The Experts below are selected from a list of 235233 Experts worldwide ranked by ideXlab platform
Eric N Olson - One of the best experts on this subject based on the ideXlab platform.
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activated notch inhibits myogenic activity of the mads box transcription factor myocyte enhancer factor 2c
Molecular and Cellular Biology, 1999Co-Authors: Jeanne Wilsonrawls, Jeffery D Molkentin, Brian L Black, Eric N OlsonAbstract:Skeletal muscle gene expression is dependent on combinatorial associations between members of the MyoD family of basic helix-loop-helix (bHLH) transcription factors and the myocyte enhancer factor 2 (MEF2) family of MADS-box transcription factors. The transmembrane receptor Notch interferes with the muscle-inducing activity of myogenic bHLH proteins, and it has been suggested that this inhibitory activity of Notch is directed at an essential cofactor that recognizes the DNA binding Domains of the myogenic bHLH proteins. Given that MEF2 proteins interact with the DNA binding Domains of myogenic bHLH factors to cooperatively regulate myogenesis, we investigated whether members of the MEF2 family might serve as targets for the inhibitory effects of Notch on myogenesis. We show that a constitutively activated form of Notch specifically blocks DNA binding by MEF2C, as well as its ability to cooperate with MyoD and myogenin to activate myogenesis. Responsiveness to Notch requires a 12-amino-acid region of MEF2C immediately adjacent to the DNA binding domain that is unique to this MEF2 isoform. Two-hybrid assays and coimmunoprecipitations show that this region of MEF2C interacts directly with the ankyrin repeat region of Notch. These findings reveal a novel mechanism for Notch-mediated inhibition of myogenesis and demonstrate that the Notch signaling pathway can discriminate between different members of the MEF2 family.
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combinatorial control of muscle development by basic helix loop helix and mads box transcription factors
Proceedings of the National Academy of Sciences of the United States of America, 1996Co-Authors: Jeffery D Molkentin, Eric N OlsonAbstract:Members of the MyoD family of muscle-specific basic helix-loop-helix (bHLH) proteins function within a genetic pathway to control skeletal muscle development. Mutational analyses of these factors suggested that their DNA binding Domains mediated interaction with a coregulator required for activation of muscle-specific transcription. Members of the myocyte enhancer binding factor 2 (MEF2) family of MADS-box proteins are expressed at high levels in muscle and neural cells and at lower levels in several other cell types. MEF2 factors are unable to activate muscle gene expression alone, but they potentiate the transcriptional activity of myogenic bHLH proteins. This potentiation appears to be mediated by direct interactions between the DNA binding Domains of these different types of transcription factors. Biochemical and genetic evidence suggests that MEF2 factors are the coregulators for myogenic bHLH proteins. The presence of MEF2 and cell-specific bHLH proteins in other cell types raises the possibility that these proteins may also cooperate to regulate other programs of cell-specific gene expression. We present a model to account for such cooperative interactions.
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cooperative activation of muscle gene expression by mef2 and myogenic bhlh proteins
Cell, 1995Co-Authors: Jeffery D Molkentin, Brian L Black, James F Martin, Eric N OlsonAbstract:Members of the myocyte enhancer factor-2 (MEF2) family of MADS domain transcription factors cannot induce myogenesis in transfected fibroblasts, but when coexpressed with the myogenic basic-helix-loop-helix (bHLH) proteins MyoD or myogenin they dramatically increase the extent of myogenic conversion above that seen with either myogenic bHLH factor alone. This cooperativity required direct interactions between the DNA-binding Domains of MEF2 and the myogenic bHLH factors, but only one of the factors needed a transactivation domain, and only one of the factors needed to be bound to DNA. These interactions allow either factor to activate transcription through the other's binding site and reveal a novel mechanism for indirect activation of gene expression via protein-protein interactions between the DNA-binding Domains of heterologous classes of transcription factors.
Michael Wierer - One of the best experts on this subject based on the ideXlab platform.
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atomic resolution mapping of transcription factor dna interactions by femtosecond laser crosslinking and mass spectrometry
Nature Communications, 2020Co-Authors: Alexander Reim, Roland Ackermann, Jofre Fontmateu, Robert Kammel, Miguel Beato, Stefan Nolte, Matthias Mann, Christoph Russmann, Michael WiererAbstract:Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding Domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding Domains, paving the way for future large scale ex vivo experiments.
Stefan Nolte - One of the best experts on this subject based on the ideXlab platform.
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atomic resolution mapping of transcription factor dna interactions by femtosecond laser crosslinking and mass spectrometry
Nature Communications, 2020Co-Authors: Alexander Reim, Roland Ackermann, Jofre Fontmateu, Robert Kammel, Miguel Beato, Stefan Nolte, Matthias Mann, Christoph Russmann, Michael WiererAbstract:Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding Domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding Domains, paving the way for future large scale ex vivo experiments.
A M Edwards - One of the best experts on this subject based on the ideXlab platform.
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crystal structure of thermotoga maritima 0065 a member of the iclr transcriptional factor family
Journal of Biological Chemistry, 2002Co-Authors: Rongguang Zhang, A M Edwards, Youngchang Kim, Tatiana Skarina, S Beasley, Roman A Laskowski, C H Arrowsmith, Andrzej Joachimiak, Alexei SavchenkoAbstract:Abstract Members of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. TheThermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two Domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn2+ ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding Domains. In the dimer, the DNA-binding Domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding Domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding Domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target.
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the crystal structure of the complex of replication protein a subunits rpa32 and rpa14 reveals a mechanism for single stranded dna binding
The EMBO Journal, 1999Co-Authors: A Bochkarev, Elena Bochkareva, Lori Frappier, A M EdwardsAbstract:Replication protein A (RPA), the eukaryote single-stranded DNA-binding protein (SSB), is a heterotrimer. The largest subunit, RPA70, which harbours the major DNA-binding activity, has two DNA-binding Domains that each adopt an OB-fold. The complex of the two smaller subunits, RPA32 and RPA14, has weak DNA-binding activity but the mechanism of DNA binding is unknown. We have determined the crystal structure of the proteolytic core of RPA32 and RPA14, which consists of the central two-thirds of RPA32 and the entire RPA14 subunit. The structure revealed that RPA14 and the central part of RPA32 are structural homologues. Each subunit contains a central OB-fold domain, which also resembles the DNA-binding Domains in RPA70; an N-terminal extension that interacts with the central OB-fold domain; and a C-terminal helix that mediate heterodimerization via a helix-helix interaction. The OB-fold of RPA32, but not RPA14, possesses additional similarity to the RPA70 DNA-binding Domains, supporting a DNA-binding role for RPA32. The discovery of a third and fourth OB-fold in RPA suggests that the quaternary structure of SSBs, which in Bacteria and Archaea are also tetramers of OB-folds, is conserved in evolution. The structure also suggests a mechanism for RPA trimer formation.
Jacques Drouin - One of the best experts on this subject based on the ideXlab platform.
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pax7 pioneer factor action requires both paired and homeo dna binding Domains
Nucleic Acids Research, 2021Co-Authors: Audrey Pelletier, A Mayran, A Gouhier, Aurelio Balsalobre, James G Omichinski, Jacques DrouinAbstract:The pioneer transcription factor Pax7 contains two DNA binding Domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 showed that each DBD binds a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed sites for both paired and homeo Domains. The present work investigated the implication of the DBDs in pioneer action. We show that the composite sequence is a higher affinity binding site and that efficient binding to this site involves both DBDs of the same Pax7 molecule. This binding is not sensitive to cytosine methylation of the DNA sites consistent with pioneer action within nucleosomal heterochromatin. Introduction of single amino acid mutations in either paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites.
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pax7 pioneer factor action requires both paired and homeo dna binding Domains
bioRxiv, 2020Co-Authors: Audrey Pelletier, A Mayran, A Gouhier, Aurelio Balsalobre, James G Omichinski, Jacques DrouinAbstract:Abstract The pioneer transcription factor Pax7 contains two DNA binding Domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 had shown that each DBD can bind a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed binding sites for both paired and homeo Domains. The present work investigated the implication of both DBDs in pioneer action. We now show that the composite sequence is a higher affinity Pax7 binding site compared to either paired or homeo binding sites and that efficient binding to this site involves both DBDs. We also show that a Pax7 monomer binds composite sites and that methylation of cytosines within the binding site does not affect binding, which is consistent with pioneer action exerted at methylated DNA sites within nucleosomal heterochromatin. Finally, introduction of single amino acid mutations in either the paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites. Significance Statement Pioneer transcription factors have the unique ability to recognize DNA target sites within closed heterochromatin and to trigger chromatin opening. Only a fraction of the heterochromatin recruitment sites of pioneers are subject to chromatin opening. The molecular basis for this selectivity is unknown and the present work addressed the importance of DNA sequence affinity for selection of sites to open. The pioneering ability of the pioneer factor Pax7 is not strictly determined by affinity or DNA sequence of binding sites, nor by number or methylation status of DNA sites. Mutation analyses showed that recruitment to heterochromatin is primarily dependent on the Pax7 paired domain whereas the ability to open chromatin requires both paired and homeo DNA binding Domains.