• Struhl is primarily known for his work on transcriptional regulatory mechanisms in yeast using molecular, genetic, biochemical, and genomic approaches. (wikipedia.org)
  • Using T7 RNA polymerase in yeast cells, Struhl demonstrated distinct chromatin-accessibility and protein-protein interaction mechanisms for transcriptional activation. (wikipedia.org)
  • Novel genetic approaches - altered-specificity mutants, protein fusions for artificial recruitment - along with chromatin immunoprecipitation (ChIP), demonstrated that transcriptional regulation in yeast occurs primarily at the level of recruitment of the RNA polymerase II transcription machinery. (wikipedia.org)
  • Furthermore, mutation analyses of Fpr1 indicated that for transcriptional function on RPG promoters, Fpr1 requires its N-terminal domain and the binding surface for rapamycin, but not peptidyl-prolyl isomerase activity. (prolekarniky.cz)
  • Rapamycin induces the G0 program of transcriptional repression in yeast by interfering with the TOR signaling pathway. (prolekarniky.cz)
  • The availability of multiple PAS in the same 3' regulatory region enables the inclusion or exclusion of 3' untranslated region (3'UTR) sequences, resulting in transcripts that may differ in particularities involving post-transcriptional processes such as stability, transport and translation ( Mayr, 2016 ), and even protein localization ( Berkovits and Mayr, 2015 ). (frontiersin.org)
  • Interestingly, tracking CTD modifications upon heat-induced transcriptional reprogramming demonstrates that Pol II with phosphorylated CTD remains paused on thousands of heat-repressed genes. (bvsalud.org)
  • Non-cleaving Cas9 (dCas9) is widely employed to manipulate specific gene loci, often with scant regard for unintended transcriptional effects. (bvsalud.org)
  • We demonstrate here that dCas9 mediates precise RNA polymerase II transcriptional pausing followed by transcription termination and potential alternative polyadenylation. (bvsalud.org)
  • Many of these pathways are highly conserved, and 53 distinct kinase functions and subfamilies appear to have been conserved between yeasts, nematodes, insects and vertebrates, with a further 91 subfamilies of kinases being seen throughout metazoan genomes. (wormbook.org)
  • Most protein kinases share a common ePK (eukaryotic protein kinase) catalytic domain, and can be identified by sequence similarity with Blast or profile hidden Markov models (HMMs). (wormbook.org)
  • We identified 438 protein kinase genes, including 20 atypical kinases, and an additional 25 kinase fragments or pseudogenes. (wormbook.org)
  • In addition, calcofluor white sensitivity of the strain was enhanced by the protein kinase inhibitor staurosporine, a phenotype shared with the Ada components of the SAGA/SLIK complex. (biomedcentral.com)
  • Lastly, Struhl showed that the Jun oncogene encodes a Gcn4 homolog that binds the same sequences and activates transcription in yeast cells. (wikipedia.org)
  • 7. Chiu MI, Katz H, Berlin V. RAPT1, a mammalian homolog of yeast Tor, interacts with the FKBP12/rapamycin complex. (prolekarniky.cz)
  • Notably, Fpr1 orthologues from other species also inhibit TORC1 when bound to rapamycin, but do not regulate transcription in yeast, which suggests that these two functions of Fpr1 are independent of each other. (prolekarniky.cz)
  • Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. (frontiersin.org)
  • Protein kinases are one of the largest and most influential of gene families: constituting some 2% of the proteome, they regulate almost all biochemical pathways and may phosphorylate up to 30% of the proteome. (wormbook.org)
  • Members of this family include the signal-transducing G protein beta subunit, as well as other proteins that regulate signal transduction, transcription, pre-mRNA splicing, cytoskeletal organization, and vesicular fusion. (embl.de)
  • Detailed genetic dissection led to the discovery of short acidic activation domains required for transcription that are functionally autonomous and can be encoded by different sequences. (wikipedia.org)
  • In the current study, extensive chromatin immunoprecipitation (ChIP) and ChIP-sequencing analyses revealed that Fpr1 associates specifically with the upstream activating sequences of nearly all RPG (ribosomal protein gene) promoters, presumably in a manner dependent on Rap1 (repressor/activator site binding protein 1). (prolekarniky.cz)
  • The specificity of the proteins is determined by the sequences outside the repeats themselves. (embl.de)
  • Jun was the first example of an oncogene that encodes a transcription factor. (wikipedia.org)
  • The mammalian genome comprises nuclear DNA (nDNA) derived from both parents and mitochondrial DNA (mtDNA) that is maternally inherited and encodes essential proteins required for oxidative phosphorylation. (regenerativemedicine.net)
  • Intriguingly, Fpr1 promotes the binding of Fhl1/Ifh1 (forkhead-like 1/interacts with forkhead 1), two key regulators of RPG transcription, to certain RPG promoters independently of and/or cooperatively with Hmo1. (prolekarniky.cz)
  • In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)
  • By phosphorylating substrate proteins, kinases modify the activity, location and affinities of up to 30% of all cellular proteins, and direct most cellular processes, particularly in signal transduction and co-ordination of complex pathways. (wormbook.org)
  • WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. (embl.de)
  • To address this problem, we combine Fab-based labeling of endogenous protein modifications with single-molecule tracking to quantify the dynamics of chromatin enriched with histone H3 lysine-27 acetylation (H3K27ac) and RNA polymerase II serine-5 phosphorylation (RNAP2-Ser5ph). (bvsalud.org)
  • The 48 kDa subunit, RETINOBLASTOMA-BINDING PROTEIN 4, is also a component of several other protein complexes involved in chromatin remodeling. (lookformedical.com)
  • A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and repression of GENETIC TRANSCRIPTION. (lookformedical.com)
  • Although initially discovered as a retinoblastoma binding protein it has an affinity for core HISTONES and is a subunit of chromatin assembly factor-1 and polycomb repressive complex 2. (lookformedical.com)
  • The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. (lookformedical.com)
  • This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS. (lookformedical.com)
  • As a graduate student, Struhl cloned and functionally expressed the first eukaryotic protein-coding gene in E.coli, a landmark in recombinant DNA technology. (wikipedia.org)
  • Using "reverse genetics" to study gene regulation in vivo, Struhl generated the first eukaryotic promoter mutants and performed a detailed analysis of the his3 gene. (wikipedia.org)
  • In one of the first examples of a eukaryotic sequence-specific binding protein, he discovered that Gcn4 coordinately activates many genes involved in amino acid biosynthesis by direct binding to bound target sites in their promoters. (wikipedia.org)
  • Protein kinases constitute one of the largest and most important of protein families, accounting for ~2% of genes in a variety of eukaryotic genomes. (wormbook.org)
  • A complex interaction between the cleavage and polyadenylation molecular complex and cis -elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. (frontiersin.org)
  • These results uncover dynamic Pol II regulation at rate-limiting steps of transcription and provide a nucleotide-resolution technique for tracking composition of engaged transcription complexes. (bvsalud.org)
  • A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1. (colorado.edu)
  • 1. Warner JR. The economics of ribosome biosynthesis in yeast. (prolekarniky.cz)
  • A histone chaperone protein that plays a role in the deposition of NUCLEOSOMES on newly synthesized DNA. (lookformedical.com)
  • and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell. (lookformedical.com)
  • It is found as a subunit of protein complexes that are in involved in the enzymatic modification of histones including the Mi2 and Sin3 histone deacetylase complexes and the polycomb repressive complex 2. (lookformedical.com)
  • Polyadenylation is essential for the stability of the transcript, preventing the mRNA from being the target of posttranscriptional gene silencing (PTGS) via RNA-dependent RNA polymerase 6 (RDR6) in plants ( Luo and Chen, 2007 ). (frontiersin.org)
  • Through APA, a single gene containing multiple PAS can generate a considerable number of transcript isoforms, thereby producing a highly diversified transcriptome ( Tian and Manley, 2013 ). (frontiersin.org)
  • Homo sapiens BUB3 mitotic checkpoint protein (BUB3), transcript variant 2, mRNA. (dbcls.jp)
  • Homo sapiens CGG triplet repeat binding protein 1 (CGGBP1), transcript variant 1, mRNA. (dbcls.jp)
  • Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. (bvsalud.org)
  • In a hmo1 Δ (high mobility group family 1-deleted) yeast strain, deletion of FPR1 induced severe growth defects, which could be alleviated by increasing the copy number of RPL25 (ribosome protein of the large subunit 25), suggesting that RPL25 expression was affected in hmo1 Δ fpr1 Δ cells. (prolekarniky.cz)
  • RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. (bvsalud.org)
  • Folding of proteins with WD-repeats: comparison of six members of the WD-repeat superfamily to the G protein beta subunit. (embl.de)
  • Here, we develop Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq), which double-selects nascent RNAs and transcription complexes, and track phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. (bvsalud.org)
  • Eukaryotes have a mechanism termed alternative polyadenylation (APA), which allows the selective use of PAS in genes containing multiple PAS. (frontiersin.org)
  • The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes. (lookformedical.com)
  • We chose proteins that include amino and carboxyl extensions as well as proteins that are made up entirely of WD-repeats. (embl.de)
  • Struhl invented "reverse biochemistry", the use of in vitro synthesized proteins to identify DNA-binding transcription factors and study protein-DNA interactions. (wikipedia.org)
  • However, the only studied example of a WD-repeat protein, G beta, synthesized in vitro in a rabbit reticulocyte lysate, is unable to fold into a native structure without its partner protein G gamma. (embl.de)
  • It is not known whether all WD-repeat proteins are unable to fold when synthesized in an in vitro system. (embl.de)
  • Together with Tom Gingeras, he used tiled microarrays to generate the first unbiased, genome-scale analysis of transcription factor binding in mammalian cells, leading to the discovery of far more transcription binding sites in vivo than predicted, including many that control non-coding RNAs. (wikipedia.org)
  • Struhl showed that the TATA-binding protein is required for transcription by all 3 nuclear RNA polymerases and defined a surface required specifically for transcription by RNA polymerase III. (wikipedia.org)
  • A family of cellular proteins that mediate the correct assembly or disassembly of polypeptides and their associated ligands. (lookformedical.com)
  • Cloned yeast genes were essential for Gerald Fink to develop transformation methods that Struhl used to co-discover DNA replication origins and to create the first vectors for molecular genetic manipulations in yeast. (wikipedia.org)
  • Recent breakthroughs have uncovered more and more DNA replication licensing machinery proteins (ORC, Cdc6, Cdt1, geminin, etc.) functioning in other cell cycle events, including centrosome replication, mitotic events, transcription and so on. (intechopen.com)
  • Structure-function analysis of Hmo1 unveils an ancestral organization of HMG-Box factors involved in ribosomal DNA transcription from yeast to human. (prolekarniky.cz)
  • These biomolecular condensates (BMCs) are 0.5 to 1 µm in diameter, have a macromolecular density of approximately 100 mg/ml, and are a consequence of a phase transition between promoter DNA and nuclear extract proteins. (bvsalud.org)
  • The precise regulations of pre-RC protein levels and assembly are effective ways to prevent reassembly of de novo MCM2-7 onto the replicated origins to re-license and re-replicate the genomic DNA in the subsequent phases of the same cell cycle ( Figure 1) . (intechopen.com)
  • Genes involved in transcription, RNA processing, mitochondrial function and membrane sorting/protein trafficking were prevalent. (biomedcentral.com)
  • Isolation of a protein target of the FKBP12-rapamycin complex in mammalian cells. (prolekarniky.cz)
  • Transcription in the nucleus occurs in a concentrated, dense environment, and no reasonable biochemical facsimile of this milieu exists. (bvsalud.org)
  • Proteins found in the nucleus of a cell. (lookformedical.com)
  • Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus. (lookformedical.com)
  • several WD40-containing proteins act as key regulators of plant-specific developmental events. (embl.de)
  • We uncover precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide (+1 nt), through early (+18 to +30 nt) and late (+31 to +60 nt) promoter-proximal pause, and into productive elongation. (bvsalud.org)
  • PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. (lookformedical.com)
  • The identity of the SSL genes also connects Tra1 with cellular stress, a result confirmed by the sensitivity of the tra1 SRR 3413 strain to a variety of stress conditions. (biomedcentral.com)
  • Violin plots show distribution of expression levels for WD_REPEATS_REGION domain-containing protein (SMED30005158) in cells (dots) of each of the 12 neoblast clusters. (stowers.org)
  • Expression of WD_REPEATS_REGION domain-containing protein (SMED30005158) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells. (stowers.org)
  • WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. (embl.de)
  • We show that unlike G beta, several proteins with WD-repeats are able to fold into globular proteins in a rabbit reticulocyte lysate. (embl.de)
  • The 3' regulatory regions have a great diversity of cis -regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. (frontiersin.org)
  • A hierarchal cluster analysis revealed that the pattern of SSL interactions for tra1 SRR 3413 most closely resembles deletions of a group of regulatory GTPases required for membrane sorting/protein trafficking. (biomedcentral.com)
  • This analysis did not identify any synthetic lethal interactions but did reveal 23 synthetic slow growth interactions, many in combination with deletions of genes involved in cell membrane/wall processes. (biomedcentral.com)
  • This analysis identified 114 genes displaying synthetic sick/lethal (SSL) interactions with tra1 SRR 3413 . (biomedcentral.com)
  • We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. (stowers.org)
  • If WD proteins form structures similar to G beta, their hydrodynamic properties should be those of compact, globular proteins, and they should be resistant to cleavage by trypsin. (embl.de)
  • In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions. (frontiersin.org)
  • Expression of each cluster's gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq. (stowers.org)
  • t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). (stowers.org)
  • We showed previously that cytoplasmic release of mtDNA activates the cGAS STING TBK1 pathway resulting in interferon-stimulated gene (ISG) expression that promotes antiviral immunity4. (regenerativemedicine.net)
  • Here, we find that persistent mtDNA stress is not associated with basally activated NF-κB signalling or interferon gene expression typical of an acute antiviral response. (regenerativemedicine.net)
  • Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. (prolekarniky.cz)
  • Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. (lookformedical.com)
  • The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. (lookformedical.com)
  • The family of WD-repeat proteins comprises over 30 different proteins that share a highly conserved repeating motif [Neer, E. J., Schmidt, C. J., Nambudripad, R., & Smith, T. F. (1994) Nature 371, 297-300]. (embl.de)
  • To put worm kinases into an evolutionary and functional context, we compared them with the distant kinomes of human, fly, and yeast. (wormbook.org)
  • In addition many of the genes have roles in the cellular response to stress. (biomedcentral.com)
  • e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens. (lookformedical.com)
  • It is very likely that all WD-repeat proteins form a similar structure. (embl.de)
  • Such radiations include genes involved in spermatogenesis, chemosensation, Wnt signaling and FGF receptor-like kinases. (wormbook.org)
  • Specific protein-binding measures are often used as assays in diagnostic assessments. (lookformedical.com)
  • Taxonomic distribution of proteins containing WD40 domain. (embl.de)