scholarly journals The human prointerleukin 1 beta gene requires DNA sequences both proximal and distal to the transcription start site for tissue-specific induction.

1993 ◽  
Vol 13 (3) ◽  
pp. 1332-1344 ◽  
Author(s):  
F Shirakawa ◽  
K Saito ◽  
C A Bonagura ◽  
D L Galson ◽  
M J Fenton ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Phorbol Myristate Acetate ◽  
Dna Sequences ◽  
Hela Cells ◽  
Start Site ◽  
Myristate Acetate ◽  
Binding Studies ◽  
Transcription Start ◽  
Specific Induction ◽  
Beta Gene

In these studies, we have identified DNA sequences and specific protein interactions necessary for transcriptional regulation of the human prointerleukin 1 beta (proIL-1 beta) gene. A cell-type-independent lipopolysaccharide (LPS)-responsive enhancer element located between -3757 and -2729 bp upstream from the transcription start site (cap site) consisted of at least six discrete subregions which were essential to the maximal induction by LPS in transfected monocytes. The enhancer also appeared to mediate phorbol myristate acetate induction in monocytes and IL-1 responsiveness in fibroblasts. Deletion and base substitution mutations along with DNA binding studies demonstrated that the enhancer contained a minimum of three functional protein binding sequences, two of which appeared to be important for gene induction. One of the essential proteins which bound to the enhancer was similar or identical to members of the C/EBP family of transcription factors required for both IL-1- and LPS-specific induction of the IL-6 gene (i.e., the NF-IL6 proteins). When ligated to the proIL-1 beta cap site-proximal region (located between -131 to +12), both the proIL-1 beta and the simian virus 40 enhancer elements functioned more efficiently in monocytes than in HeLa cells, which are not normally competent for IL-1 beta expression. When ligated to the murine c-fos promoter, however, the proIL-1 beta enhancer was inducible in phorbol myristate acetate-stimulated HeLa cells, suggesting the existence of a proIL-1 beta promoter-proximal requirement for tissue specificity.

The human prointerleukin 1 beta gene requires DNA sequences both proximal and distal to the transcription start site for tissue-specific induction

1993 ◽  
Vol 13 (3) ◽  
pp. 1332-1344 ◽  
Author(s):  
F Shirakawa ◽  
K Saito ◽  
C A Bonagura ◽  
D L Galson ◽  
M J Fenton ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Phorbol Myristate Acetate ◽  
Dna Sequences ◽  
Hela Cells ◽  
Start Site ◽  
Myristate Acetate ◽  
Binding Studies ◽  
Transcription Start ◽  
Specific Induction ◽  
Beta Gene

In these studies, we have identified DNA sequences and specific protein interactions necessary for transcriptional regulation of the human prointerleukin 1 beta (proIL-1 beta) gene. A cell-type-independent lipopolysaccharide (LPS)-responsive enhancer element located between -3757 and -2729 bp upstream from the transcription start site (cap site) consisted of at least six discrete subregions which were essential to the maximal induction by LPS in transfected monocytes. The enhancer also appeared to mediate phorbol myristate acetate induction in monocytes and IL-1 responsiveness in fibroblasts. Deletion and base substitution mutations along with DNA binding studies demonstrated that the enhancer contained a minimum of three functional protein binding sequences, two of which appeared to be important for gene induction. One of the essential proteins which bound to the enhancer was similar or identical to members of the C/EBP family of transcription factors required for both IL-1- and LPS-specific induction of the IL-6 gene (i.e., the NF-IL6 proteins). When ligated to the proIL-1 beta cap site-proximal region (located between -131 to +12), both the proIL-1 beta and the simian virus 40 enhancer elements functioned more efficiently in monocytes than in HeLa cells, which are not normally competent for IL-1 beta expression. When ligated to the murine c-fos promoter, however, the proIL-1 beta enhancer was inducible in phorbol myristate acetate-stimulated HeLa cells, suggesting the existence of a proIL-1 beta promoter-proximal requirement for tissue specificity.

scholarly journals Genetic Features of MCR-1-Producing Colistin-Resistant Escherichia coli Isolates in South Africa

2016 ◽  
Vol 60 (7) ◽  
pp. 4394-4397 ◽  
Author(s):  
Laurent Poirel ◽  
Nicolas Kieffer ◽  
Adrian Brink ◽  
Jennifer Coetze ◽  
Aurélie Jayol ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
South Africa ◽  
Transcription Start Site ◽  
Dna Sequences ◽  
Start Site ◽  
Transcription Start ◽  
Content Type ◽  
Promoter Sequences ◽  
Genetic Features ◽  
Community Patients

ABSTRACTA series of colistin-resistantEscherichia coliclinical isolates was recovered from hospitalized and community patients in South Africa. Seven clonally unrelated isolates harbored themcr-1gene located on different plasmid backbones. Two distinct plasmids were fully sequenced, and identical 2,600-bp-long DNA sequences defining amcr-1cassette were identified. Promoter sequences responsible for the expression ofmcr-1, deduced from the precise identification of the +1 transcription start site formcr-1, were characterized.

scholarly journals Characterization of Binding Sequences for Butyrolactone Autoregulator Receptors in Streptomycetes

1999 ◽  
Vol 181 (16) ◽  
pp. 5075-5080 ◽  
Author(s):  
Hiroshi Kinoshita ◽  
Tomohiro Tsuji ◽  
Hiroomi Ipposhi ◽  
Takuya Nihira ◽  
Yasuhiro Yamada
Keyword(s):  
Transcription Start Site ◽  
Dna Sequences ◽  
Target Genes ◽  
Start Codon ◽  
Receptor Protein ◽  
Upstream Region ◽  
Start Site ◽  
Transcription Start ◽  
S1 Nuclease ◽  
Nuclease Mapping

ABSTRACT BarA of Streptomyces virginiae is a specific receptor protein for a member of butyrolactone autoregulators which binds to an upstream region of target genes to control transcription, leading to the production of the antibiotic virginiamycin M1 and S. BarA-binding DNA sequences (BarA-responsive elements [BAREs]), to which BarA binds for transcriptional control, were restricted to 26 to 29-nucleotide (nt) sequences on barA and barBupstream regions by the surface plasmon resonance technique, gel shift assay, and DNase I footprint analysis. Two BAREs (BARE-1 and BARE-2) on the barB upstream region were located 57 to 29 bp (BARE-1) and 268 to 241 bp (BARE-2) upstream from the barBtranslational start codon. The BARE located on the barAupstream region (BARE-3) was found 101 to 76 bp upstream of thebarA start codon. High-resolution S1 nuclease mapping analysis revealed that BARE-1 covered the barBtranscription start site and BARE-3 covered an autoregulator-dependent transcription start site of the barA gene. Deletion and mutation analysis of BARE-2 demonstrated that at least a 19-nt sequence was required for sufficient BarA binding, and A or T residues at the edge as well as internal conserved nucleotides were indispensable. The identified binding sequences for autoregulator receptor proteins were found to be highly conserved among Streptomyces species.

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 Long-Range Transcriptional Control of Progesterone Receptor Gene Expression

2010 ◽  
Vol 24 (2) ◽  
pp. 346-358 ◽  
Author(s):  
Jamie Bonéy-Montoya ◽  
Yvonne S. Ziegler ◽  
Carol D. Curtis ◽  
Jonathan A. Montoya ◽  
Ann M. Nardulli
Keyword(s):  
Gene Expression ◽  
Progesterone Receptor ◽  
Long Range ◽  
Transcription Start Site ◽  
Dna Sequences ◽  
Receptor Gene ◽  
Start Site ◽  
Transcription Start ◽  
Dynamic Regulation ◽  
Chromosome Conformation

Abstract Estrogen receptor α (ERα) binds to specific target DNA sequences, estrogen response elements (EREs), to regulate estrogen-responsive gene expression. The progesterone receptor (PR) gene has been used extensively as a marker of estrogen responsiveness. Although we previously identified cis elements within 1 kb of the PR-B transcription start site that are associated with ERα and help to confer estrogen responsiveness, the identification of ERα binding sites far removed from the transcription start site suggested that long-range regulation of this gene may occur. We now show that eight regions of the PR gene from 311 kb upstream to 4 kb downstream of the PR-B transcription start site interact with ERα and that coactivator proteins and acetylated histones are selectively associated with these gene regions. Specific PR gene regions confer estrogen responsiveness to a heterologous reporter plasmid, and mutation of EREs within these regions diminishes estrogen-induced transactivation. Importantly, chromosome conformation capture assays reveal ERα- and ligand-dependent interactions between proximal and distal PR gene regions. Taken together, our studies suggest that distal regions of the PR gene participate in the dynamic regulation of this gene and that the coordinated action of proximal and distal PR gene regions allows cells to respond to changes in hormone levels with extraordinary versatility and sensitivity.

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

scholarly journals Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

2016 ◽  
Vol 113 (21) ◽  
pp. E2899-E2905 ◽  
Author(s):  
Irina O. Vvedenskaya ◽  
Hanif Vahedian-Movahed ◽  
Yuanchao Zhang ◽  
Deanne M. Taylor ◽  
Richard H. Ebright ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Start Site ◽  
Transcription Initiation ◽  
Specific Protein ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Bubble ◽  
Recognition Element

During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein–DNA interactions with the downstream part of the nontemplate strand of the transcription bubble (“core recognition element,” CRE). Here, we investigated whether sequence-specific RNAP–CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP–CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP–CRE interactions on TSS selection in vitro and in vivo for a library of 47 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP–CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid native-elongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP–CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP–CRE interactions determine TSS selection. Our findings establish RNAP–CRE interactions are a functional determinant of TSS selection. We propose that RNAP–CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).

Mapping of the Human Renin Transcription Start Site: Evidence for a Single Functional Promoter

1988 ◽  
Vol 10 (6) ◽  
pp. 1313-1316
Author(s):  
Martin Paul ◽  
David W. Burt ◽  
Norifumi Nakamura ◽  
Richard E. Pratt ◽  
Victor J. Dzau
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start ◽  
Human Renin
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