Genomes and Genes
Experts and Doctors on transcription factors in University Park, Florida, United States
Locale: University Park, Florida, United States
Topic: transcription factors
- Athavankar S, Peterson B. Control of gene expression with small molecules: biotin-mediated acylation of targeted lysine residues in recombinant yeast. Chem Biol. 2003;10:1245-53 pubmed..The high potency, low toxicity, and low molecular weight of biotin as a covalent CID are attractive properties for controlling cellular processes. ..
- Plumridge A, Melin P, Stratford M, Novodvorska M, Shunburne L, Dyer P, et al. The decarboxylation of the weak-acid preservative, sorbic acid, is encoded by linked genes in Aspergillus spp. Fungal Genet Biol. 2010;47:683-92 pubmed publisher..This cluster is absent from the genomes of A. fumigatus and A. clavatus and, as a consequence, neither species is capable of decarboxylating sorbic acid. ..
- Yakhnin H, Yakhnin A, Babitzke P. The trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis regulates translation initiation of ycbK, a gene encoding a putative efflux protein, by blocking ribosome binding. Mol Microbiol. 2006;61:1252-66 pubmed publisher..We also identified two dipeptide coding minigenes between the Shine-Dalgarno sequence and start codon of ycbK. Expression of one of the minigenes modestly interfered with translation of ycbK...
- Neely K, Workman J. The complexity of chromatin remodeling and its links to cancer. Biochim Biophys Acta. 2002;1603:19-29 pubmed..Their subunit composition and brief overview of their functional properties will be discussed. Also, current links between human chromatin-remodeling complexes and cell growth and cancer will be presented. ..
- Sermwittayawong D, Tan S. SAGA binds TBP via its Spt8 subunit in competition with DNA: implications for TBP recruitment. EMBO J. 2006;25:3791-800 pubmed..This simple model can explain SAGA's observed ability to both activate and repress transcription. ..
- Yakhnin A, Babitzke P. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism invitro. Proc Natl Acad Sci U S A. 2002;99:11067-72 pubmed..Finally, NusA-stimulated termination is cooperative, suggesting that binding of multiple NusA molecules influences termination. ..
- Jeffery B, Choudhury A, Horley N, Bruce M, Tomlinson S, Roberts R, et al. Peroxisome proliferator activated receptor alpha regulates a male-specific cytochrome P450 in mouse liver. Arch Biochem Biophys. 2004;429:231-6 pubmed..Thus, PPARalpha has a specific effect on constitutive expression of Cyp4a12. ..
- Patel R, Hollingshead B, Omiecinski C, Perdew G. Aryl-hydrocarbon receptor activation regulates constitutive androstane receptor levels in murine and human liver. Hepatology. 2007;46:209-18 pubmed..This study identifies a mode of up-regulating CAR and potentially expands the role of AhR in drug metabolism. This study also demonstrates in vivo up-regulation of CAR through chemical exposure. ..
- Bour B, Chakravarti M, West J, Abmayr S. Drosophila SNS, a member of the immunoglobulin superfamily that is essential for myoblast fusion. Genes Dev. 2000;14:1498-511 pubmed..To these ends, we demonstrate that the presence of SNS-expressing cells is absolutely dependent on Notch, and that expression of SNS does not require the myogenic regulatory protein MEF2. ..
- Chen B, Sysoeva T, Chowdhury S, Guo L, De Carlo S, Hanson J, et al. Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase. Structure. 2010;18:1420-30 pubmed publisher..This model provides a fresh perspective on how ATPase subunits interact within the ring-ensemble to promote transcription, directing attention to structural changes on the arginine-finger side of an ATP-bound interface. ..
- Vanden Heuvel J. The PPAR resource page. Biochim Biophys Acta. 2007;1771:1108-12 pubmed..Receiving greater than 300 unique visits per week, the PPAR resource page has become a useful tool for researchers of these important NRs. ..
- Reese J, Green M. Genetic analysis of TAF68/61 reveals links to cell cycle regulators. Yeast. 2001;18:1197-205 pubmed..The isolation of multiple genes involved in the control of a specific phase of the cell cycle argue that the arrest phenotypes of certain TAF(II) mutants reflect their role in specifically regulating cell cycle functions. ..
- Koerber R, Rhee H, Jiang C, Pugh B. Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol Cell. 2009;35:889-902 pubmed publisher..These findings suggest that nucleosomes around promoter regions have position-specific functions and that some gene regulators have position-specific nucleosomal interactions. ..
- Tomar R, Zheng S, Brunke Reese D, Wolcott H, Reese J. Yeast Rap1 contributes to genomic integrity by activating DNA damage repair genes. EMBO J. 2008;27:1575-84 pubmed publisher..We propose that Rap1 acts as a rheostat controlling nucleotide pools in response to shortened telomeres and DNA damage, providing a mechanism for fine-tuning the RNR genes during checkpoint activation. ..
- Hsu S, Gilgenast T, Bartman C, Edwards C, Stonestrom A, Huang P, et al. The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Mol Cell. 2017;66:102-116.e7 pubmed publisher..These findings indicate that BRD2 supports boundary activity, and they raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function. ..
- Costanzo A, Ades S. Growth phase-dependent regulation of the extracytoplasmic stress factor, sigmaE, by guanosine 3',5'-bispyrophosphate (ppGpp). J Bacteriol. 2006;188:4627-34 pubmed
- Gavin I, Kladde M, Simpson R. Tup1p represses Mcm1p transcriptional activation and chromatin remodeling of an a-cell-specific gene. EMBO J. 2000;19:5875-83 pubmed..We suggest that Tup1p can contribute to repression by blocking transcriptional activators, in addition to interacting with transcription machinery and stabilizing chromatin...
- Reichlen M, Vepachedu V, Murakami K, Ferry J. MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans. MBio. 2012;3:e00189-12 pubmed publisher..Finally, the results contribute to a broader understanding of transcriptional regulation in the domain Archaea...
- Lodeiro M, Uchida A, Bestwick M, Moustafa I, Arnold J, Shadel G, et al. Transcription from the second heavy-strand promoter of human mtDNA is repressed by transcription factor A in vitro. Proc Natl Acad Sci U S A. 2012;109:6513-8 pubmed publisher..Each promoter has a unique requirement for and/or response to the level of TFAM present, thus implying far greater complexity in the regulation of mammalian mitochondrial transcription than recognized to date. ..
- Gavin I, Simpson R. Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure. EMBO J. 1997;16:6263-71 pubmed..We also show that a relatively high level of SUC2 transcription can coexist with positioned nucleosomes. ..
- Ades S. Regulation by destruction: design of the sigmaE envelope stress response. Curr Opin Microbiol. 2008;11:535-40 pubmed publisher..Structural and biochemical studies of the proteases that mediate signal transduction reveal the molecular underpinnings enabling this design. ..
- Iwata Y, Lee M, Koizumi N. Analysis of a transcription factor using transient assay in Arabidopsis protoplasts. Methods Mol Biol. 2011;754:107-17 pubmed publisher..This protocol can be completed within 24 h from protoplast preparation to reporter assay. As an example, analysis of the membrane-bound transcription factor AtbZIP60 and its target BiP3 promoter is shown...
- Guo Y, Quiroga C, Chen Q, McAnulty M, Benedik M, Wood T, et al. RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli. Nucleic Acids Res. 2014;42:6448-62 pubmed publisher..Hence, our results indicate that cryptic prophage genes can be functionally divergent from their active phage counterparts after integration into the host genome...
- Nelms B, Hanna Rose W. C. elegans HIM-8 functions outside of meiosis to antagonize EGL-13 Sox protein function. Dev Biol. 2006;293:392-402 pubmed..Interactions between these genes can give insight into function of Sox family members, which are important in many aspects of metazoan development, and into functions of him-8 outside of meiosis. ..
- Qi Q, Huang W, Bai Y, Balmus G, Weiss R, August A. A unique role for ITK in survival of invariant NKT cells associated with the p53-dependent pathway in mice. J Immunol. 2012;188:3611-9 pubmed publisher..Our results suggest that TXK plays an overlapping role with ITK in iNKT cell development and function but that ITK also has a unique function in the survival of iNKT cells, likely via a p53-dependent pathway. ..
- Zhang Z, Reese J. Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae. EMBO J. 2004;23:2246-57 pubmed..Our study has revealed a novel collaboration between two nucleosome-positioning activities in vivo, and suggests that disruption of nucleosome positioning is insufficient to cause a high level of transcription. ..
- Hu L, Allison S, Phillips A. Identification of multiple repressor recognition sites in the hut system of Pseudomonas putida. J Bacteriol. 1989;171:4189-95 pubmed..A roughly 40-base-pair portion was identified which contained a 16-base-pair region of dyad symmetry located near the transcription initiation site for this operon. ..
- Rohrbaugh M, Ramos E, Nguyen D, Price M, Wen Y, Lai Z. Notch activation of yan expression is antagonized by RTK/pointed signaling in the Drosophila eye. Curr Biol. 2002;12:576-81 pubmed..This competition illustrates a potential mechanism for RTK and Notch signals to oppose each other. Thus, yan serves as a common target of Notch/Su(H) and RTK/Pointed signaling pathways during cell fate specification. ..
- Yen K, Vinayachandran V, Batta K, Koerber R, Pugh B. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 2012;149:1461-73 pubmed publisher..Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays. ..
- Zhang Z, Buchman A. Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Mol Cell Biol. 1997;17:5461-72 pubmed..These results suggest that DIS1 may contribute to making the silenced DNA template at HM loci more accessible during the mating-type switching process. ..
- Zhu Y, Mahon B, Froicu M, Cantorna M. Calcium and 1 alpha,25-dihydroxyvitamin D3 target the TNF-alpha pathway to suppress experimental inflammatory bowel disease. Eur J Immunol. 2005;35:217-24 pubmed..The data support a model where dietary calcium and 1,25D3 treatment directly and indirectly inhibit the TNF-alpha pathway and suppress IBD. ..
- Jones L, Earley C, Allen R, Jones B. Of mice and men, periodic limb movements and iron: how the human genome informs the mouse genome. Genes Brain Behav. 2008;7:513-4 pubmed publisher..In a homologous region in mouse, an area containing btbd9 was also identified as being related to iron homeostasis. This finding is important as iron status in brain has been implicated in restless legs syndrome. ..
- Allison S, Phillips A. Nucleotide sequence of the gene encoding the repressor for the histidine utilization genes of Pseudomonas putida. J Bacteriol. 1990;172:5470-6 pubmed..A second open reading frame (ORF2) would encode a 21,155-dalton protein, but because this region could be deleted with only a slight effect on repressor activity, it is not likely to be involved in repressor function or structure...
- Zhang D, Johnson M, Miller C, Pircher T, Geiger J, Wojchowski D. An optimized system for studies of EPO-dependent murine pro-erythroblast development. Exp Hematol. 2001;29:1278-88 pubmed..Objectives were to develop new means to isolate useful numbers of primary progenitor cells and to quantitatively assay the stepwise maturation of erythroblasts...
- Walter P, Owen Hughes T, Cote J, Workman J. Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer. Mol Cell Biol. 1995;15:6178-87 pubmed..Thus, histone displacement in this instance occurred by transfer of complete histone octamers, a mechanism distinct from that mediated by the histone-binding proteins nucleoplasmin and NAP-1. ..
- Stoner M, Auerbach S, Zamule S, Strom S, Omiecinski C. Transactivation of a DR-1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites. Nucleic Acids Res. 2007;35:2177-90 pubmed
- Zhang J, Nei M. Evolution of Antennapedia-class homeobox genes. Genetics. 1996;142:295-303 pubmed
- Ghosh S, Missra A, Gilmour D. Negative elongation factor accelerates the rate at which heat shock genes are shut off by facilitating dissociation of heat shock factor. Mol Cell Biol. 2011;31:4232-43 pubmed publisher..Activators are typically viewed as controlling Pol II. Our results reveal a possible reciprocal relationship in which paused Pol II influences the activator. ..
- Yakhnin A, Yakhnin H, Babitzke P. Function of the Bacillus subtilis transcription elongation factor NusG in hairpin-dependent RNA polymerase pausing in the trp leader. Proc Natl Acad Sci U S A. 2008;105:16131-6 pubmed publisher..Overexpression of nusG reduces trp operon expression to a larger extent than overexpression of nusA...
- Nelson K, Wang F, Boyd E, Selander R. Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli. Genetics. 1997;147:1509-20 pubmed
- Flaveny C, Reen R, Kusnadi A, Perdew G. The mouse and human Ah receptor differ in recognition of LXXLL motifs. Arch Biochem Biophys. 2008;471:215-23 pubmed publisher..These findings suggest that the human and mouse AhR may display differential recruitment of coactivators and hence may exhibit divergent regulation of target genes. ..
- Achary B, Campbell K, Co I, Gilmour D. RNAi screen in Drosophila larvae identifies histone deacetylase 3 as a positive regulator of the hsp70 heat shock gene expression during heat shock. Biochim Biophys Acta. 2014;1839:355-63 pubmed publisher..Additionally, we show that HDAC3 and SMRTER contribute to hsp70 gene expression at a step subsequent to HSF-mediated activation and release of the paused Pol II that resides at the promoter prior to heat shock induction. ..
- Neely K, Hassan A, Brown C, Howe L, Workman J. Transcription activator interactions with multiple SWI/SNF subunits. Mol Cell Biol. 2002;22:1615-25 pubmed..Thus, three distinct subunits of the SWI/SNF complex contribute to its interactions with activation domains. ..
- Hays T, Rusyn I, Burns A, Kennett M, Ward J, Gonzalez F, et al. Role of peroxisome proliferator-activated receptor-alpha (PPARalpha) in bezafibrate-induced hepatocarcinogenesis and cholestasis. Carcinogenesis. 2005;26:219-27 pubmed..Results from these studies demonstrate that the PPARalpha is required to mediate hepatocarcinogenesis induced by bezafibrate, and that PPARalpha protects against potential cholestasis...
- Chitikila C, Huisinga K, Irvin J, Basehoar A, Pugh B. Interplay of TBP inhibitors in global transcriptional control. Mol Cell. 2002;10:871-82 pubmed..These findings reveal that transcriptional output is limited in part by a collaboration of different combinations of TBP inhibitory mechanisms. ..
- Hassan A, Prochasson P, Neely K, Galasinski S, Chandy M, Carrozza M, et al. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell. 2002;111:369-79 pubmed..Thus, bromodomains within the catalytic subunits of SAGA and SWI/SNF anchor these complexes to acetylated promoter nucleosomes. ..
- Brown C, Howe L, Sousa K, Alley S, Carrozza M, Tan S, et al. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science. 2001;292:2333-7 pubmed..These data demonstrate that the essential Tra1 protein serves as a common target for activators in both SAGA and NuA4 acetyltransferases. ..
- Costanzo A, Nicoloff H, Barchinger S, Banta A, Gourse R, Ades S. ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms. Mol Microbiol. 2008;67:619-32 pubmed..However, ppGpp and its cofactor DksA can also activate transcription by EsigmaEin vitro, suggesting that the effects of ppGpp on sigmaE activity are both direct and indirect. ..
- Molete J, Petrykowska H, Sigg M, Miller W, Hardison R. Functional and binding studies of HS3.2 of the beta-globin locus control region. Gene. 2002;283:185-97 pubmed..GATA1 and Oct1 also bind in the HS cores of the LCR and to promoters in HBBC. Their binding to this minor HS suggests that they may be used in assembly of a large complex containing multiple regulatory sequences. ..
- Chung W, Albert R, Albert I, Nekrutenko A, Makova K. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinformatics. 2006;7:46 pubmed..Duplicate genes rapidly diverge in their expression profiles in the network and play similar role in maintaining the network robustness as compared with singletons. ..
- Chang G, Noegel A, Mavrich T, Muller R, Tomsho L, Ward E, et al. Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Res. 2012;22:1098-106 pubmed publisher..Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and +1 nucleosome positioning may have coevolved in animals. ..
- Grant P, Duggan L, Cote J, Roberts S, Brownell J, Candau R, et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997;11:1640-50 pubmed..e., tbp). ..
- Ades S. Control of the alternative sigma factor sigmaE in Escherichia coli. Curr Opin Microbiol. 2004;7:157-62 pubmed..This mechanism of signal transduction, regulated intramembrane proteolysis, is used in transmembrane signaling pathways from bacteria to humans. ..
- Purnell B, Gilmour D. Contribution of sequences downstream of the TATA element to a protein-DNA complex containing the TATA-binding protein. Mol Cell Biol. 1993;13:2593-603 pubmed..The results suggest that specific contacts downstream of the TATA element could play a key role in establishing the transcriptional potential of a gene by contributing to the interaction of the TATA-binding protein. ..
- Feng B, Lu D, Ma X, Peng Y, Sun Y, Ning G, et al. Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development. Plant J. 2012;72:612-24 pubmed publisher..Our results demonstrate the important role of DYT1 in regulating anther transcriptome and function, and supporting normal pollen development...
- Peters J, Aoyama T, Burns A, Gonzalez F. Bezafibrate is a dual ligand for PPARalpha and PPARbeta: studies using null mice. Biochim Biophys Acta. 2003;1632:80-9 pubmed..In contrast to other PPARalpha ligands such as WY-14,643, induction of some target genes by bezafibrate can also be modulated in the absence of a functional PPARalpha. ..
- Nguyen D, Rohrbaugh M, Lai Z. The Drosophila homolog of Onecut homeodomain proteins is a neural-specific transcriptional activator with a potential role in regulating neural differentiation. Mech Dev. 2000;97:57-72 pubmed..In support of this notion, overexpression of a putative dominant negative form of D-Onecut during eye development does not affect early cell fate specification, but severely affects photoreceptor differentiation. ..
- Taggart A, Pugh B. Dimerization of TFIID when not bound to DNA. Science. 1996;272:1331-3 pubmed..These findings suggest that dimerization through TBP is the physiological state of TFIID when not bound to DNA. Thus, the inefficiency of TFIID binding to a promoter may be partly attributable to the competitive effect of dimerization. ..
- Stock D, Ellies D, Zhao Z, Ekker M, Ruddle F, Weiss K. The evolution of the vertebrate Dlx gene family. Proc Natl Acad Sci U S A. 1996;93:10858-63 pubmed..Determination of the linkage relationship of these additional zebrafish Dlx genes to Hox clusters should help resolve this issue. ..
- Li J, Gilmour D. Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J. 2013;32:1829-41 pubmed publisher..In contrast to M1BP and GAF genes, a significant portion of TATA box genes appear to be controlled at preinitiation complex formation. ..
- Shimada T, Ross A, Muccio D, Brouillette W, Shealy Y. Regulation of hepatic lecithin:retinol acyltransferase activity by retinoic acid receptor-selective retinoids. Arch Biochem Biophys. 1997;344:220-7 pubmed..920). These data implicate the RARs in the induction of hepatic LRAT and suggest a predominant role for RAR-alpha-active ligands. ..
- Cote J, Quinn J, Workman J, Peterson C. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994;265:53-60 pubmed..A direct ATP-dependent interaction between the SWI/SNF complex and nucleosomal DNA was detected. These observations suggest that a primary role of the SWI/SNF complex is to promote activator binding to nucleosomal DNA. ..
- Keller C, Erickson M, Abmayr S. Misexpression of nautilus induces myogenesis in cardioblasts and alters the pattern of somatic muscle fibers. Dev Biol. 1997;181:197-212 pubmed..In summary, we suggest that nautilus induces myogenic differentiation in vivo when ectopically expressed in developing cardioblasts and may affect the myogenic differentiation program of specific muscle fibers. ..
- Steger D, Workman J. Stable co-occupancy of transcription factors and histones at the HIV-1 enhancer. EMBO J. 1997;16:2463-72 pubmed..Thus, the constitutive DHSs identified at the HIV-1 enhancer in native chromatin may reflect the presence of a ternary complex composed of transcriptional activators, histones and DNA. ..
- Weber J, Taxman D, Lu Q, Gilmour D. Molecular architecture of the hsp70 promoter after deletion of the TATA box or the upstream regulation region. Mol Cell Biol. 1997;17:3799-808 pubmed..GAGA factor alone might be capable of establishing an open chromatin structure that encompasses the upstream regulatory region as well as the core promoter region, thus facilitating the binding of TFIID. ..
- Grant P, Schieltz D, Pray Grant M, Steger D, Reese J, Yates J, et al. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell. 1998;94:45-53 pubmed..These results illustrate a role for certain TAF(II) proteins in the regulation of gene expression at the level of chromatin modification that is distinct from the TFIID complex and TAF(II)145. ..
- Neely K, Hassan A, Wallberg A, Steger D, Cairns B, Wright A, et al. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol Cell. 1999;4:649-55 pubmed..The similarity of activation domain interactions and transcriptional stimulation between SWI/SNF and the SAGA histone acetyltransferase complex may account for their apparent overlapping functions in vivo. ..
- Nekrutenko A, He J. Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames. Trends Genet. 2006;22:645-8 pubmed..Our study provides a novel evolutionary framework for the analysis of loci with overlapping reading frames, which can be used for identification and analyses of novel dual-coding genes. ..
- Peters J, Park Y, Gonzalez F, Pariza M. Influence of conjugated linoleic acid on body composition and target gene expression in peroxisome proliferator-activated receptor alpha-null mice. Biochim Biophys Acta. 2001;1533:233-42 pubmed
- Steitz M, Wickenheisser J, Siegfried E. Overexpression of zeste white 3 blocks wingless signaling in the Drosophila embryonic midgut. Dev Biol. 1998;197:218-33 pubmed
- Kim D, Akiyama T, Harman F, Burns A, Shan W, Ward J, et al. Peroxisome proliferator-activated receptor beta (delta)-dependent regulation of ubiquitin C expression contributes to attenuation of skin carcinogenesis. J Biol Chem. 2004;279:23719-27 pubmed..These results strongly suggest that activation of PPARbeta-dependent target genes provides a novel strategy to inhibit tumor promotion and carcinogenesis. ..