scholarly journals Computational Identification of Site-Specific Transcription Factors in Drosophila

Fly ◽  
2007 ◽  
Vol 1 (3) ◽  
pp. 142-145 ◽  
Author(s):  
Boris Adryan ◽  
Sarah A. Teichmann
Keyword(s):  
Transcription Factors ◽  
Site Specific ◽  
Computational Identification

scholarly journals Distinct Roles for Interfacial Hydration in Site-Specific DNA Recognition by ETS-Family Transcription Factors

2017 ◽  
Vol 121 (13) ◽  
pp. 2748-2758 ◽  
Author(s):  
Suela Xhani ◽  
Shingo Esaki ◽  
Kenneth Huang ◽  
Noa Erlitzki ◽  
Gregory M. K. Poon
Keyword(s):  
Transcription Factors ◽  
Dna Recognition ◽  
Site Specific ◽  
Ets Family

Computational Identification of Key Biological Modules and Transcription Factors in Acute Lung Injury

2006 ◽  
Vol 173 (6) ◽  
pp. 653-658 ◽  
Author(s):  
Sina A. Gharib ◽  
W. Conrad Liles ◽  
Gustavo Matute-Bello ◽  
Robb W. Glenny ◽  
Thomas R. Martin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Acute Lung Injury ◽  
Lung Injury ◽  
Computational Identification ◽  
Biological Modules

scholarly journals Ternary Complex Factors Elk-1 and Sap-1a Mediate Growth Hormone-Induced Transcription of Egr-1 (Early Growth Response Factor-1) in 3T3-F442A Preadipocytes

1999 ◽  
Vol 13 (4) ◽  
pp. 619-631 ◽  
Author(s):  
Richard W. E. Clarkson ◽  
Catherine A. Shang ◽  
Linda K. Levitt ◽  
Tammy Howard ◽  
Michael J. Waters
Keyword(s):  
Transcription Factors ◽  
Ternary Complex ◽  
Growth Response ◽  
Early Growth ◽  
Ternary Complexes ◽  
Response Factor ◽  
Site Specific ◽  
Early Growth Response ◽  
Ets Factors ◽  
Serum Response

Abstract In our search for transcription factors induced by GH, we have analyzed immediate early gene activation in a model of GH-dependent differentiation. Here we describe the activation of early growth response factor-1 (egr-1) in GH-stimulated 3T3-F442A preadipocytes and the transcription factors responsible for its transactivation. Binding activity of egr-1 in electrophoretic mobility shift assay (EMSA) increased transiently 1 h after GH stimulation, accompanied by a concomitant increase in egr-1 mRNA. egr-1 induction appeared not to be related to proliferation since it was amplified in quiescent preadipocytes at a time when cells were refractive to GH-stimulated DNA synthesis. Truncations of the proximal 1 kb of the egr-1 promoter revealed that a 374-bp region (−624 to −250) contributes about 80% of GH inducibility in 3T3-F442A cells and approximately 90% inducibility in CHO-K1 cells. This region contains three juxtaposed SRE (serum response element)/Ets site pairs known to be important for egr-1 activity in response to exogenous stimuli. Site-specific mutations of individual SRE and Ets sites within this region each reduced GH inducibility of the promoter. Use of these site-specific mutations in EMSA showed that disruption of either Ets or SRE sites abrogated ternary complex formation at the composite sites. DNA binding of ternary complexes, but not binary complexes, in EMSA was rapidly and transiently increased by GH. EMSA supershifts indicated these ternary complexes contained serum response factor (SRF) and the Ets factors Elk-1 and Sap-1a. Coexpression of Sap-1a and Elk-1 resulted in a marked increase in GH induction of egr-1 promoter activity, although transfection with expression vectors for either Ets factor alone did not significantly enhance the GH response. We conclude that GH stimulates transcription of egr-1 primarily through activation of these Ets factors at multiple sites on the promoter and that stabilization of ternary complexes with SRF at these sites maximizes this response.

Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

2010 ◽  
Vol 4 (3) ◽  
pp. 247-255 ◽  
Author(s):  
ChangKug Kim ◽  
Shoshi Kikuchi ◽  
YeonKi Kim ◽  
SungHan Park ◽  
UngHan Yoon ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Black Rice ◽  
Computational Identification ◽  
Anthocyanin Production

Novel application of S-nitrosoglutathione–Sepharose to identify proteins that are potential targets for S-nitrosoglutathione-induced mixed-disulphide formation

2000 ◽  
Vol 349 (2) ◽  
pp. 567-578
Author(s):  
Peter KLATT ◽  
Estela PINEDA MOLINA ◽  
Dolores PÉREZ-SALA ◽  
Santiago LAMAS
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Camp Response Element Binding ◽  
Cysteine Residue ◽  
Activator Protein 1 ◽  
Site Specific ◽  
Binding Domains ◽  
Nuclear Extracts ◽  
Protein Thiols

Site-specific S-glutathionylation is emerging as a novel mechanism by which S-nitrosoglutathione (GSNO) may modify functionally important protein thiols. Here, we show that GSNO-Sepharose mimicks site-specific S-glutathionylation of the transcription factors c-Jun and p50 by free GSNO in vitro. Both c-Jun and p50 were found to bind to immobilized GSNO through the formation of a mixed disulphide, involving a conserved cysteine residue located in the DNA-binding domains of these transcription factors. Furthermore, we show that c-Jun, p50, glycogen phosphorylase b, glyceraldehyde-3-phosphate dehydrogenase, creatine kinase, glutaredoxin and caspase-3 can be precipitated from a mixture of purified thiol-containing proteins by the formation of a mixed-disulphide bond with GSNO-Sepharose. With few exceptions, protein binding to this matrix correlated well with the susceptibility of the investigated proteins to undergo GSNO- but not diamide-induced mixed-disulphide formation in vitro. Finally, it is shown that covalent GSNO-Sepharose chromatography of HeLa cell nuclear extracts results in the enrichment of proteins which incorporate glutathione in response to GSNO treatment. As suggested by DNA-binding assays, this group of nuclear proteins include the transcription factors activator protein-1, nuclear factor-ĸB and cAMP-response-element-binding protein. In conclusion, we introduce GSNO-Sepharose as a probe for site-specific S-glutathionylation and as a novel and potentially useful tool to isolate and identify proteins which are candidate targets for GSNO-induced mixed-disulphide formation.

scholarly journals Evidence for Site-Specific Occupancy of the Mitochondrial Genome by Nuclear Transcription Factors

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e84713 ◽  
Author(s):  
Georgi K. Marinov ◽  
Yun E. Wang ◽  
David Chan ◽  
Barbara J. Wold
Keyword(s):  
Transcription Factors ◽  
Mitochondrial Genome ◽  
Site Specific

scholarly journals Cross-talk between Site-specific Transcription Factors and DNA Methylation States

2013 ◽  
Vol 288 (48) ◽  
pp. 34287-34294 ◽  
Author(s):  
Adam Blattler ◽  
Peggy J. Farnham
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Cross Talk ◽  
Site Specific
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