scholarly journals FIS activatesglnAp2 inEscherichia coli: role of a DNA bend centered at −55, upstream of the transcription start site

2006 ◽  
Vol 257 (1) ◽  
pp. 99-105 ◽  
Author(s):  
Yi-Xin Huo ◽  
Bei-Yan Nan ◽  
Cong-Hui You ◽  
Zhe-Xian Tian ◽  
Annie Kolb ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Inescherichia Coli ◽  
Start Site ◽  
Transcription Start

The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning

2021 ◽  
pp. 166813
Author(s):  
Eric J. Tomko ◽  
Olivia Luyties ◽  
Jenna K. Rimel ◽  
Chi-Lin Tsai ◽  
Jill O. Fuss ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start

Role of the Sulfolobus shibatae viral T6 initiator in conferring promoter strength and in influencing transcription start site selection

2006 ◽  
Vol 52 (11) ◽  
pp. 1136-1140 ◽  
Author(s):  
Sohail A Qureshi
Keyword(s):  
Transcription Start Site ◽  
Dna Sequences ◽  
Site Selection ◽  
Core Promoter ◽  
Promoter Strength ◽  
Start Site ◽  
Transcription Start ◽  
Recognition Element ◽  
Sulfolobus Shibatae

Archaeal promoters contain a TATA-box, an adjacent upstream TFB-recognition element (BRE), and a downstream initiator (INR) region from which transcription originates. While the contribution of A-box and BRE to promoter strength is well established, the role of DNA sequences within the INR region and its vicinity on transcription efficiency and start site selection remains unclear. Here, I demonstrate using the strong Sulfolobus shibatae viral T6 promoter that either substitution of its natural sequence from –17 and beyond with plasmid DNA or introduction of point transversion mutations at +3, –2, –4, and –5 positions reduce promoter strength dramatically, whereas +1, –1, and –2 mutations influence the transcription start site. These data therefore reveal that the INR region plays a role as important as the BRE and the A-box in T6 gene transcription. Key words: Archaea, transcription, initiator (INR), Sulfolobus shibatae, core promoter.

scholarly journals Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch

2013 ◽  
Vol 42 (4) ◽  
pp. 2171-2184 ◽  
Author(s):  
Richard Patryk Ngondo ◽  
Philippe Carbon
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Start Site ◽  
Regulatory Mechanism ◽  
Start Site ◽  
Transcription Start ◽  
Aberrant Expression ◽  
Alternative Transcription ◽  
Activating Transcription Factor

Abstract A transcriptional feedback loop is the simplest and most direct means for a transcription factor to provide an increased stability of gene expression. In this work performed in human cells, we reveal a new negative auto-regulatory mechanism involving an alternative transcription start site (TSS) usage. Using the activating transcription factor ZNF143 as a model, we show that the ZNF143 low-affinity binding sites, located downstream of its canonical TSS, play the role of protein sensors to induce the up- or down-regulation of ZNF143 gene expression. We uncovered that the TSS switch that mediates this regulation implies the differential expression of two transcripts with an opposite protein production ability due to their different 5′ untranslated regions. Moreover, our analysis of the ENCODE data suggests that this mechanism could be used by other transcription factors to rapidly respond to their own aberrant expression level.

scholarly journals Function and Transcriptional Regulation of Bovine TORC2 Gene in Adipocytes: Roles of C/EBP, XBP1, INSM1 and ZNF263

2019 ◽  
Vol 20 (18) ◽  
pp. 4338 ◽  
Author(s):  
Khan ◽  
Raza ◽  
Junjvlieke ◽  
Xiaoyu ◽  
Garcia ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Promoter Region ◽  
Binding Protein ◽  
Cell Counting ◽  
Luciferase Reporter ◽  
Marker Genes ◽  
Start Site ◽  
Transcription Start ◽  
Bovine Adipocytes

The TORC2 gene is a member of the transducer of the regulated cyclic adenosine monophosphate (cAMP) response element binding protein gene family, which plays a key role in metabolism and adipogenesis. In the present study, we confirmed the role of TORC2 in bovine preadipocyte proliferation through cell cycle staining flow cytometry, cell counting assay, 5-ethynyl-2′-deoxyuridine staining (EdU), and mRNA and protein expression analysis of proliferation-related marker genes. In addition, Oil red O staining analysis, immunofluorescence of adiponectin, mRNA and protein level expression of lipid related marker genes confirmed the role of TORC2 in the regulation of bovine adipocyte differentiation. Furthermore, the transcription start site and sub-cellular localization of the TORC2 gene was identified in bovine adipocytes. To investigate the underlying regulatory mechanism of the bovine TORC2, we cloned a 1990 bp of the 5' untranslated region (5′UTR) promoter region into a luciferase reporter vector and seven vector fragments were constructed through serial deletion of the 5′UTR flanking region. The core promoter region of the TORC2 gene was identified at location −314 to −69 bp upstream of the transcription start site. Based on the results of the transcriptional activities of the promoter vector fragments, luciferase activities of mutated fragments and siRNAs interference, four transcription factors (CCAAT/enhancer-binding protein C/BEP, X-box binding protein 1 XBP1, Insulinoma-associated 1 INSM1, and Zinc finger protein 263 ZNF263) were identified as the transcriptional regulators of TORC2 gene. These findings were further confirmed through Electrophoretic Mobility Shift Assay (EMSA) within nuclear extracts of bovine adipocytes. Furthermore, we also identified that C/EBP, XBP1, INSM1 and ZNF263 regulate TORC2 gene as activators in the promoter region. We can conclude that TORC2 gene is potentially a positive regulator of adipogenesis. These findings will not only provide an insight for the improvement of intramuscular fat in cattle, but will enhance our understanding regarding therapeutic intervention of metabolic syndrome and obesity in public health as well.

scholarly journals Role of a small RNA pol II subunit in TATA to transcription start site spacing

1994 ◽  
Vol 22 (23) ◽  
pp. 4932-4936 ◽  
Author(s):  
Elizabeth M. Furter-Graves ◽  
Benjamin D. Hall ◽  
Rolf Furter
Keyword(s):  
Transcription Start Site ◽  
Small Rna ◽  
Start Site ◽  
Transcription Start ◽  
Rna Pol Ii ◽  
Pol Ii

scholarly journals A cis Repression Sequence Adjacent to the Transcription Start Site of the Human Cytomegalovirus US3 Gene Is Required To Down Regulate Gene Expression at Early and Late Times after Infection

1998 ◽  
Vol 72 (12) ◽  
pp. 9575-9584 ◽  
Author(s):  
Philip E. Lashmit ◽  
Mark F. Stinski ◽  
Eain A. Murphy ◽  
Grant C. Bullock
Keyword(s):  
Gene Expression ◽  
Viral Replication ◽  
Transcription Start Site ◽  
Human Cytomegalovirus ◽  
Maximum Level ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
Recombinant Viruses

ABSTRACT Human cytomegalovirus has two enhancer-containing immediate-early (IE) promoters with a cis repression sequence (CRS) positioned immediately upstream of the transcription start site, designated the major IE (MIE) promoter and the US3 promoter. The role of the CRS upstream of the US3 transcription start site in the context of the viral genome was determined by comparing the levels of transcription from these two enhancer-containing promoters in recombinant viruses with a wild-type or mutant CRS. Upstream of the CRS of the US3 promoter was either the endogenous enhancer (R2) or silencer (R1). The downstream US3 gene was replaced with the indicator gene chloramphenicol acetyltransferase (CAT). Infected permissive human fibroblast cells or nonpermissive, undifferentiated monocytic THP-1 cells were analyzed for expression from the US3 promoter containing either the wild-type or mutant CRS. With the wild-type CRS, the maximum level of transcription in permissive cells was detected within 4 to 6 h after infection and then declined. With the mutant CRS and the R2 enhancer upstream, expression from the US3 promoter continued to increase throughout the viral replication cycle to levels 20- to 40-fold higher than for the wild type. In nonpermissive or permissive monocytic THP-1 cells, expression from the US3 promoter was also significantly higher when the CRS was mutated. Less expression was obtained when only the R1 element was present, but expression was higher when the CRS was mutated. Thus, the CRS in the enhancer-containing US3 promoter appears to allow for a short burst of US3 gene expression followed by repression at early and late times after infection. Overexpression of US3 may be detrimental to viral replication, and its level of expression must be stringently controlled. The role of the CRS and the viral IE86 protein in controlling enhancer-containing promoters is discussed.

scholarly journals Stable DNA Opening within Open Promoter Complexes Is Mediated by the RNA Polymerase β′-Jaw Domain

2005 ◽  
Vol 280 (43) ◽  
pp. 36176-36184 ◽  
Author(s):  
Siva. R. Wigneshweraraj ◽  
Patricia C. Burrows ◽  
Konstantin Severinov ◽  
Martin Buck
Keyword(s):  
Rna Polymerase ◽  
Complex Network ◽  
Transcription Start Site ◽  
Functional Domain ◽  
Regulatory Domain ◽  
Start Site ◽  
Transcription Start ◽  
Bacterial Rna ◽  
Promoter Complex

DNA opening for transcription-competent open promoter complex (OC) formation by the bacterial RNA polymerase (RNAP) relies upon a complex network of interactions between the structurally conserved and flexible modules of the catalytic β and β′-subunits, RNAP-associated σ-subunit, and the DNA. Here, we show that one such module, the β′-jaw, functions to stabilize the OC. In OCs formed by the major σ70-RNAP, the stabilizing role of the β′-jaw is not restricted to any particular melted DNA segment. In contrast, in OCs formed by the major variant σ54-RNAP, the β′-jaw and a conserved σ54 regulatory domain co-operate to stabilize the melted DNA segment immediately upstream of the transcription start site. Clearly, regulated communication between the mobile modules of the RNAP and the functional domain(s) of the σ subunit is required for stable DNA opening.

scholarly journals The Role of Human TFIIB in Transcription Start Site Selectionin Vitroandin Vivo

1999 ◽  
Vol 274 (20) ◽  
pp. 14337-14343 ◽  
Author(s):  
Nicola A. Hawkes ◽  
Stefan G. E. Roberts
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start
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