ORCID Profile
0000-0002-4023-7876
Current Organisations
Ruprecht Karls University Heidelberg
,
European Molecular Biology Laboratory
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Publications
Translational control of dosage compensation in Drosophila by Sex-lethal: Cooperative silencing via the 5' and 3' UTRs of msl-2 mRNA is independent of the poly(A) tail
Publisher: Wiley
Date: 11-1999
From cis-regulatory elements to complex RNPs and back
Publisher: Cold Spring Harbor Laboratory
Date: 07-2012
Erratum to: Insights into the design and interpretation of iCLIP experiments
Publisher: Springer Science and Business Media LLC
Date: 15-08-2017
Circular RNAs: Splicing's enigma variations
Publisher: Wiley
Date: 05-03-2013
From factors to mechanisms: translation and translational control in eukaryotes
Publisher: Elsevier BV
Date: 10-1999
DOI: 10.1016/S0959-437X(99)00005-2
Abstract: Biochemical and genetic studies are revealing a network of interactions between eukaryotic translation initiation factors, further refining or redefining perceptions of their function. The notion of translated mRNA as a 'closed-loop' has gained support from the identification of physical and functional interactions between the two mRNA ends and their associated factors. Translational control mechanisms are beginning to unravel in sufficient detail to pinpoint the affected step in the initiation pathway.
A brave new world of RNA-binding proteins
Publisher: Springer Science and Business Media LLC
Date: 17-01-2018
DOI: 10.1038/NRM.2017.130
Abstract: RNA-binding proteins (RBPs) are typically thought of as proteins that bind RNA through one or multiple globular RNA-binding domains (RBDs) and change the fate or function of the bound RNAs. Several hundred such RBPs have been discovered and investigated over the years. Recent proteome-wide studies have more than doubled the number of proteins implicated in RNA binding and uncovered hundreds of additional RBPs lacking conventional RBDs. In this Review, we discuss these new RBPs and the emerging understanding of their unexpected modes of RNA binding, which can be mediated by intrinsically disordered regions, protein-protein interaction interfaces and enzymatic cores, among others. We also discuss the RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA.
RNA-binding proteins in Mendelian disease
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.TIG.2013.01.004
Abstract: RNA-binding proteins (RBPs) control all aspects of RNA fate, and defects in their function underlie a broad spectrum of human pathologies. We focus here on two recent studies that uncovered the in vivo mRNA interactomes of human cells, jointly implicating over 1100 proteins in RNA binding. Surprisingly, over 350 of these RBPs had no prior RNA binding-related annotation or domain homology. The datasets also contain many proteins that, when mutated, cause Mendelian diseases, prominently neurological, sensory, and muscular disorders and cancers. Disease mutations in these proteins occur throughout their domain architectures and many are found in non-classical RNA-binding domains and in disordered regions. In some cases, mutations might cause disease through perturbing previously unknown RNA-related protein functions. These studies have thus expanded our knowledge of RBPs and their role in genetic diseases. We also expect that mRNA interactome capture approaches will aid further exploration of RNA systems biology in varied physiological and pathophysiological settings.
The REM phase of gene regulation
Publisher: Elsevier BV
Date: 08-2010
DOI: 10.1016/J.TIBS.2010.05.009
Abstract: 'Classic' enzymes carry out the housekeeping functions of intermediary metabolism. The past decades have seen a steady trickle of reports of several of these enzymes 'moonlighting' as RNA-binding proteins. Although evidence for a physiological role for RNA binding is strong in a few in idual ex les, no systematic concept has been proposed for the overall phenomenon. We suggest that these erse observations might herald the existence of currently hidden post-transcriptional regulatory networks between intermediary metabolism and gene expression based on RNA, enzyme and metabolite interactions. We briefly summarize the evidence in support of such networks and discuss how current approaches can be employed for systematic analyses and integration into our understanding of cellular biology, given the technical and conceptual advances of the 'omics' age.
Translational activation of uncapped mRNAs by the central part of human elF4G is 5' end-dependent
Publisher: Cold Spring Harbor Laboratory
Date: 07-1998
DOI: 10.1017/S1355838298980372
Abstract: Translation initiation factor (eIF) 4G represents a critical link between mRNAs and 40S ribosomal subunits during translation initiation. It interacts directly with the cap-binding protein eIF4E through its N-terminal part, and binds eIF3 and eIF4A through the central and C-terminal region. We expressed and purified recombinant variants of human eIF4G lacking the N-terminal domain as GST-fusion proteins, and studied their function in cell-free translation reactions. Both eIF4G lacking its N-terminal part (aa 486-1404) and the central part alone (aa 486-935) exert a dominant negative effect on the translation of capped mRNAs. Furthermore, these polypeptides potently stimulate the translation of uncapped mRNAs. Although this stimulation is cap-independent, it is shown to be dependent on the accessibility of the mRNA 5' end. These results reveal two unexpected features of eIF4G-mediated translation. First, the C-terminal eIF4A binding site is dispensable for activation of uncapped mRNA translation. Second, translation of uncapped mRNA still requires 5' end-dependent ribosome binding. These new findings are incorporated into existing models of mammalian translation initiation.
Tethered-function analysis reveals that eIF4E can recruit ribosomes independent of its binding to the cap structure
Publisher: Cold Spring Harbor Laboratory
Date: 2001
DOI: 10.1017/S1355838201000577
Abstract: The cap-binding complex elF4F is involved in ribosome recruitment during the initiation phase of translation and is composed of three subunits: elF4E, -4G, and -4A. The m7GpppN cap-binding subunit eIF4E binds the N-terminal region of eIF4G, which in turn contacts eIF4A through its central and C-terminal regions. We have previously shown, through a tethered-function approach in transfected HeLa cells, that the binding of eIF4G to an mRNA is sufficient to drive productive translation (De Gregorio et al., EMBO J, 1999, 18:4865-4874). Here we exploit this approach to assess which of the other subunits of elF4F can exert this function. eIF4AI or mutant forms of eIF4E were fused to the RNA-binding domain of the lambda phage antiterminator protein N to generate the chimeric proteins lambda4A, lambda4E-102 (abolished cap binding), and lambda4E-73-102 (impaired binding to both, the cap and eIF4G). The fusion proteins were directed to a bicistronic reporter mRNA by means of interaction with a specific lambda-N binding site (boxB) in the intercistronic space. We show that lambda4E-102, but neither the double mutant lambda4E-73-102 nor lambda4A, suffices to promote translation of the downstream gene in this assay. Coimmunoprecipitation analyses confirmed that all lambda-fusion proteins are capable of interacting with the appropriate endogenous eIF4F subunits. These results reveal that eIF4E, as well as eIF4G, can drive ribosome recruitment independent of a physical link to the cap structure. In spite of its interaction with endogenous eIF4G, lambda4A does not display this property. eIF4A thus appears to supply an essential auxiliary function to eIF4F that may require its ability to cycle into and out of this complex.
The interaction of the cap-binding complex (CBC) with eIF4G is dispensable for translation in yeast
Publisher: Cold Spring Harbor Laboratory
Date: 06-2003
DOI: 10.1261/RNA.5100903
Abstract: In eukaryotes, the m 7 GpppN cap structure is added to all nascent RNA polymerase II transcripts, and serves important functions at multiple steps of RNA metabolism. The predominantly nuclear cap-binding complex (CBC) binds to the cap during RNA synthesis. The predominantly cytoplasmic eukaryotic initiation factor 4F (eIF4F) is thought to replace CBC after export of mature mRNA to the cytoplasm, and mediates the bulk of cellular translation. Yeast as well as mammalian CBC interacts in vitro with eIF4G, a subunit of eIF4F. In this work, we investigate a potential role of this interaction during translation in yeast. We identify a mutation (DR548/9AA) in Tif4631p, one of two isoforms of yeast eIF4G, that abolishes its binding to CBC. Cells expressing this mutant protein as the sole source of eIF4G grow at wild-type rates, and bulk cellular translation, as assessed by metabolic labeling and polysome profile analysis, is unchanged. Importantly, we find that the DR548/9AA mutation neither diminishes nor delays the translation of newly induced reporter mRNA. Finally, microarray analysis reveals marked transcriptome alterations in CBC subunit deletion strains, whereas eIF4G point mutants have essentially a wild-type transcriptome composition. Collectively, these data suggest that in yeast, the phenotypic consequences of CBC deletions are separable from its interaction with eIF4G, and that the CBC–eIF4G interaction is dispensable for a potential “pioneering round” of translation in yeast.
Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system
Publisher: Cold Spring Harbor Laboratory
Date: 12-2000
DOI: 10.1017/S1355838200001679
Abstract: In eukaryotic cells, efficient translation of most cellular mRNAs requires the synergistic interplay between the m7GpppN cap structure and the poly(A) tail during initiation. We have developed and characterized a cell-free system from human HeLa cells that recapitulates this important feature, displaying more than one order of magnitude of translational synergism between the cap structure and the poly(A) tail. The stimulation of cap-dependent translation by the poly(A) tail is length-dependent, but not mediated by changes in mRNA stability. Using this system, we investigated the effect of the poly(A) tail on the translation of picornaviral RNAs, which are naturally polyadenylated but initiate translation via internal ribosome entry sites (IRESs). We show that translation driven by the IRESs of poliovirus (PV), encephalomyocarditis virus (EMCV), and hepatitis A virus is also significantly augmented by a poly(A) tail, ranging from an approximately 3-fold stimulation for the EMCV-IRES to a more than 10-fold effect for the PV IRES. These results raise interesting questions concerning the underlying molecular mechanism(s). The cell-free system described here should prove useful in studying these questions as well as providing a general biochemical tool to examine the translation initiation pathway in a more physiological setting.
Identification of RNA-binding Proteins in Macrophages by Interactome Capture
Publisher: Elsevier BV
Date: 08-2016
Drosophila miR2 Primarily Targets the m7GpppN Cap Structure for Translational Repression
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.MOLCEL.2009.09.009
Abstract: Understanding the molecular mechanism(s) of how miRNAs repress mRNA translation is a fundamental challenge in RNA biology. Here we use a validated cell-free system from Drosophila embryos to investigate how miR2 inhibits translation initiation. By screening a library of chemical m7GpppN cap structure analogs, we identified defined modifications of the triphosphate backbone that augment miRNA-mediated inhibition of translation initiation but are "neutral" toward general cap-dependent translation. Interestingly, these caps also augment inhibition by 4E-BP. Kinetic dissection of translational repression and miR2-induced deadenylation shows that both processes proceed largely independently, with establishment of the repressed state involving a slow step. Our data demonstrate a primary role for the m7GpppN cap structure in miRNA-mediated translational inhibition, implicate structural determinants outside the core eIF4E-binding region in this process, and suggest that miRNAs may target cap-dependent translation through a mechanism related to the 4E-BP class of translational regulators.
Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock
Publisher: Springer Science and Business Media LLC
Date: 09-11-2003
DOI: 10.1038/NSB1015
Insights into the design and interpretation of iCLIP experiments
Publisher: Springer Science and Business Media LLC
Date: 16-01-2017
In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings
Publisher: Oxford University Press (OUP)
Date: 10-2016
DOI: 10.1105/TPC.16.00562
Poly(A)-tail-promoted translation in yeast: Implications for translational control
Publisher: Cold Spring Harbor Laboratory
Date: 11-1998
DOI: 10.1017/S1355838298980669
Abstract: The cap structure and the poly(A) tail synergistically activate mRNA translation in vivo. Recent work using Saccharomyces cerevisiae spheroplasts and a yeast cell-free translation system revealed that the poly(A) tail can function as an independent promotor for ribosome recruitment, to internal initiation sites within an mRNA. This raises the question of how regulatory upstream open reading frames and translational repressor proteins binding to the 5'UTR can function, as well as how regulated polyadenylation can support faithful activation of protein synthesis. We investigated the function of the regulatory upstream open reading frame 4 from the yeast GCN 4 gene and the effect of IRP-1 binding to an iron-responsive element introduced into the 5' UTR of reporter mRNAs. Both manipulations effectively block cap-dependent translation, whereas ribosome recruitment promoted by the poly(A) tail under non-competitive conditions can efficiently bypass both blocks. We show that the synergistic use of both, the cap structure and the poly-A tail enforced by mRNA competition reinstates the full extent of translational control by both types of 5' UTR regulatory elements. With a view towards regulated polyadenylation, we studied the function of poly(A) tails of defined length on the translation of capped mRNAs. We find that poly(A) tail elongation increases translational efficiency, particularly under competitive conditions. Our results integrate recent findings on the function of the poly(A) tail into an understanding of translational control.
microRNA-Mediated Messenger RNA Deadenylation Contributes to Translational Repression in Mammalian Cells
Publisher: Public Library of Science (PLoS)
Date: 27-08-2009
Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins
Publisher: Elsevier BV
Date: 12-2015
Translation driven by an eIF4G core domain in vivo
Publisher: Wiley
Date: 09-1999
Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
Publisher: Elsevier BV
Date: 06-2012
DOI: 10.1016/J.CELL.2012.04.031
Abstract: RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and comprehensive approach, termed "interactome capture," to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.
Dual function of the messenger RNA cap structure in poly(A)-tail- promoted translation in yeast
Publisher: Springer Science and Business Media LLC
Date: 04-1998
DOI: 10.1038/33192
Abstract: The messenger RNA 3' poly(A) tail critically affects the initiation and control of translation in eukaryotes. By analogy to elements involved in transcription initiation, the poly(A) tail has been described as a 'translational enhancer' that enhances the 'translational promoter' activity of the mRNA 5'-cap structure. Elongation or shortening of the poly(A) tail regulates translation during development. Here we show, using cell-free and in vivo translation analyses in Saccharomyces cerevisiae, that the poly(A) tail can act as an independent 'translational promoter', delivering ribosomes to uncapped mRNAs even if their 5' end is blocked. When mRNAs compete for ribosome binding, neither the cap structure nor the poly(A) tail alone is enough to drive efficient translation, but together they synergize and direct ribosome entry to the 5' end. The cap structure both promotes ribosome recruitment, together with the poly(A) tail, and tethers recruited ribosomes to the 5' end. Correct choice of translation initiation codons and the function of translational regulators acting on the 5' untranslated region are thus ensured by the functional interaction of the poly(A) tail with the cap structure.
The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease
Publisher: Elsevier BV
Date: 08-2016
Related Organisations
University Of Oxford Radcliffe Department Of Medicine
Location: United Kingdom of Great Britain and Northern Ireland
University Of Glasgow School Of Medicine
Location: United Kingdom of Great Britain and Northern Ireland
University Of Cambridge Medicine
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
No related grants have been discovered for Matthias Hentze.