DNA-dependent protein kinase interacts functionally with the RNA
... Recruitment of DNA-PK at the HIV LTR As it is known that DNA-PK phosphorylates the CTD of RNAP II (Dvir et al., 1993; Trigon et al., 1998), we performed chromatin immunoprecipitation (ChIP) assays to investigate the possible presence of this enzyme at the HIV LTR. These assays were performed by usin ...
... Recruitment of DNA-PK at the HIV LTR As it is known that DNA-PK phosphorylates the CTD of RNAP II (Dvir et al., 1993; Trigon et al., 1998), we performed chromatin immunoprecipitation (ChIP) assays to investigate the possible presence of this enzyme at the HIV LTR. These assays were performed by usin ...
Dual function of Swc5 in SWR remodeling ATPase activation and
... is required to couple substrate recognition to ATPase activation. A biochemical complementation assay was developed to show that a unique, conserved domain at the C-terminus of Swc5, called Bucentaur (BCNT), is essential for the histone exchange activity of SWR, whereas an acidic region at the N-ter ...
... is required to couple substrate recognition to ATPase activation. A biochemical complementation assay was developed to show that a unique, conserved domain at the C-terminus of Swc5, called Bucentaur (BCNT), is essential for the histone exchange activity of SWR, whereas an acidic region at the N-ter ...
The identification of transcription factors expressed in the notochord
... Ciona intestinalis at various stages of embryonic development. Four of these transcription factors, Fos-a, NFAT5, AFF and Klf15, have not been directly associated with the notochord in previous studies, while the others, including Spalt-like-a, Lmx-like, and STAT5/6-b, display evolutionarily conserv ...
... Ciona intestinalis at various stages of embryonic development. Four of these transcription factors, Fos-a, NFAT5, AFF and Klf15, have not been directly associated with the notochord in previous studies, while the others, including Spalt-like-a, Lmx-like, and STAT5/6-b, display evolutionarily conserv ...
Role of hsp90 and the hsp90-binding immunophilins in signalling
... effective at reducing GR hormone binding affinity and reporter gene expression. In contrast to these observations, Patel et al. [44] found that the human GR has a normal dose response for transactivation regardless of whether it is expressed in New World or Old World primate cells. They cloned the G ...
... effective at reducing GR hormone binding affinity and reporter gene expression. In contrast to these observations, Patel et al. [44] found that the human GR has a normal dose response for transactivation regardless of whether it is expressed in New World or Old World primate cells. They cloned the G ...
Word document
... structure is being probed by these assays (Dillon and Grosveld, 1994). Nevertheless, these studies reveal that regions of nuclease accessible, or “open” chromatin often correlate with gene regulatory regions. In some cases, a more widespread increase in accessibility is observed over entire chromati ...
... structure is being probed by these assays (Dillon and Grosveld, 1994). Nevertheless, these studies reveal that regions of nuclease accessible, or “open” chromatin often correlate with gene regulatory regions. In some cases, a more widespread increase in accessibility is observed over entire chromati ...
Clockwork green—the circadian oscillator in
... levels are reduced in the gi mutant. As GI reaches its highest level around dusk, it may be a positive regulator of TOC1. The reduced TOC1 levels in turn would result in lower expression of CCA1 and LHY, as, indeed, is observed in gi (Park et al. 1999). GIGANTEA was also recovered as an interaction ...
... levels are reduced in the gi mutant. As GI reaches its highest level around dusk, it may be a positive regulator of TOC1. The reduced TOC1 levels in turn would result in lower expression of CCA1 and LHY, as, indeed, is observed in gi (Park et al. 1999). GIGANTEA was also recovered as an interaction ...
Myocyte Enhancer Factor 2 Transcription Factors in Heart
... In contrast to the MADS and MEF2 domains, the Cterminal regions of MEF2 proteins are highly-divergent and also highly-variable within a single gene, as a result of regulated RNA splicing. MEF2 primary transcripts are subjected to alternative splicing, skip splicing and cryptic splice site selection, ...
... In contrast to the MADS and MEF2 domains, the Cterminal regions of MEF2 proteins are highly-divergent and also highly-variable within a single gene, as a result of regulated RNA splicing. MEF2 primary transcripts are subjected to alternative splicing, skip splicing and cryptic splice site selection, ...
The AMP-activated protein kinase pathway – new
... Second, AMP binding makes AMPK a better substrate for the upstream kinase. The upstream kinase, recently identified as the tumour suppressor LKB1 (see below), activates the kinase by phosphorylation of the α subunit at a specific threonine residue (Thr172) (Hawley et al., 1996) in the socalled activ ...
... Second, AMP binding makes AMPK a better substrate for the upstream kinase. The upstream kinase, recently identified as the tumour suppressor LKB1 (see below), activates the kinase by phosphorylation of the α subunit at a specific threonine residue (Thr172) (Hawley et al., 1996) in the socalled activ ...
RFX2 is broadly required for ciliogenesis during
... (Huangfu et al., 2003). Substantial studies have now revealed that defects in cilia structure or function lie at the root of a wide range of human diseases, such as primary ciliary dyskinesia, polycystic kidney disease, and Bardet–Biedl and Meckel–Gruber syndromes (Baker and Beales, 2009; Hildebrand ...
... (Huangfu et al., 2003). Substantial studies have now revealed that defects in cilia structure or function lie at the root of a wide range of human diseases, such as primary ciliary dyskinesia, polycystic kidney disease, and Bardet–Biedl and Meckel–Gruber syndromes (Baker and Beales, 2009; Hildebrand ...
AMP-activated protein kinase phosphorylates transcription factors of
... LKB1 is not expressed in muscle (Fig. 1B). Although phosphoAMPK did not appear to be increased 1 h following the final injection with AICAR, phospho-ACC was markedly increased in wild-type but not in MLKB1-KO mice (Fig. 1A). This provides evidence for the ZMP-triggered allosteric activation of phosp ...
... LKB1 is not expressed in muscle (Fig. 1B). Although phosphoAMPK did not appear to be increased 1 h following the final injection with AICAR, phospho-ACC was markedly increased in wild-type but not in MLKB1-KO mice (Fig. 1A). This provides evidence for the ZMP-triggered allosteric activation of phosp ...
Write on zinc fingers
... The most straightforward method to generate new zinc finger arrays is to combine smaller zinc finger "modules" of known specificity. The structure of the zinc finger protein Zif268 bound to DNA described by Pavletich and Pabo in their 1991 publication has been key to much of this work and describes ...
... The most straightforward method to generate new zinc finger arrays is to combine smaller zinc finger "modules" of known specificity. The structure of the zinc finger protein Zif268 bound to DNA described by Pavletich and Pabo in their 1991 publication has been key to much of this work and describes ...
Genome-Wide Distribution of Yeast RNA Polymerase II and Its
... have identified the Sen1 protein as a Pol II termination factor that functions with the RNA-binding proteins Nrd1 and Nab3 on noncoding RNA genes (Steinmetz and Brow, 1996; Steinmetz et al., 2001). Sen1 is an essential 252 kDa superfamily 1 helicase that is most similar to Upf1/SMG-2 and SDE3/Armita ...
... have identified the Sen1 protein as a Pol II termination factor that functions with the RNA-binding proteins Nrd1 and Nab3 on noncoding RNA genes (Steinmetz and Brow, 1996; Steinmetz et al., 2001). Sen1 is an essential 252 kDa superfamily 1 helicase that is most similar to Upf1/SMG-2 and SDE3/Armita ...
Chapter 1
... of transcription factors in controlling the stomatal opening and closure (as reviewed by Cominelli et al., 2010) [4]. MYB proteins are a class of transcription factors that are present in all eukaryotes, and share a common DNA-binding domain. In plants, the most highly represented MYB protein group ...
... of transcription factors in controlling the stomatal opening and closure (as reviewed by Cominelli et al., 2010) [4]. MYB proteins are a class of transcription factors that are present in all eukaryotes, and share a common DNA-binding domain. In plants, the most highly represented MYB protein group ...
Crosstalk in NF-κB signaling pathways
... of IRF3 (ref. 28). The relative contribution to this process of TRAFs and other E3 ligases needs further investigation under physiological conditions. Furthermore, it remains unclear whether the requirement for TRAF3 in interferon production likewise depends on its E3 ligase activity. As it would se ...
... of IRF3 (ref. 28). The relative contribution to this process of TRAFs and other E3 ligases needs further investigation under physiological conditions. Furthermore, it remains unclear whether the requirement for TRAF3 in interferon production likewise depends on its E3 ligase activity. As it would se ...
Transcriptional Control of Endothelial Cell Development
... well-characterized roles in endothelial gene expression and each bind to the enhancers and activate the expression of numerous endothelial genes (Table 1). Knockdown of either Ets1 or Erg expression in endothelial cells in culture results in decreased endothelial cell migration and tube formation (B ...
... well-characterized roles in endothelial gene expression and each bind to the enhancers and activate the expression of numerous endothelial genes (Table 1). Knockdown of either Ets1 or Erg expression in endothelial cells in culture results in decreased endothelial cell migration and tube formation (B ...
WW Domains Provide a Platform for the
... during 25 min with a total run time of 45 min. Data were analyzed in batch using the Mascot search engine (57), and proteins were considered “hits” if two independent peptides or a single peptide with a Mascot score of 50 or higher was found. Protein hits were converted to gene identifiers (GeneIDs) ...
... during 25 min with a total run time of 45 min. Data were analyzed in batch using the Mascot search engine (57), and proteins were considered “hits” if two independent peptides or a single peptide with a Mascot score of 50 or higher was found. Protein hits were converted to gene identifiers (GeneIDs) ...
A Per-ARNT-Sim-Like Sensor Domain Uniquely
... which ZPR proteins act to negatively regulate HD-ZIP III activity by preventing their dimerization. The structure of HD-ZIP III proteins suggests additional mechanisms of posttranslational regulation. In addition to the homeodomain and leucine zipper domain, HD-ZIP III proteins contain, in order fro ...
... which ZPR proteins act to negatively regulate HD-ZIP III activity by preventing their dimerization. The structure of HD-ZIP III proteins suggests additional mechanisms of posttranslational regulation. In addition to the homeodomain and leucine zipper domain, HD-ZIP III proteins contain, in order fro ...
ANALYSIS OF A BACTERIAL SERINE/THREONINE KINASE
... Protein kinase activity was first detected in Salmonella by Wang and Koshland Jr. (1978) in the late 1970s. Since that time several protein kinases have been characterized in this organism particularly those which are part of the canonical two-component system. Phosphorylation of protein and non-pro ...
... Protein kinase activity was first detected in Salmonella by Wang and Koshland Jr. (1978) in the late 1970s. Since that time several protein kinases have been characterized in this organism particularly those which are part of the canonical two-component system. Phosphorylation of protein and non-pro ...
NF-kB as a primary regulator of the stress response
... facilitating recruitment of aPKCs to the TNF receptor complex. The aPKCs then function to directly activate IKK2 and consequently NF-kB. The precise mechanism by which intracellular signals are relayed from the cell membrane to the nucleus are complex and varied. One theme involves the integration o ...
... facilitating recruitment of aPKCs to the TNF receptor complex. The aPKCs then function to directly activate IKK2 and consequently NF-kB. The precise mechanism by which intracellular signals are relayed from the cell membrane to the nucleus are complex and varied. One theme involves the integration o ...
Gre factors-mediated control of hilD transcription is essential for the
... that infects both humans and animals, is extensively used as a model organism in pathogenicity studies [1,2]. S. Typhimurium infection is asymptomatic in poultry, but causes gastroenteritis in humans [3]. Its infectious cycle is complex and requires the expression of a large number of virulence fact ...
... that infects both humans and animals, is extensively used as a model organism in pathogenicity studies [1,2]. S. Typhimurium infection is asymptomatic in poultry, but causes gastroenteritis in humans [3]. Its infectious cycle is complex and requires the expression of a large number of virulence fact ...
Ammonium utilization in Bacillus subtilis: transport and regulatory
... alternative nitrogen sources such as ammonium can be used. Ammonium utilization involves the uptake of the gas or the ammonium ion, the synthesis of glutamine by the glutamine synthetase and the recycling of the glutamate by the glutamate synthase. In this work, ammonium transport in B. subtilis was ...
... alternative nitrogen sources such as ammonium can be used. Ammonium utilization involves the uptake of the gas or the ammonium ion, the synthesis of glutamine by the glutamine synthetase and the recycling of the glutamate by the glutamate synthase. In this work, ammonium transport in B. subtilis was ...
A Dominant Negative Mutant of Cyclin-Dependent
... coding sequence to distinguish the protein encoded by this gene (CDKA-WT) from the endogenous CDKA. A mutation in the coding sequence of CDKA-WT that converted Asp146 to Asn146 was made by site-directed mutagenesis, creating the CDKA-DN gene. As a consequence of this mutation, the ATP-dependent phos ...
... coding sequence to distinguish the protein encoded by this gene (CDKA-WT) from the endogenous CDKA. A mutation in the coding sequence of CDKA-WT that converted Asp146 to Asn146 was made by site-directed mutagenesis, creating the CDKA-DN gene. As a consequence of this mutation, the ATP-dependent phos ...
Document
... been revised from 5154 to 2222… – FANTOM/RIKEN Consortium Science, March 2006 Brendan Frey ...
... been revised from 5154 to 2222… – FANTOM/RIKEN Consortium Science, March 2006 Brendan Frey ...
osa and brahma interact in Drosophila - Development
... steps involved in maintaining HOM gene function (such as transcriptional activation, posttranslational modification of HOM proteins, and expression of required HOM protein cofactors) the trxG genes are expected to be far more heterogeneous in function than the PcG genes, which all appear to repress ...
... steps involved in maintaining HOM gene function (such as transcriptional activation, posttranslational modification of HOM proteins, and expression of required HOM protein cofactors) the trxG genes are expected to be far more heterogeneous in function than the PcG genes, which all appear to repress ...
The nonenzymatic subunit of pseutarin C, a
... complex” with the nonenzymatic cofactor factor Va (FVa), calcium ions, and phospholipid membranes.1 Phospholipids stimulate prothrombin activation by lowering the Km for prothrombin2-4 and provide a surface on which FXa, FVa, and prothrombin bind in the presence of Ca2⫹, leading to a productive enzy ...
... complex” with the nonenzymatic cofactor factor Va (FVa), calcium ions, and phospholipid membranes.1 Phospholipids stimulate prothrombin activation by lowering the Km for prothrombin2-4 and provide a surface on which FXa, FVa, and prothrombin bind in the presence of Ca2⫹, leading to a productive enzy ...
Histone acetylation and deacetylation
Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation. Histone acetylation and deacetylation are essential parts of gene regulation. These reactions are typically catalysed by enzymes with ""histone acetyltransferase"" (HAT) or ""histone deacetylase"" (HDAC) activity. Acetylation is the process where an acetyl functional group is transferred from one molecule (in this case, Acetyl-Coenzyme A) to another. Deacetylation is simply the reverse reaction where an acetyl group is removed from a molecule.Acetylated histones, octameric proteins that organize chromatin into nucleosomes and ultimately higher order structures, represent a type of epigenetic marker within chromatin. Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity. Relaxed, transcriptionally active DNA is referred to as euchromatin. More condensed (tightly packed) DNA is referred to as heterochromatin. Condensation can be brought about by processes including deacetylation and methylation; the action of methylation is indirect and has no effect upon charge.