scholarly journals Structural organization of upstream exons and distribution of transcription start sites in the chicken c-myb gene.

1989 ◽  
Vol 9 (2) ◽  
pp. 837-843 ◽  
Author(s):  
S L Hahn ◽  
M Hahn ◽  
W S Hayward
Keyword(s):  
Binding Sites ◽  
Noncoding Region ◽  
Open Reading Frames ◽  
Transcription Start ◽  
S1 Nuclease ◽  
Transcription Start Sites ◽  
Conserved Sequence ◽  
Myb Gene ◽  
Putative Transcription Factor ◽  
Myb Genes

We mapped and sequenced three upstream exons of the chicken c-myb gene and the regions flanking the first coding exon. We found multiple potential binding sites for transcription factors in the 5'-noncoding region, a T-rich stretch of 78 base pairs (bp) (68% T) in the first intron, and four fairly long open reading frames in the antisense direction of the first coding exon and its flanking regions. Three major transcription start sites, contained within a single 11-bp region, were identified by S1 nuclease analysis and primer extension. A sequence comparison of the avian and murine c-myb genes revealed a highly conserved sequence of 124 bp in the 5'-noncoding region. Its location between the putative transcription factor binding sites and the major transcription start sites suggests that it may play an important regulatory role in c-myb expression.

Structural organization of upstream exons and distribution of transcription start sites in the chicken c-myb gene

1989 ◽  
Vol 9 (2) ◽  
pp. 837-843
Author(s):  
S L Hahn ◽  
M Hahn ◽  
W S Hayward
Keyword(s):  
Binding Sites ◽  
Noncoding Region ◽  
Open Reading Frames ◽  
Transcription Start ◽  
S1 Nuclease ◽  
Transcription Start Sites ◽  
Conserved Sequence ◽  
Myb Gene ◽  
Putative Transcription Factor ◽  
Myb Genes

We mapped and sequenced three upstream exons of the chicken c-myb gene and the regions flanking the first coding exon. We found multiple potential binding sites for transcription factors in the 5'-noncoding region, a T-rich stretch of 78 base pairs (bp) (68% T) in the first intron, and four fairly long open reading frames in the antisense direction of the first coding exon and its flanking regions. Three major transcription start sites, contained within a single 11-bp region, were identified by S1 nuclease analysis and primer extension. A sequence comparison of the avian and murine c-myb genes revealed a highly conserved sequence of 124 bp in the 5'-noncoding region. Its location between the putative transcription factor binding sites and the major transcription start sites suggests that it may play an important regulatory role in c-myb expression.

scholarly journals Extended Region of Nodulation Genes in Rhizobium meliloti 1021. II. Nucleotide Sequence, Transcription Start Sites and Protein Products

Genetics ◽  
1987 ◽  
Vol 117 (2) ◽  
pp. 191-201
Author(s):  
Robert F Fisher ◽  
Jean A Swanson ◽  
John T Mulligan ◽  
Sharon R Long
Keyword(s):  
Binding Site ◽  
Rhizobium Meliloti ◽  
Open Reading Frames ◽  
Translation System ◽  
Transcription Start ◽  
Nod Genes ◽  
Transcription Start Sites ◽  
Conserved Sequence ◽  
Reading Frames

ABSTRACT We have established the DNA sequence and analyzed the transcription and translation products of a series of putative nodulation (nod) genes in Rhizobium meliloti strain 1021. Four loci have been designated nodF, nodE, nodG and nodH. The correlation of transposon insertion positions with phenotypes and open reading frames was confirmed by sequencing the insertion junctions of the transposons. The protein products of these nod genes were visualized by in vitro expression of cloned DNA segments in a R. meliloti transcription-translation system. In addition, the sequence for nodG was substantiated by creating translational fusions in all three reading frames at several points in the sequence; the resulting fusions were expressed in vitro in both E. coli and R. meliloti transcription-translation systems. A DNA segment bearing several open reading frames downstream of nodG corresponds to the putative nod gene mutated in strain nod-216. The transcription start sites of nodF and nodH were mapped by primer extension of RNA from cells induced with the plant flavone, luteolin. Initiation of transcription occurs approximately 25 bp downstream from the conserved sequence designated the "nod box," suggesting that this conserved sequence acts as an upstream regulator of inducible nod gene expression. Its distance from the transcription start site is more suggestive of an activator binding site rather than an RNA polymerase binding site.

scholarly journals Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7526 ◽  
Author(s):  
Alfredo Mendoza-Vargas ◽  
Leticia Olvera ◽  
Maricela Olvera ◽  
Ricardo Grande ◽  
Leticia Vega-Alvarado ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
E Coli ◽  
Factor Binding ◽  
Genome Wide

scholarly journals Genome-Wide Identification of Estrogen Receptor α-Binding Sites in Mouse Liver

2008 ◽  
Vol 22 (1) ◽  
pp. 10-22 ◽  
Author(s):  
Hui Gao ◽  
Susann Fält ◽  
Albin Sandelin ◽  
Jan-Åke Gustafsson ◽  
Karin Dahlman-Wright
Keyword(s):  
Estrogen Receptor ◽  
Binding Sites ◽  
Mouse Liver ◽  
Estrogen Receptor Α ◽  
Estrogen Signaling ◽  
Transcription Start ◽  
Expression Levels ◽  
Transcription Start Sites ◽  
Genome Wide ◽  
Binding Regions

Abstract We report the genome-wide identification of estrogen receptor α (ERα)-binding regions in mouse liver using a combination of chromatin immunoprecipitation and tiled microarrays that cover all nonrepetitive sequences in the mouse genome. This analysis identified 5568 ERα-binding regions. In agreement with what has previously been reported for human cell lines, many ERα-binding regions are located far away from transcription start sites; approximately 40% of ERα-binding regions are located within 10 kb of annotated transcription start sites. Almost 50% of ERα-binding regions overlap genes. The majority of ERα-binding regions lie in regions that are evolutionarily conserved between human and mouse. Motif-finding algorithms identified the estrogen response element, and variants thereof, together with binding sites for activator protein 1, basic-helix-loop-helix proteins, ETS proteins, and Forkhead proteins as the most common motifs present in identified ERα-binding regions. To correlate ERα binding to the promoter of specific genes, with changes in expression levels of the corresponding mRNAs, expression levels of selected mRNAs were assayed in livers 2, 4, and 6 h after treatment with ERα-selective agonist propyl pyrazole triol. Five of these eight selected genes, Shp, Stat3, Pdgds, Pck1, and Pdk4, all responded to propyl pyrazole triol after 4 h treatment. These results extend our previous studies using gene expression profiling to characterize estrogen signaling in mouse liver, by characterizing the first step in this signaling cascade, the binding of ERα to DNA in intact chromatin.

scholarly journals The Promoter of the Yeast INO4Regulatory Gene: a Model of the Simplest Yeast Promoter

2000 ◽  
Vol 182 (10) ◽  
pp. 2746-2752 ◽  
Author(s):  
Kelly A. Robinson ◽  
John M. Lopes
Keyword(s):  
Promoter Activity ◽  
Small Region ◽  
Transcription Start ◽  
Additional Element ◽  
S1 Nuclease ◽  
Activator Proteins ◽  
Transcription Start Sites ◽  
S1 Nuclease Mapping ◽  
Nuclease Mapping ◽  
Yeast Genes

ABSTRACT In Saccharomyces cerevisiae, the phospholipid biosynthetic genes are transcriptionally regulated in response to inositol and choline. This regulation requires the transcriptional activator proteins Ino4p and Ino2p, which form a heterodimer that binds to the UAS INO element. We have previously shown that the promoters of the INO4 and INO2 genes are among the weakest promoters characterized in yeast. Because little is known about the promoters of weakly expressed yeast genes, we report here the analysis of the constitutive INO4 promoter. Promoter deletion constructs scanning 1,000 bp upstream of theINO4 gene identified a small region (−58 to −46) that is absolutely required for expression. S1 nuclease mapping shows that this region contains the transcription start sites for the INO4gene. An additional element (−114 to −86) modestly enhancesINO4 promoter activity (fivefold). Thus, the region required for INO4 transcription is limited to 68 bp. These studies also found that INO4 gene expression is not autoregulated by Ino2p and Ino4p, despite the presence of a putative UAS INO element in the INO4promoter. We further report that the INO4 steady-state transcript levels and Ino4p levels are regulated twofold in response to inositol and choline, suggesting a posttranscriptional mechanism of regulation.

scholarly journals ExsA Recruits RNA Polymerase to an Extended −10 Promoter by Contacting Region 4.2 of Sigma-70

2010 ◽  
Vol 192 (14) ◽  
pp. 3597-3607 ◽  
Author(s):  
Christopher A. Vakulskas ◽  
Evan D. Brutinel ◽  
Timothy L. Yahr
Keyword(s):  
Rna Polymerase ◽  
Binding Sites ◽  
Type Iii Secretion ◽  
Transcription Initiation ◽  
Additional Contribution ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Collective Data ◽  
Sigma 70

ABSTRACT ExsA is a member of the AraC family of transcriptional activators and is required for expression of the Pseudomonas aeruginosa type III secretion system (T3SS). ExsA-dependent promoters consist of two binding sites for monomeric ExsA located approximately 50 bp upstream of the transcription start sites. Binding to both sites is required for recruitment of σ70-RNA polymerase (RNAP) to the promoter. ExsA-dependent promoters also contain putative −35 hexamers that closely match the σ70 consensus but are atypically spaced 21 or 22 bp from the −10 hexamer. Because several nucleotides located within the putative −35 region are required for ExsA binding, it is unclear whether the putative −35 region makes an additional contribution to transcription initiation. In the present study we demonstrate that the putative −35 hexamer is dispensable for ExsA-independent transcription from the P exsC promoter and that deletion of σ70 region 4.2, which contacts the −35 hexamer, has no effect on ExsA-independent transcription from P exsC . Region 4.2 of σ70, however, is required for ExsA-dependent activation of the P exsC and P exsD promoters. Genetic data suggest that ExsA directly contacts region 4.2 of σ70, and several amino acids were found to contribute to the interaction. In vitro transcription assays demonstrate that an extended −10 element located in the P exsC promoter is important for overall promoter activity. Our collective data suggest a model in which ExsA compensates for the lack of a −35 hexamer by interacting with region 4.2 of σ70 to recruit RNAP to the promoter.

scholarly journals The human carbonic anhydrase I gene has two promoters with different tissue specificities

1991 ◽  
Vol 277 (3) ◽  
pp. 903-905 ◽  
Author(s):  
H J M Brady ◽  
N Lowe ◽  
J C Sowden ◽  
M Edwards ◽  
P H W Butterworth
Keyword(s):  
Carbonic Anhydrase ◽  
Sequence Similarity ◽  
Transcription Start ◽  
S1 Nuclease ◽  
Transcription Start Sites ◽  
Similar Region ◽  
Carbonic Anhydrase I ◽  
Mrna Transcripts ◽  
Human Carbonic Anhydrase ◽  
Strong Sequence Similarity

Primer extension and S1 nuclease analysis of human carbonic anhydrase I (HCA1) mRNA transcripts in erythroid and non-erythroid tissues show that the HCA1 gene has two promoters with different tissue specificities, separated by 36 kb of DNA. The promoter of the HCA1 gene which is active in non-erythroid tissue shows strong sequence similarity with a similar region in the mouse CA1 gene, but has two equally used transcription start sites.

scholarly journals Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expression

2020 ◽  
Author(s):  
Mitra Ansariola ◽  
Valerie N. Fraser ◽  
Sergei A. Filichkin ◽  
Maria G. Ivanchenko ◽  
Zachary A. Bright ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Open Chromatin ◽  
Transcription Start ◽  
Tissue Specific ◽  
Transcription Start Sites ◽  
Tissue Specific Gene ◽  
Specific Gene Expression

AbstractAcross tissues, gene expression is regulated by a combination of determinants, including the binding of transcription factors (TFs), along with other aspects of cellular state. Recent studies emphasize the importance of both genetic and epigenetic states – TF binding sites and binding site chromatin accessibility have emerged as potentially causal determinants of tissue specificity. To investigate the relative contributions of these determinants, we constructed three genome-scale datasets for both root and shoot tissues of the same Arabidopsis thaliana plants: TSS-seq data to identify Transcription Start Sites, OC-seq data to identify regions of Open Chromatin, and RNA-seq data to assess gene expression levels. For genes that are differentially expressed between root and shoot, we constructed a machine learning model predicting tissue of expression from chromatin accessibility and TF binding information upstream of TSS locations. The resulting model was highly accurate (over 90% auROC and auPRC), and our analysis of model contributions (feature weights) strongly suggests that patterns of TF binding sites within ∼500 nt TSS-proximal regions are predominant explainers of tissue of expression in most cases. Thus, in plants, cis-regulatory control of tissue-specific gene expression appears to be primarily determined by TSS-proximal sequences, and rarely by distal enhancer-like accessible chromatin regions. This study highlights the exciting future possibility of a native TF site-based design process for the tissue-specific targeting of plant gene promoters.

scholarly journals Molecular Characterization of the PhoP-PhoQ Two-Component System in Escherichia coli K-12: Identification of Extracellular Mg2+-Responsive Promoters

1999 ◽  
Vol 181 (17) ◽  
pp. 5516-5520 ◽  
Author(s):  
Akinori Kato ◽  
Hiroyuki Tanabe ◽  
Ryutaro Utsumi
Keyword(s):  
Escherichia Coli ◽  
Direct Repeat ◽  
Two Component System ◽  
Transcription Start ◽  
Promoter Regions ◽  
S1 Nuclease ◽  
Transcription Start Sites ◽  
Two Component ◽  
K 12

ABSTRACT We identified Mg2+-responsive promoters of thephoPQ, mgtA, and mgrB genes ofEscherichia coli K-12 by S1 nuclease analysis. Expression of these genes was induced by magnesium limitation and depended on PhoP and PhoQ. The transcription start sites were also determined, which allowed us to find a (T/G)GTTTA direct repeat in their corresponding promoter regions.

scholarly journals Alternative promoters and cardiac muscle cell-specific expression of the Na+/Ca2+exchanger gene

1998 ◽  
Vol 274 (1) ◽  
pp. H217-H232 ◽  
Author(s):  
Susanne B. Nicholas ◽  
Weidong Yang ◽  
Shwu-Luan Lee ◽  
Hong Zhu ◽  
Kenneth D. Philipson ◽  
...  
Keyword(s):  
Binding Sites ◽  
Alternative Promoters ◽  
Limited Data ◽  
Transcription Start ◽  
Specific Expression ◽  
Tissue Specific ◽  
Transcription Start Sites ◽  
Gata Factors ◽  
Specific Alternative ◽  
Specific Factors

Many studies have investigated the regulation of the Na+/Ca2+exchanger, NCX1, but limited data exist on transcriptional regulation of the NCX1 gene. We have identified the transcription start sites of three tissue-specific alternative promoters of NCX1 transcripts from rat heart, kidney, and brain. We have characterized the cardiac NCX1 promoter, from which the most abundant quantities of NCX1 transcripts are expressed. Transfection of primary cardiac myocytes, CHO cells, and COS-7 cells with overlapping genomic DNA fragments spanning the NCX1 cardiac transcription start site has uncovered a cardiac cell-specific minimum promoter from −137 to +85. The cardiac NCX1 promoter is TATA-less but has putative binding sites for cardiac-specific GATA factors, an E box, and an Inr as well as multiple active enhancers. The kidney NCX1 promoter has a typical TATA box and binding sites for several tissue-specific factors. The brain NCX1 promoter is very GC-rich and possesses several Sp-1 binding sites consistent with its ubiquitous expression.

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