1
|
Grzybowska EA, Wakula M. Protein Binding to Cis-Motifs in mRNAs Coding Sequence Is Common and Regulates Transcript Stability and the Rate of Translation. Cells 2021; 10:2910. [PMID: 34831133 PMCID: PMC8616275 DOI: 10.3390/cells10112910] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
Protein binding to the non-coding regions of mRNAs is relatively well characterized and its functionality has been described in many examples. New results obtained by high-throughput methods indicate that binding to the coding sequence (CDS) by RNA-binding proteins is also quite common, but the functions thereof are more obscure. As described in this review, CDS binding has a role in the regulation of mRNA stability, but it has also a more intriguing role in the regulation of translational efficiency. Global approaches, which suggest the significance of CDS binding along with specific examples of CDS-binding RBPs and their modes of action, are outlined here, pointing to the existence of a relatively less-known regulatory network controlling mRNA stability and translation on yet another level.
Collapse
Affiliation(s)
- Ewa A. Grzybowska
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland;
| | | |
Collapse
|
2
|
Xu L, Zhao Q, Li D, Luo J, Ma W, Jin Y, Li C, Chen J, Zhao K, Zheng Y, Yu D. MicroRNA-760 resists ambient PM 2.5-induced apoptosis in human bronchial epithelial cells through elevating heme-oxygenase 1 expression. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117213. [PMID: 33933780 DOI: 10.1016/j.envpol.2021.117213] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
PM2.5 (particles matter smaller aerodynamic diameter of 2.5 μm) exposure, a major environmental risk factor for the global burden of diseases, is associated with high risks of respiratory diseases. Heme-oxygenase 1 (HMOX1) is one of the major molecular antioxidant defenses to mediate cytoprotective effects against diverse stressors, including PM2.5-induced toxicity; however, the regulatory mechanism of HMOX1 expression still needs to be elucidated. In this study, using PM2.5 as a typical stressor, we explored whether microRNAs (miRNAs) might modulate HMOX1 expression in lung cells. Systematic bioinformatics analysis showed that seven miRNAs have the potentials to target HMOX1 gene. Among these, hsa-miR-760 was identified as the most responsive miRNA to PM2.5 exposure. More importantly, we revealed a "non-conventional" miRNA function in hsa-miR-760 upregulating HMOX1 expression, by targeting the coding region and interacting with YBX1 protein. In addition, we observed that exogenous hsa-miR-760 effectively elevated HMOX1 expression, reduced the reactive oxygen agents (ROS) levels, and rescued the lung cells from PM2.5-induced apoptosis. Our results revealed that hsa-miR-760 might play an important role in protecting lung cells against PM2.5-induced toxicity, by elevating HMOX1 expression, and offered new clues to elucidate the diverse functions of miRNAs.
Collapse
Affiliation(s)
- Lin Xu
- School of Public Health, Qingdao University, Qingdao, China
| | - Qianwen Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Daochuan Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Wanli Ma
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China
| | - Chuanhai Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Jing Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Kunming Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuxin Zheng
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China.
| |
Collapse
|
3
|
Albarqi MMY, Ryder SP. The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans. PLoS Genet 2021; 17:e1009775. [PMID: 34424904 PMCID: PMC8412283 DOI: 10.1371/journal.pgen.1009775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/02/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
RNA regulation is essential to successful reproduction. Messenger RNAs delivered from parent to progeny govern early embryonic development. RNA-binding proteins (RBPs) are the key effectors of this process, regulating the translation and stability of parental transcripts to control cell fate specification events prior to zygotic gene activation. The KH-domain RBP MEX-3 is conserved from nematode to human. It was first discovered in Caenorhabditis elegans, where it is essential for anterior cell fate and embryo viability. Here, we show that loss of the endogenous mex-3 3´UTR disrupts its germline expression pattern. An allelic series of 3´UTR deletion variants identify repressing regions of the UTR and demonstrate that repression is not precisely coupled to reproductive success. We also show that several RBPs regulate mex-3 mRNA through its 3´UTR to define its unique germline spatiotemporal expression pattern. Additionally, we find that both poly(A) tail length control and the translation initiation factor IFE-3 contribute to its expression pattern. Together, our results establish the importance of the mex-3 3´UTR to reproductive health and its expression in the germline. Our results suggest that additional mechanisms control MEX-3 function when 3´UTR regulation is compromised. In sexually reproducing organisms, germ cells undergo meiosis and differentiate to form oocytes or sperm. Coordination of this process requires a gene regulatory program that acts while the genome is undergoing chromatin condensation. As such, RNA regulatory pathways are an important contributor. The germline of the nematode Caenorhabditis elegans is a suitable model system to study germ cell differentiation. Several RNA-binding proteins (RBPs) coordinate each transition in the germline such as the transition from mitosis to meiosis. MEX-3 is a conserved RNA-binding protein found in most animals including humans. In C. elegans, MEX-3 displays a highly restricted pattern of expression. Here, we define the importance of the 3´UTR in regulating MEX-3 expression pattern in vivo and characterize the RNA-binding proteins involved in this regulation. Our results show that deleting various mex-3 3´UTR regions alter the pattern of expression in the germline in various ways. These mutations also reduced—but did not eliminate—reproductive capacity. Finally, we demonstrate that multiple post-transcriptional mechanisms control MEX-3 levels in different domains of the germline. Our data suggest that coordination of MEX-3 activity requires multiple layers of regulation to ensure reproductive robustness.
Collapse
Affiliation(s)
- Mennatallah M. Y. Albarqi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sean P. Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
4
|
Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
5
|
Rose J, Kraft T, Brenner B, Montag J. Hypertrophic cardiomyopathy MYH7 mutation R723G alters mRNA secondary structure. Physiol Genomics 2020; 52:15-19. [PMID: 31790337 DOI: 10.1152/physiolgenomics.00100.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Point mutation R723G in the MYH7 gene causes hypertrophic cardiomyopathy (HCM). Heterozygous patients with this mutation exhibit a comparable allelic imbalance of the MYH7 gene. On average 67% of the total MYH7 mRNA are derived from the MYH7R723G-allele and 33% from the MYH7WT allele. Mechanisms underlying mRNA allelic imbalance are largely unknown. We suggest that a different mRNA lifetime of the alleles may cause the allelic drift in R723G patients. A potent regulator of mRNA lifetime is its secondary structure. To test for alterations in the MYH7R723G mRNA structure we used selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. We show significantly different SHAPE reactivity of wild-type and MYH7R723G RNA, which is in accordance with bioinformatically predicted structures. Thus, we provide the first experimental evidence for mRNA secondary structure alterations by the HCM point mutation. We assume that this may result in a prolonged lifetime of MYH7R723G mRNA in vivo and subsequently in the determined allelic imbalance.
Collapse
Affiliation(s)
- J Rose
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - T Kraft
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - B Brenner
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - J Montag
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| |
Collapse
|
6
|
Theil K, Herzog M, Rajewsky N. Post-transcriptional Regulation by 3' UTRs Can Be Masked by Regulatory Elements in 5' UTRs. Cell Rep 2019; 22:3217-3226. [PMID: 29562178 DOI: 10.1016/j.celrep.2018.02.094] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/20/2017] [Accepted: 02/23/2018] [Indexed: 11/29/2022] Open
Abstract
In mRNA sequences, 3' UTRs are thought to contain most elements that specifically regulate localization, turnover, and translation. Although high-throughput experiments indicate that many RNA-binding proteins (RBPs) also bind 5' UTRs, much less is known about specific post-transcriptional control exerted by 5' UTRs. GLD-1 is a conserved RBP and a translational repressor with essential roles in Caenorhabditis elegans germ cell development. Previously, we showed that GLD-1 binds highly conserved sites in both 3' and 5' UTRs. Here, by targeted single-copy insertion of transgenes, we systematically tested in vivo functionality of 5' and 3' UTR binding sites individually and in combination. Our data show that sites in 5' UTRs mediate specific and strong translational repression, independent of exact position. Intriguingly, we found that the functionality of 3' UTR sites can be masked by 5' UTR sites and vice versa. We conclude that it is important to study both UTRs simultaneously.
Collapse
Affiliation(s)
- Kathrin Theil
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Margareta Herzog
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.
| |
Collapse
|
7
|
MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death Differ 2019; 26:2157-2178. [PMID: 30728462 DOI: 10.1038/s41418-019-0291-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/22/2023] Open
Abstract
Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many RBPs are conserved between Caenorhabditis elegans and humans, and several are known to regulate apoptosis in the adult C. elegans germ line. How these RBPs control apoptosis is, however, largely unknown. Here, we identify mina-1(C41G7.3) in a RNA interference-based screen as a novel regulator of apoptosis, which is exclusively expressed in the adult germ line. The absence of MINA-1 causes a dramatic increase in germ cell apoptosis, a reduction in brood size, and an impaired P granules organization and structure. In vivo crosslinking immunoprecipitation experiments revealed that MINA-1 binds a set of mRNAs coding for RBPs associated with germ cell development. Additionally, a system-wide analysis of a mina-1 deletion mutant compared with wild type, including quantitative proteome and transcriptome data, hints to a post-transcriptional regulatory RBP network driven by MINA-1 during germ cell development in C. elegans. In particular, we found that the germline-specific Argonaute WAGO-4 protein levels are increased in mina-1 mutant background. Phenotypic analysis of double mutant mina-1;wago-4 revealed that contemporary loss of MINA-1 and WAGO-4 strongly rescues the phenotypes observed in mina-1 mutant background. To strengthen this functional interaction, we found that upregulation of WAGO-4 in mina-1 mutant animals causes hypersensitivity to exogenous RNAi. Our comprehensive experimental approach allowed us to describe a phenocritical interaction between two RBPs controlling germ cell apoptosis and exogenous RNAi. These findings broaden our understanding of how RBPs can orchestrate different cellular events such as differentiation and death in C. elegans.
Collapse
|
8
|
Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex. Dev Biol 2018; 446:193-205. [PMID: 30599151 DOI: 10.1016/j.ydbio.2018.11.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 01/26/2023]
Abstract
Proper germ cell sex determination in Caenorhabditis nematodes requires a network of RNA-binding proteins (RBPs) and their target mRNAs. In some species, changes in this network enabled limited XX spermatogenesis, and thus self-fertility. In C. elegans, one of these selfing species, the global sex-determining gene tra-2 is regulated in germ cells by a conserved RBP, GLD-1, via the 3' untranslated region (3'UTR) of its transcript. A C. elegans-specific GLD-1 cofactor, FOG-2, is also required for hermaphrodite sperm fate, but how it modifies GLD-1 function is unknown. Germline feminization in gld-1 and fog-2 null mutants has been interpreted as due to cell-autonomous elevation of TRA-2 translation. Consistent with the proposed role of FOG-2 in translational control, the abundance of nearly all GLD-1 target mRNAs (including tra-2) is unchanged in fog-2 mutants. Epitope tagging reveals abundant TRA-2 expression in somatic tissues, but an undetectably low level in wild-type germ cells. Loss of gld-1 function elevates germline TRA-2 expression to detectable levels, but loss of fog-2 function does not. A simple quantitative model of tra-2 activity constrained by these results can successfully sort genotypes into normal or feminized groups. Surprisingly, fog-2 and gld-1 activity enable the sperm fate even when GLD-1 cannot bind to the tra-2 3' UTR. This suggests the GLD-1-FOG-2 complex regulates uncharacterized sites within tra-2, or other mRNA targets. Finally, we quantify the RNA-binding capacities of dominant missense alleles of GLD-1 that act genetically as "hyper-repressors" of tra-2 activity. These variants bind RNA more weakly in vitro than does wild-type GLD-1. These results indicate that gld-1 and fog-2 regulate germline sex via multiple interactions, and that our understanding of the control and evolution of germ cell sex determination in the C. elegans hermaphrodite is far from complete.
Collapse
|
9
|
West SM, Mecenas D, Gutwein M, Aristizábal-Corrales D, Piano F, Gunsalus KC. Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline. Genome Biol 2018; 19:8. [PMID: 29368663 PMCID: PMC5784609 DOI: 10.1186/s13059-017-1369-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 12/03/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation. RESULTS We show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3'UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases. CONCLUSIONS These results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.
Collapse
Affiliation(s)
- Sean M West
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Desirea Mecenas
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Michelle Gutwein
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - David Aristizábal-Corrales
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Fabio Piano
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
10
|
Vaklavas C, Blume SW, Grizzle WE. Translational Dysregulation in Cancer: Molecular Insights and Potential Clinical Applications in Biomarker Development. Front Oncol 2017; 7:158. [PMID: 28798901 PMCID: PMC5526920 DOI: 10.3389/fonc.2017.00158] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 01/04/2023] Open
Abstract
Although transcript levels have been traditionally used as a surrogate measure of gene expression, it is increasingly recognized that the latter is extensively and dynamically modulated at the level of translation (messenger RNA to protein). Over the recent years, significant progress has been made in dissecting the complex posttranscriptional mechanisms that regulate gene expression. This advancement in knowledge came hand in hand with the progress made in the methodologies to study translation both at gene-specific as well as global genomic level. The majority of translational control is exerted at the level of initiation; nonetheless, protein synthesis can be modulated at the level of translation elongation, termination, and recycling. Sequence and structural elements and epitranscriptomic modifications of individual transcripts allow for dynamic gene-specific modulation of translation. Cancer cells usurp the regulatory mechanisms that govern translation to carry out translational programs that lead to the phenotypic hallmarks of cancer. Translation is a critical nexus in neoplastic transformation. Multiple oncogenes and signaling pathways that are activated, upregulated, or mutated in cancer converge on translation and their transformative impact "bottlenecks" at the level of translation. Moreover, this translational dysregulation allows cancer cells to adapt to a diverse array of stresses associated with a hostile microenviroment and antitumor therapies. All elements involved in the process of translation, from the transcriptional template, the components of the translational machinery, to the proteins that interact with the transcriptome, have been found to be qualitatively and/or quantitatively perturbed in cancer. This review discusses the regulatory mechanisms that govern translation in normal cells and how translation becomes dysregulated in cancer leading to the phenotypic hallmarks of malignancy. We also discuss how dysregulated mediators or components of translation can be utilized as biomarkers with potential diagnostic, prognostic, or predictive significance. Such biomarkers have the potential advantage of uniform applicability in the face of inherent tumor heterogeneity and deoxyribonucleic acid instability. As translation becomes increasingly recognized as a process gone awry in cancer and agents are developed to target it, the utility and significance of these potential biomarkers is expected to increase.
Collapse
Affiliation(s)
- Christos Vaklavas
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Scott W Blume
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - William E Grizzle
- Department of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
11
|
Subasic D, Stoeger T, Eisenring S, Matia-González AM, Imig J, Zheng X, Xiong L, Gisler P, Eberhard R, Holtackers R, Gerber AP, Pelkmans L, Hengartner MO. Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes Dev 2017; 30:2213-2225. [PMID: 27798844 PMCID: PMC5088569 DOI: 10.1101/gad.285726.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/16/2016] [Indexed: 12/03/2022]
Abstract
In this study, Subasic et al. investigated the post-transcriptional control of caspases. The authors describe four conserved RNA-binding proteins (RBPs) that sequentially repress the CED-3 caspase in distinct regions of the C. elegans germline and identify seven RBPs that regulate human caspase-3 expression and/or activation, suggesting that translational inhibition of executioner caspases by RBPs might be a general strategy used widely across the animal kingdom to control apoptosis. Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)—PUF-8, MEX-3, GLD-1, and CGH-1—that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3′ untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3′ UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.
Collapse
Affiliation(s)
- Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Stoeger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Systems Biology PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Seline Eisenring
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ana M Matia-González
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Jochen Imig
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Lei Xiong
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Pascal Gisler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ralf Eberhard
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - René Holtackers
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - André P Gerber
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Lucas Pelkmans
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
12
|
Jiang H, Lv X, Lei X, Yang Y, Yang X, Jiao J. Immune Regulator MCPIP1 Modulates TET Expression during Early Neocortical Development. Stem Cell Reports 2016; 7:439-453. [PMID: 27523618 PMCID: PMC5031990 DOI: 10.1016/j.stemcr.2016.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 07/10/2016] [Accepted: 07/11/2016] [Indexed: 12/15/2022] Open
Abstract
MCPIP1 is a recently identified immune regulator that plays critical roles in preventing immune disorders, and is also present in the brain. Currently an unresolved question remains as to how MCPIP1 performs its non-immune functions in normal brain development. Here, we report that MCPIP1 is abundant in neural progenitor cells (NPCs) and newborn neurons during the early stages of neurogenesis. The suppression of MCPIP1 expression impairs normal neuronal differentiation, cell-cycle exit, and concomitant NPC proliferation. MCPIP1 is important for maintenance of the NPC pool. Notably, we demonstrate that MCPIP1 reduces TET (TET1/TET2/TET3) levels and then decreases 5-hydroxymethylcytosine levels. Furthermore, the MCPIP1 interaction with TETs is involved in neurogenesis and in establishing the proper number of NPCs in vivo. Collectively, our findings not only demonstrate that MCPIP1 plays an important role in early cortical neurogenesis but also reveal an unexpected link between neocortical development, immune regulators, and epigenetic modification. MCPIP1 is abundant during early neocortical development MCPIP1 suppression impairs normal neocortical neurogenesis MCPIP1 directly targets Tets and regulates TET expression levels
Collapse
Affiliation(s)
- Huihui Jiang
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Lv
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuepei Lei
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
13
|
Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev 2015; 29:501-12. [PMID: 25737280 PMCID: PMC4358403 DOI: 10.1101/gad.258483.115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/06/2015] [Indexed: 12/14/2022]
Abstract
Cellular morphology is an essential determinant of cellular function in all kingdoms of life, yet little is known about how cell shape is controlled. Here we describe a molecular program that controls the early morphology of neurons through a metazoan-specific zinc finger protein, Unkempt. Depletion of Unkempt in mouse embryos disrupts the shape of migrating neurons, while ectopic expression confers neuronal-like morphology to cells of different nonneuronal lineages. We found that Unkempt is a sequence-specific RNA-binding protein and identified its precise binding sites within coding regions of mRNAs linked to protein metabolism and trafficking. RNA binding is required for Unkempt-induced remodeling of cellular shape and is directly coupled to a reduced production of the encoded proteins. These findings link post-transcriptional regulation of gene expression with cellular shape and have general implications for the development and disease of multicellular organisms.
Collapse
Affiliation(s)
- Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yawei J Yang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA;
| | - Omer Durak
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Elisabeth A Murphy
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Sihem Cheloufi
- Cancer Center, Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Johannes Zuber
- The Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jernej Ule
- Department of Molecular Neuroscience, University College London Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; UCL Genetics Institute, Department of Genetics, Environment, and Evolution, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| |
Collapse
|
14
|
Nicastro G, Taylor IA, Ramos A. KH-RNA interactions: back in the groove. Curr Opin Struct Biol 2015; 30:63-70. [PMID: 25625331 DOI: 10.1016/j.sbi.2015.01.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/20/2014] [Accepted: 01/08/2015] [Indexed: 12/30/2022]
Abstract
The hnRNP K-homology (KH) domain is a single stranded nucleic acid binding domain that mediates RNA target recognition by a large group of gene regulators. The structure of the KH fold is well characterised and some initial rules for KH-RNA recognition have been drafted. However, recent findings have shown that these rules need to be revisited and have now provided a better understanding of how the domain can recognise a sequence landscape larger than previously thought as well as revealing the diversity of structural expansions to the KH domain. Finally, novel structural and functional data show how multiple KH domains act in a combinatorial fashion to both allow recognition of longer RNA motifs and remodelling of the RNA structure. These advances set the scene for a detailed molecular understanding of KH selection of the cellular targets.
Collapse
Affiliation(s)
- Giuseppe Nicastro
- Division of Molecular Structure, MRC National Institute for Medical Research, London, UK
| | - Ian A Taylor
- Division of Molecular Structure, MRC National Institute for Medical Research, London, UK
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, London, UK; Division of Molecular Structure, MRC National Institute for Medical Research, London, UK.
| |
Collapse
|
15
|
Abstract
RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA–protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA–protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.
Collapse
|
16
|
Beadell AV, Haag ES. Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. Genome Biol Evol 2014; 7:314-35. [PMID: 25502909 PMCID: PMC4316625 DOI: 10.1093/gbe/evu272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2014] [Indexed: 12/17/2022] Open
Abstract
Given the large number of RNA-binding proteins and regulatory RNAs within genomes, posttranscriptional regulation may be an underappreciated aspect of cis-regulatory evolution. Here, we focus on nematode germ cells, which are known to rely heavily upon translational control to regulate meiosis and gametogenesis. GLD-1 belongs to the STAR-domain family of RNA-binding proteins, conserved throughout eukaryotes, and functions in Caenorhabditis elegans as a germline-specific translational repressor. A phylogenetic analysis across opisthokonts shows that GLD-1 is most closely related to Drosophila How and deuterostome Quaking, both implicated in alternative splicing. We identify messenger RNAs associated with C. briggsae GLD-1 on a genome-wide scale and provide evidence that many participate in aspects of germline development. By comparing our results with published C. elegans GLD-1 targets, we detect nearly 100 that are conserved between the two species. We also detected several hundred Cbr-GLD-1 targets whose homologs have not been reported to be associated with C. elegans GLD-1 in either of two independent studies. Low expression in C. elegans may explain the failure to detect most of them, but a highly expressed subset are strong candidates for Cbr-GLD-1-specific targets. We examine GLD-1-binding motifs among targets conserved in C. elegans and C. briggsae and find that most, but not all, display evidence of shared ancestral binding sites. Our work illustrates both the conservative and the dynamic character of evolution at the posttranslational level of gene regulation, even between congeners.
Collapse
Affiliation(s)
- Alana V Beadell
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Present address: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL
| | - Eric S Haag
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Department of Biology, University of Maryland, College Park
| |
Collapse
|
17
|
Daubner GM, Brümmer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FHT. Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Res 2014; 42:8092-105. [PMID: 24838563 PMCID: PMC4081071 DOI: 10.1093/nar/gku445] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/04/2014] [Accepted: 05/06/2014] [Indexed: 01/13/2023] Open
Abstract
The STAR family comprises ribonucleic acid (RNA)-binding proteins that play key roles in RNA-regulatory processes. RNA recognition is achieved by a KH domain with an additional α-helix (QUA2) that seems to extend the RNA-binding surface to six nucleotides for SF1 (Homo sapiens) and seven nucleotides for GLD-1 (Caenorhabditis elegans). To understand the structural basis of this probable difference in specificity, we determined the solution structure of GLD-1 KH-QUA2 with the complete consensus sequence identified in the tra-2 gene. Compared to SF1, the GLD-1 KH-QUA2 interface adopts a different conformation resulting indeed in an additional sequence-specific binding pocket for a uracil at the 5'end. The functional relevance of this binding pocket is emphasized by our bioinformatics analysis showing that GLD-1 binding sites with this 5'end uracil are more predictive for the functional response of the messenger RNAs to gld-1 knockout. We further reveal the importance of the KH-QUA2 interface in vitro and that its alteration in vivo affects the level of translational repression dependent on the sequence of the GLD-1 binding motif. In conclusion, we demonstrate that the QUA2 domain distinguishes GLD-1 from other members of the STAR family and contributes more generally to the modulation of RNA-binding affinity and specificity of KH domain containing proteins.
Collapse
Affiliation(s)
- Gerrit M Daubner
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Anneke Brümmer
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Cristina Tocchini
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
| | - Stefan Gerhardy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
| | | | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
18
|
Brümmer A, Hausser J. MicroRNA binding sites in the coding region of mRNAs: extending the repertoire of post-transcriptional gene regulation. Bioessays 2014; 36:617-26. [PMID: 24737341 DOI: 10.1002/bies.201300104] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is well established that microRNAs (miRNAs) induce mRNA degradation by binding to 3' untranslated regions (UTRs). The functionality of sites in the coding domain sequence (CDS), on the other hand, remains under discussion. Such sites have limited impact on target mRNA abundance and recent work suggests that miRNAs bind in the CDS to inhibit translation. What then could be the regulatory benefits of translation inhibition through CDS targeting compared to mRNA degradation following 3' UTR binding? We propose that these domain-dependent effects serve to diversify the functional repertoire of post-transcriptional gene expression control. Possible regulatory benefits may include tuning the time-scale and magnitude of post-transcriptional regulation, regulating protein abundance depending on or independently of the cellular state, and regulation of the protein abundance of alternative splice variants. Finally, we review emerging evidence that these ideas may generalize to RNA-binding proteins beyond miRNAs and Argonaute proteins.
Collapse
|
19
|
Biyanee A, Ohnheiser J, Singh P, Klempnauer KH. A novel mechanism for the control of translation of specific mRNAs by tumor suppressor protein Pdcd4: inhibition of translation elongation. Oncogene 2014; 34:1384-92. [PMID: 24681950 DOI: 10.1038/onc.2014.83] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 02/10/2014] [Accepted: 02/24/2014] [Indexed: 12/12/2022]
Abstract
The tumor suppressor gene Pdcd4 (programmed cell death gene 4) has drawn considerable attention because its downregulation is involved in the development of several types of cancer. Because Pdcd4 interacts with the translation initiation factor eIF4A and inhibits its helicase activity, Pdcd4 has been implicated in the translational suppression of cellular mRNAs containing structured 5'-untranslated regions. However, Pdcd4's role in translation regulation is still poorly understood, because only very few physiological Pdcd4 target mRNAs are known. By using a Pdcd4-deficient clone of the chicken B-cell line DT40, we have discovered that the mRNA of the A-myb proto-oncogene is a novel Pdcd4 target RNA whose translation is suppressed by Pdcd4. Interestingly, the inhibitory effect of Pdcd4 is independent of the Pdcd4-eIF4A interaction, but is dependent on an RNA-binding domain at the N terminus of Pdcd4 and on sequences located within the coding region of A-myb mRNA, indicating that Pdcd4 suppresses A-myb translation by a novel mechanism. Our data show that the Pdcd4 RNA-binding domain preferentially recognizes an RNA secondary structure element formed by the part of the A-myb coding region that mediates Pdcd4-dependent suppression. Previously, we have shown that Pdcd4 also suppresses the translation of the c-myb mRNA by a similar mechanism involving binding of Pdcd4 to RNA secondary structure formed by the c-myb coding region. Surprisingly, our data show that Pdcd4 exerts its inhibitory activity only when the target region of Pdcd4 in A-myb and c-myb mRNA is itself translated, consistent with a mechanism in which Pdcd4 suppresses translation by interfering with translation elongation. Taken together, our work reveals a novel mechanism by which Pdcd4 affects the translational of cellular RNAs. Furthermore, as c-myb and A-myb are members of the Myb proto-oncogene family whose deregulation has been implicated in tumorigenesis, inhibiting their translation might contribute to the tumor-suppressive activity of Pdcd4.
Collapse
Affiliation(s)
- A Biyanee
- 1] Institute for Biochemistry, Westfälische-Wilhelms-Universität Münster, Münster, Germany [2] Graduate School of Chemistry (GSC-MS), Westfälische-Wilhelms-Universität Münster, Münster, Germany
| | - J Ohnheiser
- Institute for Biochemistry, Westfälische-Wilhelms-Universität Münster, Münster, Germany
| | - P Singh
- Institute for Biochemistry, Westfälische-Wilhelms-Universität Münster, Münster, Germany
| | - K-H Klempnauer
- Institute for Biochemistry, Westfälische-Wilhelms-Universität Münster, Münster, Germany
| |
Collapse
|
20
|
Li X, Kazan H, Lipshitz HD, Morris QD. Finding the target sites of RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:111-30. [PMID: 24217996 PMCID: PMC4253089 DOI: 10.1002/wrna.1201] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 12/15/2022]
Abstract
RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201
Collapse
Affiliation(s)
- Xiao Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | |
Collapse
|