation of Helix-C and the subsequent contact with RNA through conformational selection, although the stabilization of the U1A-RNA complex is caused by induced fit. We further propose a modification to the conventional assumption regarding the mechanism of U1A-RNA molecular recognition.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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30
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Wickramasinghe VO, Andrews R, Ellis P, Langford C, Gurdon JB, Stewart M, Venkitaraman AR, Laskey RA. Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP. Nucleic Acids Res 2014; 42:5059-71. [PMID: 24510098 PMCID: PMC4005691 DOI: 10.1093/nar/gku095] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 01/21/2023] Open
Abstract
The nuclear phase of the gene expression pathway culminates in the export of mature messenger RNAs (mRNAs) to the cytoplasm through nuclear pore complexes. GANP (germinal- centre associated nuclear protein) promotes the transfer of mRNAs bound to the transport factor NXF1 to nuclear pore complexes. Here, we demonstrate that GANP, subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex, promotes selective nuclear export of a specific subset of mRNAs whose transport depends on NXF1. Genome-wide gene expression profiling showed that half of the transcripts whose nuclear export was impaired following NXF1 depletion also showed reduced export when GANP was depleted. GANP-dependent transcripts were highly expressed, yet short-lived, and were highly enriched in those encoding central components of the gene expression machinery such as RNA synthesis and processing factors. After injection into Xenopus oocyte nuclei, representative GANP-dependent transcripts showed faster nuclear export kinetics than representative transcripts that were not influenced by GANP depletion. We propose that GANP promotes the nuclear export of specific classes of mRNAs that may facilitate rapid changes in gene expression.
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Affiliation(s)
- Vihandha O. Wickramasinghe
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Robert Andrews
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Peter Ellis
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Cordelia Langford
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - John B. Gurdon
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Murray Stewart
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ashok R. Venkitaraman
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ronald A. Laskey
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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31
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Leppek K, Stoecklin G. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. Nucleic Acids Res 2013; 42:e13. [PMID: 24157833 PMCID: PMC3902943 DOI: 10.1093/nar/gkt956] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Determining the composition of messenger ribonucleoprotein (mRNP) particles is essential for a comprehensive understanding of the complex mechanisms underlying mRNA regulation, but is technically challenging. Here we present an RNA-based method to identify RNP components using a modified streptavidin (SA)-binding RNA aptamer termed S1m. By optimizing the RNA aptamer S1 in structure and repeat conformation, we improved its affinity for SA and found a 4-fold repeat of S1m (4×S1m) to be more efficient than the established MS2 and PP7 systems from bacteriophages. We then attached the AU-rich element (ARE) of tumor necrosis factor alpha (TNFα), a well-known RNA motif that induces mRNA degradation, via 4×S1m to a SA matrix, and used the resulting RNA affinity column to purify ARE-binding proteins (BPs) from cellular extracts. By quantitative mass spectrometry using differential dimethyl labeling, we identified the majority of established ARE-BPs and detected several RNA-BPs that had previously not been associated with AREs. For two of these proteins, Rbms1 and Roxan, we confirmed specific binding to the TNFα ARE. The optimized 4×S1m aptamer, therefore, provides a powerful tool for the discovery of mRNP components in a single affinity purification step.
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Affiliation(s)
- Kathrin Leppek
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany and DKFZ-ZMBH Alliance
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32
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Papadodima O, Chatziioannou A, Patrinou-Georgoula M, Kolisis FN, Pletsa V, Guialis A. HuR-regulated mRNAs associated with nuclear hnRNP A1-RNP complexes. Int J Mol Sci 2013; 14:20256-81. [PMID: 24152440 PMCID: PMC3821614 DOI: 10.3390/ijms141020256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 09/06/2013] [Accepted: 09/16/2013] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicating their concerted function in mRNA metabolism.
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Affiliation(s)
- Olga Papadodima
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
| | - Aristotelis Chatziioannou
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
| | - Meropi Patrinou-Georgoula
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece; E-Mail:
| | - Vasiliki Pletsa
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
- Authors to whom correspondence should be addressed; E-Mails: (V.P.); (A.G.); Tel.: +30-210-7273-754 (V.P. & A.G.); Fax: +30-210-7273-677 (V.P. & A.G.)
| | - Apostolia Guialis
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
- Authors to whom correspondence should be addressed; E-Mails: (V.P.); (A.G.); Tel.: +30-210-7273-754 (V.P. & A.G.); Fax: +30-210-7273-677 (V.P. & A.G.)
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33
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Ho JJD, Marsden PA. Competition and collaboration between RNA-binding proteins and microRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:69-86. [PMID: 24124109 DOI: 10.1002/wrna.1197] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/21/2013] [Accepted: 08/27/2013] [Indexed: 01/08/2023]
Abstract
Posttranscriptional regulation of mRNA species represents a major regulatory checkpoint in the control of gene expression. Historically, RNA-binding proteins (RBPs) have been regarded as the primary regulators of mRNA stability and translation. More recently, however, microRNAs have emerged as a class of potent and pervasive posttranscriptional rheostats that similarly affect mRNA stability and translation. The observation that both microRNAs and RBPs regulate mRNA stability and translation has initiated a newer area of research that involves the examination of dynamic interactions between these two important classes of posttranscriptional regulators, the myriad of factors that influence these biological interactions, and ultimately, their effects on target mRNAs. Specifically, microRNAs and RBPs can act synergistically to effect mRNA destabilization and translational inhibition. They can also engage in competition with each other and exert opposing effects on target mRNAs. To date, several key studies have provided critical details regarding the mechanisms and principles of interaction between these molecules. Additionally, these findings raise important questions regarding the regulation of these interactions, including the roles of posttranslational modification, subcellular localization, target inhibition versus activation, and changes in expression levels of these regulatory factors, especially under stimulus- and cell-specific conditions. Indeed, further experimentation is warranted to address these key issues that pertain to the collaboration and competition between microRNAs and RBPs. Significantly, the elucidation of these important details bears critical implications for disease management, especially for those diseases in which these cellular factors are dysregulated.
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Affiliation(s)
- J J David Ho
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
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Yamanishi M, Ito Y, Kintaka R, Imamura C, Katahira S, Ikeuchi A, Moriya H, Matsuyama T. A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae provides a ″terminatome″ toolbox. ACS Synth Biol 2013; 2:337-47. [PMID: 23654277 DOI: 10.1021/sb300116y] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The terminator regions of eukaryotes encode functional elements in the 3' untranslated region (3'-UTR) that influence the 3'-end processing of mRNA, mRNA stability, and translational efficiency, which can modulate protein production. However, the contribution of these terminator regions to gene expression remains unclear, and therefore their utilization in metabolic engineering or synthetic genetic circuits has been limited. Here, we comprehensively evaluated the activity of 5302 terminator regions from a total of 5880 genes in the budding yeast Saccharomyces cerevisiae by inserting each terminator region downstream of the P TDH3 - green fluorescent protein (GFP) reporter gene and measuring the fluorescent intensity of GFP. Terminator region activities relative to that of the PGK1 standard terminator ranged from 0.036 to 2.52, with a mean of 0.87. We thus could isolate the most and least active terminator regions. The activities of the terminator regions showed a positive correlation with mRNA abundance, indicating that the terminator region is a determinant of mRNA abundance. The least active terminator regions tended to encode longer 3'-UTRs, suggesting the existence of active degradation mechanisms for those mRNAs. The terminator regions of ribosomal protein genes tended to be the most active, suggesting the existence of a common regulator of those genes. The ″terminatome″ (the genome-wide set of terminator regions) thus not only provides valuable information to understand the modulatory roles of terminator regions on gene expression but also serves as a useful toolbox for the development of metabolically and genetically engineered yeast.
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Affiliation(s)
| | | | - Reiko Kintaka
- Research Core for Interdisciplinary
Sciences, Okayama University, 3-1-1 Tsushima-Naka,
Kita-ku, Okayama, 700-8530, Japan
| | | | | | | | - Hisao Moriya
- Research Core for Interdisciplinary
Sciences, Okayama University, 3-1-1 Tsushima-Naka,
Kita-ku, Okayama, 700-8530, Japan
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35
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York A, Fodor E. Biogenesis, assembly, and export of viral messenger ribonucleoproteins in the influenza A virus infected cell. RNA Biol 2013; 10:1274-82. [PMID: 23807439 PMCID: PMC3817148 DOI: 10.4161/rna.25356] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The flow of genetic information from sites of transcription within the nucleus to the cytoplasmic translational machinery of eukaryotic cells is obstructed by a physical blockade, the nuclear double membrane, which must be overcome in order to adhere to the central dogma of molecular biology, DNA makes RNA makes protein. Advancement in the field of cellular and molecular biology has painted a detailed picture of the molecular mechanisms from transcription of genes to mRNAs and their processing that is closely coupled to export from the nucleus. The rules that govern delivering messenger transcripts from the nucleus must be obeyed by influenza A virus, a member of the Orthomyxoviridae that has adopted a nuclear replication cycle. The negative-sense genome of influenza A virus is segmented into eight individual viral ribonucleoprotein (vRNP) complexes containing the viral RNA-dependent RNA polymerase and single-stranded RNA encapsidated in viral nucleoprotein. Influenza A virus mRNAs fall into three major categories, intronless, intron-containing unspliced and spliced. During evolutionary history, influenza A virus has conceived a way of negotiating the passage of viral transcripts from the nucleus to cytoplasmic sites of protein synthesis. The major mRNA nuclear export NXF1 pathway is increasingly implicated in viral mRNA export and this review considers and discusses the current understanding of how influenza A virus exploits the host mRNA export pathway for replication.
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Affiliation(s)
- Ashley York
- Sir William Dunn School of Pathology; University of Oxford; Oxford, United Kingdom
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36
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Aparicio LA, Abella V, Valladares M, Figueroa A. Posttranscriptional regulation by RNA-binding proteins during epithelial-to-mesenchymal transition. Cell Mol Life Sci 2013; 70:4463-77. [PMID: 23715860 PMCID: PMC3827902 DOI: 10.1007/s00018-013-1379-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/10/2013] [Accepted: 05/16/2013] [Indexed: 12/22/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT), one of the crucial steps for carcinoma cells to acquire invasive capacity, results from the disruption of cell–cell contacts and the acquisition of a motile mesenchymal phenotype. Although the transcriptional events controlling EMT have been extensively studied, in recent years, several posttranscriptional mechanisms have emerged as critical in the regulation of EMT during tumor progression. In this review, we highlight the regulation of posttranscriptional events in EMT by RNA-binding proteins (RBPs). RBPs are responsible for controlling pre-mRNA splicing, capping, and polyadenylation, as well as mRNA export, turnover, localization, and translation. We discuss the most relevant aspects of RBPs controlling the metabolism of EMT-related mRNAs, and describe the implication of novel posttranscriptional mechanisms regulating EMT in response to different signaling pathways. Novel insight into posttranscriptional regulation of EMT by RBPs is uncovering new therapeutic targets in cancer invasion and metastasis.
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Affiliation(s)
- Luis A Aparicio
- Servizo de Oncología Médica, Complejo Hospitalario Universitario A Coruña (CHUAC), SERGAS, A Coruña, Spain
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Zhou HL, Geng C, Luo G, Lou H. The p97-UBXD8 complex destabilizes mRNA by promoting release of ubiquitinated HuR from mRNP. Genes Dev 2013; 27:1046-58. [PMID: 23618873 DOI: 10.1101/gad.215681.113] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The assembly and disassembly of ribonucleoproteins (RNPs) are dynamic processes that control every step of RNA metabolism, including mRNA stability. However, our knowledge of how RNP remodeling is achieved is largely limited to RNA helicase functions. Here, we report a previously unknown mechanism that implicates the ATPase p97, a protein-remodeling machine, in the dynamic regulation of mRNP disassembly. We found that p97 and its cofactor, UBXD8, destabilize p21, MKP-1, and SIRT1, three established mRNA targets of the RNA-binding protein HuR, by promoting release of HuR from mRNA. Importantly, ubiquitination of HuR with a short K29 chain serves as the signal for release. When cells are subjected to stress conditions, the steady-state levels of HuR ubiquitination change, suggesting a new mechanism through which HuR mediates the stress response. Our studies reveal a new paradigm in RNA biology: nondegradative ubiquitin signaling-dependent disassembly of mRNP promoted by the p97-UBXD8 complex to control mRNA stability.
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Affiliation(s)
- Hua-Lin Zhou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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Shao J, Zhang J, Zhang Z, Jiang H, Lou X, Huang B, Foltz G, Lan Q, Huang Q, Lin B. Alternative polyadenylation in glioblastoma multiforme and changes in predicted RNA binding protein profiles. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:136-49. [PMID: 23421905 DOI: 10.1089/omi.2012.0098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Alternative polyadenylation (APA) is widely present in the human genome and plays a key role in carcinogenesis. We conducted a comprehensive analysis of the APA products in glioblastoma multiforme (GBM, one of the most lethal brain tumors) and normal brain tissues and further developed a computational pipeline, RNAelements (http://sysbio.zju.edu.cn/RNAelements/), using covariance model from known RNA binding protein (RBP) targets acquired by RNA Immunoprecipitation (RIP) analysis. We identified 4530 APA isoforms for 2733 genes in GBM, and found that 182 APA isoforms from 148 genes showed significant differential expression between normal and GBM brain tissues. We then focused on three genes with long and short APA isoforms that show inconsistent expression changes between normal and GBM brain tissues. These were myocyte enhancer factor 2D, heat shock factor binding protein 1, and polyhomeotic homolog 1 (Drosophila). Using the RNAelements program, we found that RBP binding sites were enriched in the alternative regions between the first and the last polyadenylation sites, which would result in the short APA forms escaping regulation from those RNA binding proteins. To the best of our knowledge, this report is the first comprehensive APA isoform dataset for GBM and normal brain tissues. Additionally, we demonstrated a putative novel APA-mediated mechanism for controlling RNA stability and translation for APA isoforms. These observations collectively lay a foundation for novel diagnostics and molecular mechanisms that can inform future therapeutic interventions for GBM.
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Affiliation(s)
- Jiaofang Shao
- Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, Hangzhou, China
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Simone LE, Keene JD. Mechanisms coordinating ELAV/Hu mRNA regulons. Curr Opin Genet Dev 2013; 23:35-43. [PMID: 23312841 PMCID: PMC3617084 DOI: 10.1016/j.gde.2012.12.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/05/2012] [Accepted: 12/12/2012] [Indexed: 12/25/2022]
Abstract
The 5' and 3' untranslated regions (UTRs) of messenger RNAs (mRNAs) function as platforms that can determine the fate of each mRNA individually and in aggregate. Multiple mRNAs that encode proteins that are functionally related often interact with RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) that coordinate their expression in time and space as RNA regulons within the ribonucleoprotein (RNP) infrastructure we term the ribonome. Recent ribonomic methods have emerged that can determine which mRNAs are bound and regulated by RBPs and ncRNAs, some of which act in combination to determine global outcomes. ELAV/Hu proteins bind to AU-rich elements (ARE) in mRNAs and regulate their stability from splicing to translation, and the ubiquitous HuR protein has been implicated in cancerous cell growth. Recent work is focused on mechanistic models of how ELAV/Hu proteins increase mRNA stability and translation by repressing microRNAs (miRs) and the RNA induced silencing complex (RISC) via ARE-based ribonucleosomes that may affect global functions of mRNA regulons.
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Affiliation(s)
- Laura E. Simone
- Department of Molecular Genetics & Microbiology Duke University Medical Center Durham, NC 27710
| | - Jack D. Keene
- Department of Molecular Genetics & Microbiology Duke University Medical Center Durham, NC 27710
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Krauss S, Griesche N, Jastrzebska E, Chen C, Rutschow D, Achmüller C, Dorn S, Boesch SM, Lalowski M, Wanker E, Schneider R, Schweiger S. Translation of HTT mRNA with expanded CAG repeats is regulated by the MID1-PP2A protein complex. Nat Commun 2013; 4:1511. [PMID: 23443539 DOI: 10.1038/ncomms2514] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/18/2013] [Indexed: 11/08/2022] Open
Abstract
Expansion of CAG repeats is a common feature of various neurodegenerative disorders, including Huntington's disease. Here we show that expanded CAG repeats bind to a translation regulatory protein complex containing MID1, protein phosphatase 2A and 40S ribosomal S6 kinase. Binding of the MID1-protein phosphatase 2A protein complex increases with CAG repeat size and stimulates translation of the CAG repeat expansion containing messenger RNA in a MID1-, protein phosphatase 2A- and mammalian target of rapamycin-dependent manner. Our data indicate that pathological CAG repeat expansions upregulate protein translation leading to an overproduction of aberrant protein and suggest that the MID1-complex may serve as a therapeutic target for the treatment of CAG repeat expansion disorders.
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Affiliation(s)
- Sybille Krauss
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 25, 53127 Bonn, Germany.
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41
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Hussey GS, Link LA, Brown AS, Howley BV, Chaudhury A, Howe PH. Establishment of a TGFβ-induced post-transcriptional EMT gene signature. PLoS One 2012; 7:e52624. [PMID: 23285117 PMCID: PMC3527574 DOI: 10.1371/journal.pone.0052624] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/20/2012] [Indexed: 12/31/2022] Open
Abstract
A major challenge in the clinical management of human cancers is to accurately stratify patients according to risk and likelihood of a favorable response. Stratification is confounded by significant phenotypic heterogeneity in some tumor types, often without obvious criteria for subdivision. Despite intensive transcriptional array analyses, the identity and validation of cancer specific ‘signature genes’ remains elusive, partially because the transcriptome does not mirror the proteome. The simplification associated with transcriptomic profiling does not take into consideration changes in the relative expression among transcripts that arise due to post-transcriptional regulatory events. We have previously shown that TGFβ post-transcriptionally regulates epithelial-mesenchymal transition (EMT) by causing increased expression of two transcripts, Dab2 and ILEI, by modulating hnRNP E1 phosphorylation. Using a genome-wide combinatorial approach involving expression profiling and RIP-Chip analysis, we have identified a cohort of translationally regulated mRNAs that are induced during TGFβ-mediated EMT. Coordinated translational regulation by hnRNP E1 constitutes a post-transcriptional regulon inhibiting the expression of related EMT-facilitating genes, thus enabling the cell to rapidly and coordinately regulate multiple EMT-facilitating genes.
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Affiliation(s)
- George S. Hussey
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Laura A. Link
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Andrew S. Brown
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Breege V. Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Philip H. Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail:
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Cassar PA, Stanford WL. Integrating post-transcriptional regulation into the embryonic stem cell gene regulatory network. J Cell Physiol 2012; 227:439-49. [PMID: 21503874 DOI: 10.1002/jcp.22787] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Stem cell behavior is orchestrated as a multilayered, concert of gene regulatory mechanisms collectively referred to as the gene regulatory network (GRN). Via cooperative mechanisms, transcriptional, epigenetic, and post-transcriptional regulators activate and repress gene expression to finely regulate stem cell self-renewal and commitment. Due to their tractability, embryonic stem cells (ESCs) serve as the model stem cell to dissect the complexities of the GRN, and discern its relation to stem cell fate. By way of high-throughput genomic analysis, targets of individual gene regulators have been established in ESCs. The compilation of these discrete networks has revealed convergent, multi-dimensional gene regulatory mechanisms involving transcription factors, epigenetic modifiers, non-coding RNA (ncRNA), and RNA-binding proteins. Here we highlight the seminal genomic studies that have shaped our understanding of the ESC GRN and describe alternate post-transcriptional gene regulatory mechanisms that require in depth analyses to draft networks that fully model ESC behavior.
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Affiliation(s)
- Paul A Cassar
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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McLennan Y, Polussa J, Tassone F, Hagerman R. Fragile x syndrome. Curr Genomics 2011; 12:216-24. [PMID: 22043169 PMCID: PMC3137006 DOI: 10.2174/138920211795677886] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 02/03/2023] Open
Abstract
Recent data from a national survey highlighted a significant difference in obesity rates in young fragile X males (31%) compared to age matched controls (18%). Fragile X syndrome (FXS) is the most common cause of intellectual disability in males and the most common single gene cause of autism. This X-linked disorder is caused by an expansion of a trinucleotide CGG repeat (>200) on the promotor region of the fragile X mental retardation 1 gene (FMR1). As a result, the promotor region often becomes methylated which leads to a deficiency or absence of the FMR1 protein (FMRP). Common characteristics of FXS include mild to severe cognitive impairments in males but less severe cognitive impairment in females. Physical features of FXS include an elongated face, prominent ears, and post-pubertal macroorchidism. Severe obesity in full mutation males is often associated with the Prader-Willi phenotype (PWP) which includes hyperphagia, lack of satiation after meals, and hypogonadism or delayed puberty; however, there is no deletion at 15q11-q13 nor uniparental maternal disomy. Herein, we discuss the molecular mechanisms leading to FXS and the Prader-Willi phenotype with an emphasis on mouse FMR1 knockout studies that have shown the reversal of weight increase through mGluR antagonists. Finally, we review the current medications used in treatment of FXS including the atypical antipsychotics that can lead to weight gain and the research regarding the use of targeted treatments in FXS that will hopefully have a significantly beneficial effect on cognition and behavior without weight gain.
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Affiliation(s)
- Yingratana McLennan
- Medical Investigation of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California Davis Health System, Sacramento, California, USA
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Brandt S, Raffetseder U, Djudjaj S, Schreiter A, Kadereit B, Michele M, Pabst M, Zhu C, Mertens PR. Cold shock Y-box protein-1 participates in signaling circuits with auto-regulatory activities. Eur J Cell Biol 2011; 91:464-71. [PMID: 21962637 DOI: 10.1016/j.ejcb.2011.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/04/2011] [Accepted: 07/06/2011] [Indexed: 02/07/2023] Open
Abstract
The cold shock protein Y-box (YB) binding-1 is an example of a highly regulated protein with pleiotropic functions. Besides activities as a transcription factor in the nucleus or regulator of translation in the cytoplasm, recent findings indicate extracellular effects and secretion via a non-classical secretion pathway. This review summarizes regulatory pathways in which YB-1 participates, all iterating auto-regulatory loops. Schematics are developed that elucidate the cold shock protein activities in (i) fine-tuning its own expression level following platelet-derived growth factor-B-, thrombin- or interferon-γ-dependent signaling, (ii) as a component of the messenger ribonucleoprotein (mRNP) complex for interleukin-2 synthesis in T-cell commitment/activation, (iii) pro-fibrogenic cell phenotypic changes mediated by transforming growth factor-β, and (iv) receptor Notch-3 cleavage and signal transduction. Emphasis is put forward on subcellular protein translocation mechanisms and underlying signaling pathways. These have mostly been analysed in cell culture systems and rarely in experimental models. In sum, YB-1 seems to fulfill a pacemaker role in diverse diseases, both inflammatory/pro-fibrogenic as well as tumorigenic. A clue towards potential intervention strategies may reside in the understanding of the outlined auto-regulatory loops and means to interfere with cycling pathways.
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Affiliation(s)
- Sabine Brandt
- Department of Nephrology, Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany
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45
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Vogel C, Silva GM, Marcotte EM. Protein expression regulation under oxidative stress. Mol Cell Proteomics 2011; 10:M111.009217. [PMID: 21933953 DOI: 10.1074/mcp.m111.009217] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress is known to affect both translation and protein turnover, but very few large scale studies describe protein expression under stress. We measure protein concentrations in Saccharomyces cerevisiae over the course of 2 h in response to a mild oxidative stress induced by diamide, providing detailed time-resolved information for 815 proteins, with additional data for another ~1,100 proteins. For the majority of proteins, we discover major differences between the global transcript and protein response. Although mRNA levels often return to baseline 1 h after treatment, protein concentrations continue to change. Integrating our data with features of translation and protein degradation, we are able to predict expression patterns for 41% of the proteins in the core data set. Predictive features include, among others, targeting by RNA-binding proteins (Lhp1 and Khd1), RNA secondary structures, RNA half-life, and translation efficiency under unperturbed conditions and in response to oxidative reagents, but not chaperone binding. We are able to both describe general dynamics of protein concentration changes and suggest possible regulatory mechanisms for individual proteins.
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Affiliation(s)
- Christine Vogel
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA.
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46
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Mechanisms of dendritic mRNA transport and its role in synaptic tagging. EMBO J 2011; 30:3540-52. [PMID: 21878995 DOI: 10.1038/emboj.2011.278] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 07/20/2011] [Indexed: 11/08/2022] Open
Abstract
The localization of RNAs critically contributes to many important cellular processes in an organism, such as the establishment of polarity, asymmetric division and migration during development. Moreover, in the central nervous system, the local translation of mRNAs is thought to induce plastic changes that occur at synapses triggered by learning and memory. Here, we will critically review the physiological functions of well-established dendritically localized mRNAs and their associated factors, which together form ribonucleoprotein particles (RNPs). Second, we will discuss the life of a localized transcript from transcription in the nucleus to translation at the synapse and introduce the concept of the 'RNA signature' that is characteristic for each transcript. Finally, we present the 'sushi belt model' of how localized RNAs within neuronal RNPs may dynamically patrol multiple synapses rather than being anchored at a single synapse. This new model integrates our current understanding of synaptic function ranging from synaptic tagging and capture to functional and structural reorganization of the synapse upon learning and memory.
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47
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Chaudhury A, Hussey GS, Howe PH. 3'-UTR-mediated post-transcriptional regulation of cancer metastasis: beginning at the end. RNA Biol 2011; 8:595-9. [PMID: 21654215 PMCID: PMC3360070 DOI: 10.4161/rna.8.4.16018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 04/19/2011] [Accepted: 04/28/2011] [Indexed: 02/03/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) and the underlying mechanisms and signaling pathways regulating such transitions have generated a lot of interest among cancer researchers. Much of this can be attributed to the apparent similarities in the molecular processes regulating embryonic EMT that can be recapitulated during tumor progression and metastasis. It appears that both embryonic and oncogenic EMT are regulated by an intricate interplay of transcriptional and post-transcriptional programs, and the recent discovery of a transcript-selective translational regulatory pathway controlling expression of EMT-associated mRNAs demonstrates the high fidelity and tight regulation associated with the process of EMT and metastatic progression. Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) is emerging as a critical and integral modulator of TGFβ-induced EMT and subsequent tumor metastasis. Through its RNA-binding ability, hnRNP E1 binds distinct 3'-UTR structural elements present in mRNA transcripts required for EMT and translationally silences their expression. Translational silencing, mediated by hnRNP E1, occurs specifically at the translation elongation step through effects on the eukaryotic elongation factor-1 A1 (eEF1A1), and is relieved by Akt2-mediated phosphorylation. Interestingly, modulation of either the steady-state expression or the posttranscriptional modification of hnRNP E1 has a temporo-spatial effect on translational repression, tumorigenesis and cancer metastasis.
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Affiliation(s)
- Arindam Chaudhury
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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Pancaldi V, Bähler J. In silico characterization and prediction of global protein-mRNA interactions in yeast. Nucleic Acids Res 2011; 39:5826-36. [PMID: 21459850 PMCID: PMC3152324 DOI: 10.1093/nar/gkr160] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Post-transcriptional gene regulation is mediated through complex networks of protein-RNA interactions. The targets of only a few RNA binding proteins (RBPs) are known, even in the well-characterized budding yeast. In silico prediction of protein-RNA interactions is therefore useful to guide experiments and to provide insight into regulatory networks. Computational approaches have identified RBP targets based on sequence binding preferences. We investigate here to what extent RBP-RNA interactions can be predicted based on RBP and mRNA features other than sequence motifs. We analyze global relationships between gene and protein properties in general and between selected RBPs and known mRNA targets in particular. Highly translated RBPs tend to bind to shorter transcripts, and transcripts bound by the same RBP show high expression correlation across different biological conditions. Surprisingly, a given RBP preferentially binds to mRNAs that encode interaction partners for this RBP, suggesting coordinated post-transcriptional auto-regulation of protein complexes. We apply a machine-learning approach to predict specific RBP targets in yeast. Although this approach performs well for RBPs with known targets, predictions for uncharacterized RBPs remain challenging due to limiting experimental data. We also predict targets of fission yeast RBPs, indicating that the suggested framework could be applied to other species once more experimental data are available.
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Affiliation(s)
- Vera Pancaldi
- Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, Gower Street, London WC1E 6BT, UK.
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49
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Vogel C, Abreu RDS, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 2011; 6:400. [PMID: 20739923 PMCID: PMC2947365 DOI: 10.1038/msb.2010.59] [Citation(s) in RCA: 458] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 06/29/2010] [Indexed: 11/23/2022] Open
Abstract
We provide a large-scale dataset on absolute protein and matching mRNA concentrations from the human medulloblastoma cell line Daoy. The correlation between mRNA and protein concentrations is significant and positive (Rs=0.46, R2=0.29, P-value<2e16), although non-linear. Out of ∼200 tested sequence features, sequence length, frequency and properties of amino acids, as well as translation initiation-related features are the strongest individual correlates of protein abundance when accounting for variation in mRNA concentration. When integrating mRNA expression data and all sequence features into a non-parametric regression model (Multivariate Adaptive Regression Splines), we were able to explain up to 67% of the variation in protein concentrations. Half of the contributions were attributed to mRNA concentrations, the other half to sequence features relating to regulation of translation and protein degradation. The sequence features are primarily linked to the coding and 3′ untranslated region. To our knowledge, this is the most comprehensive predictive model of human protein concentrations achieved so far.
mRNA decay, translation regulation and protein degradation are essential parts of eukaryotic gene expression regulation (Hieronymus and Silver, 2004; Mata et al, 2005), which enable the dynamics of cellular systems and their responses to external and internal stimuli without having to rely exclusively on transcription regulation. The importance of these processes is emphasized by the generally low correlation between mRNA and protein concentrations. For many prokaryotic and eukaryotic organisms, <50% of variation in protein abundance variation is explained by variation in mRNA concentrations (de Sousa Abreu et al, 2009). Given the plethora of regulatory mechanisms involved, most studies have focused so far on individual regulators and specific targets. Particularly in human, we currently lack system-wide, quantitative analyses that evaluate the relative contribution of regulatory elements encoded in the mRNA and protein sequence. Existing studies have been carried out only in bacteria and yeast (Nie et al, 2006; Brockmann et al, 2007; Tuller et al, 2007; Wu et al, 2008). Here, we present the first comprehensive analysis on the impact of translation and protein degradation on protein abundance variation in a human cell line. For this purpose, we experimentally measured absolute protein and mRNA concentrations in the Daoy medulloblastoma cell line, using shotgun proteomics and microarrays, respectively (Figure 1). These data comprise one of the largest such sets available today for human. We focused on sequence features that likely impact protein translation and protein degradation, including length, nucleotide composition, structure of the untranslated regions (UTRs), coding sequence, composition of the translation initiation site, presence of upstream open reading frames putative target sites of miRNAs, codon usage, amino-acid composition and protein degradation signals. Three types of tests have been conducted: (a) we examined partial Spearman's rank correlation of numerical features (e.g. length) with protein concentration, accounting for variation in mRNA concentrations; (b) for numerical and categorical features (e.g. function), we compared two extreme populations with Welch's t-test and (c) using a Multivariate Adaptive Regression Splines model, we analyzed the combined contributions of mRNA expression and sequence features to protein abundance variation (Figure 1). To account for the non-linearity of many relationships, we use non-parametric approaches throughout the analysis. We observed a significant positive correlation between mRNA and protein concentrations, larger than many previous measurements (de Sousa Abreu et al, 2009). We also show that the contribution of translation and protein degradation is at least as important as the contribution of mRNA transcription and stability to the abundance variation of the final protein products. Although variation in mRNA expression explains ∼25–30% of the variation in protein abundance, another 30–40% can be accounted for by characteristics of the sequences, which we identified in a comparative assessment of global correlates. Among these characteristics, sequence length, amino-acid frequencies and also nucleotide frequencies in the coding region are of strong influence (Figure 3A). Characteristics of the 3′UTR and of the 5′UTR, that is length, nucleotide composition and secondary structures, describe another part of the variation, leaving 33% expression variation unexplained. The unexplained fraction may be accounted for by mechanisms not considered in this analysis (e.g. regulation by RNA-binding proteins or gene-specific structural motifs), as well as expression and measurement noise. Our combined model including mRNA concentration and sequence features can explain 67% of the variation of protein abundance in this system—and thus has the highest predictive power for human protein abundance achieved so far (Figure 3B). Transcription, mRNA decay, translation and protein degradation are essential processes during eukaryotic gene expression, but their relative global contributions to steady-state protein concentrations in multi-cellular eukaryotes are largely unknown. Using measurements of absolute protein and mRNA abundances in cellular lysate from the human Daoy medulloblastoma cell line, we quantitatively evaluate the impact of mRNA concentration and sequence features implicated in translation and protein degradation on protein expression. Sequence features related to translation and protein degradation have an impact similar to that of mRNA abundance, and their combined contribution explains two-thirds of protein abundance variation. mRNA sequence lengths, amino-acid properties, upstream open reading frames and secondary structures in the 5′ untranslated region (UTR) were the strongest individual correlates of protein concentrations. In a combined model, characteristics of the coding region and the 3′UTR explained a larger proportion of protein abundance variation than characteristics of the 5′UTR. The absolute protein and mRNA concentration measurements for >1000 human genes described here represent one of the largest datasets currently available, and reveal both general trends and specific examples of post-transcriptional regulation.
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Affiliation(s)
- Christine Vogel
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78229-3900, USA.
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50
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Kanitz A, Gerber AP. Circuitry of mRNA regulation. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:245-251. [PMID: 20836026 DOI: 10.1002/wsbm.55] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Some of the classical paradigms of gene regulation have been challenged by global-scale analysis of eukaryotic transcriptional and post-transcriptional gene regulation (PTGR), made possible by the development of genomics and proteomics tools. Post-transcriptional events in particular are increasingly being recognized as important sources of gene regulation. The hundreds of regulatory RNA-binding proteins that exist in eukaryotes may regulate dozens to hundreds of functionally related RNA targets. Likewise, the expression of considerable fractions of many eukaryotic genomes is affected by hundreds of non-coding RNAs, e.g., microRNAs. These findings suggest an enormous regulatory potential for PTGR that may affect virtually every message in a cell. All gene regulatory systems are composed of simple network circuits that coordinate the transfer of regulatory signals to a target gene/message.
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Affiliation(s)
| | - André P Gerber
- Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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