Characterization of sequences downstream from transcriptional start site ofRhizobium meliloti nifHDK promoter

1997 ◽  
Vol 40 (2) ◽  
pp. 217-224 ◽  
Author(s):  
Yunfeng Gao ◽  
Tong Wu ◽  
Jiabi Zhu ◽  
Guanqiao Yu ◽  
Shanjiong Shen
Keyword(s):  
Transcriptional Start Site ◽  
Start Site ◽  
Ofrhizobium Meliloti

scholarly journals Troglitazone, a Ligand of Peroxisome Proliferator-Activated Receptor-γ, Stabilizes NUCB2 (Nesfatin) mRNA by Activating the ERK1/2 Pathway: Isolation and Characterization of the Human NUCB2 Gene

Endocrinology ◽  
2010 ◽  
Vol 151 (6) ◽  
pp. 2494-2503 ◽  
Author(s):  
Masanobu Yamada ◽  
Kazuhiko Horiguchi ◽  
Ryohei Umezawa ◽  
Koshi Hashimoto ◽  
Tetsurou Satoh ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Transcriptional Start Site ◽  
Peroxisome Proliferator ◽  
Start Site ◽  
Peroxisome Proliferator Activated Receptor ◽  
Isolation And Characterization ◽  
Precursor Peptide ◽  
Translational Start ◽  
Derivatives Of

We recently identified a novel satiety peptide, nesfatin-1, containing 82 amino acids derived from the precursor peptide, nucleobindin 2 (NUCB2), from a troglitazone (TZ)-induced cDNA library. We examined the molecular mechanism underlying TZ-induced NUCB2 mRNA expression. Although TZ induced the mRNA expression in HTB185 cells, a nuclear run-on assay revealed no significant change in the transcription of the gene. Surprisingly, HTB185 cells possessed no functional peroxisome proliferator-activated receptor-γ. We therefore examined the effect of TZ on the mRNA’s stability. The half-life of NUCB2 mRNA was approximately 6 h, and incubation with TZ increased this to 27 h. Furthermore, this increase was completely inhibited by an ERK inhibitor, PD98059, and phosphorylated ERK1/2 was significantly increased after 30 min incubation with TZ. In addition, we cloned the entire NUCB2 gene and identified four adenylate/uridylate-rich elements (AREs) in the 3′ untranslated region (UTR), to which several proteins of HTB185 extracts treated with TZ bound. The reporter assay fused with 3′UTR showed that the second and third AREs were crucial. Furthermore, the human NUCB2 gene spanned 55 kb and contained 14 exons and 13 introns. The transcriptional start site formed clusters around 246 bp upstream from the translational start site. We confirmed that a construct containing 5889 bp of the promoter region was very active in neuron-derived cell lines but not stimulated by TZ. These findings demonstrated a novel action of derivatives of thiazolidinediones, oral insulin-sensitizing antidiabetic agents, to stabilize the mRNA of NUCB2 through AREs in the 3′UTR by activating the ERK1/2 pathway independently of peroxisome proliferator-activated receptor-γ.

Nucleotide Structure and Characterization of the Murine Gene Encoding Anticoagulant Protein C

1998 ◽  
Vol 79 (02) ◽  
pp. 310-316 ◽  
Author(s):  
Louise Jalbert ◽  
Elliot Rosen ◽  
Ann Lissens ◽  
Peter Carmeliet ◽  
Désiré Collen ◽  
...  
Keyword(s):  
Protein C ◽  
Stop Codon ◽  
Transcriptional Start Site ◽  
Consensus Sequence ◽  
Start Site ◽  
Gene Encoding ◽  
Exon 2 ◽  
Exon 1 ◽  
Translation Stop Codon

SummaryThe 15,160 bp murine gene encoding anticoagulation protein C (PC) was cloned and sequenced, including 414 bp upstream of exon 1 and 80 bp downstream of the translation stop codon. Nine exons and eight introns were identified. The first exon was untranslated and contained the major transcriptional start site, the surrounding nucleotide sequence of which matched reasonably well with the consensus eukaryotic Cap element sequence. The translational initiator methio-nine residue was located in exon 2. The other introns were positioned as splices between the major domain units of the protein. The 5’ untranslated region contained two possible CCAAT sequences and GC boxes, but no TATA box was obvious within the optimal range of distances from the transcription start site. The 3’-flanking nucleotides included a probable polyadenylation site (ATTAAA), beginning 80 nucleotides downstream of the translation stop codon, and a downstream consensus sequence (AGTGTTTC) required for the efficient formation of a 3’ terminus of mRNA. Several high probability transcription factor recognition sequences, including proteins that are enriched in, or specific to, the liver, such as C/EBP, C/EBP, HNF1, and HNF3, have been located in the 5’ region of the gene. These results indicate that all elements are present for liver-based transcription of the gene for murine PC.

scholarly journals Molecular characterization of a beta zero-thalassemia resulting from a 1.4 kilobase deletion

Blood ◽  
1988 ◽  
Vol 72 (2) ◽  
pp. 636-641 ◽  
Author(s):  
R Anand ◽  
CD Boehm ◽  
HH Jr Kazazian ◽  
EF Vanin
Keyword(s):  
Transcriptional Start Site ◽  
Globin Gene ◽  
Event Analysis ◽  
Beta Globin ◽  
Base Pairs ◽  
Dna Polymerase Alpha ◽  
Beta Globin Gene ◽  
American Black ◽  
The Individual

Abstract We report the characterization of a beta zero-thalassemia in an American Black with unusually high HbA2 and HbF levels. Genomic southern analysis indicated that the individual was heterozygous for a deletion that began within the second intervening sequence of the beta- globin gene and extended approximately 1.4 kb in the 5′ direction. A clone spanning the breakpoint on the abnormal chromosome was isolated and further mapped, and the deletion joint was sequenced. Comparison of the normal beta-globin gene and its 5′ flanking region with the deletion joint sequence indicated that the 5′ breakpoint for this deletion was 484 base pairs (bp) 5′ to the transcriptional start site for the beta-globin gene and the 3′ breakpoint was 908 bp into the beta- globin gene; the deletion removed a total of 1,393 bp. Comparison of the normal 5′ and 3′ breakpoint sequences indicated that this deletion was the result of a “clean” nonhomologous breakage and reunion event; ie, no spurious bases were added during the recombinational event. Analysis of the breakpoints of this deletion together with the breakpoints of two other small deletions involving the beta-globin gene suggests that the breakpoints may occur at DNA polymerase alpha pause sites.

scholarly journals Characterization of the Overlapping Promoters of nolB and nolW, Two Soybean Cultivar Specificity Genes from Rhizobium fredii Strain USDA257

1997 ◽  
Vol 10 (1) ◽  
pp. 138-141 ◽  
Author(s):  
Jun Gu ◽  
Pedro A. Balatti ◽  
Hari B. Krishnan ◽  
Steven G. Pueppke
Keyword(s):  
Regulatory Gene ◽  
Initiation Site ◽  
Dual Control ◽  
Start Site ◽  
Rhizobium Fredii ◽  
Normal Expression ◽  
Transcript Initiation ◽  
Cultivar Specificity ◽  
Transcript Start Site

The transcripts of nolW and nolB, two divergently oriented cultivar specificity genes of Rhizobium fredii strain USDA257, are known to be initiated 14 bp apart from promoters that face one another. We show here that expression of nolB is dependent both on induction with flavonoid signals and on the regulatory gene, nodD1. Expression of nolW is constitutive and independent of flavonoids and nodD1. Normal expression of nolB is retained with a promoter that extends only 61 bp upstream of the transcript start site, but it is lost if an additional 24 bp are removed. Substantial expression of nolW is retained with a promoter that contains only 34 bp of DNA upstream from the transcript initiation site. The dual control region for the two genes is thus only about 109 bp in length.

The two isozymes of rat intestinal alkaline phosphatase are products of two distinct genes

2000 ◽  
Vol 3 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Q. XIE ◽  
D. H. ALPERS
Keyword(s):  
Alkaline Phosphatase ◽  
Transcriptional Start Site ◽  
In Vivo Studies ◽  
Peroxisome Proliferator ◽  
Start Site ◽  
Intestinal Alkaline Phosphatase ◽  
Promoter Regions ◽  
Flanking Regions

Xie, Q., and D. H. Alpers. The two isozymes of rat intestinal alkaline phosphatase are products of two distinct genes. Physiol Genomics 3: 1–8, 2000.—Rat intestinal alkaline phosphatases (IAP-I and -II) differ in primary structure, substrate specificity, tissue localization, and response to fat feeding. This study identifies two distinct genes (∼5–6 kb) corresponding to each isozyme and containing 11 exons of nearly identical size. The exon-intron junctions are identical with those found in IAP genes from other species. The 1.7 and 1.2 bp of 5′ flanking regions isolated from each gene, respectively, contain Sp1 and gut-enriched Kruppel-like factor (GKLF) binding sites, but otherwise show little identity. There is a potential CAAT-box 14 bp 5′ to the transcriptional start site, 36 bp upstream from IAP-I, and a TATA-box 31 bp 5′ to the transcriptional start site, 55 bp upstream from IAP-II. Transfection of these promoter regions (linked to luciferase as a reporter gene) into a kidney cell line, COS-7, produced the differential response to oleic acid expected from in vivo studies, i.e., threefold increase using the 5′ flanking region of IAP-II, but not IAP-I. This response was not reproduced by 5,8,11,14-eicosatetraynoic acid (ETYA) or clofibrate, suggesting that peroxisome proliferator response elements are not involved. Isolation of the IAP-II gene will allow determination of the sequences responsible for dietary fat response in the enterocyte.

scholarly journals Characterization of PmfR, the Transcriptional Activator of the pAO1-Borne purU-mabO-folD Operon of Arthrobacter nicotinovorans

2005 ◽  
Vol 187 (9) ◽  
pp. 3062-3070 ◽  
Author(s):  
Calin B. Chiribau ◽  
Cristinel Sandu ◽  
Gabor L. Igloi ◽  
Roderich Brandsch
Keyword(s):  
Binding Site ◽  
Transcriptional Start Site ◽  
Transcriptional Activator ◽  
Open Reading Frames ◽  
Start Site ◽  
Gene Encoding ◽  
Chloramphenicol Resistance ◽  
Nuclease Digestion ◽  
Arthrobacter Nicotinovorans

ABSTRACT Nicotine catabolism by Arthrobacter nicotinovorans is linked to the presence of the megaplasmid pAO1. Genes involved in this catabolic pathway are arranged on the plasmid into gene modules according to function. During nicotine degradation γ-N-methylaminobutyrate is formed from the pyrrolidine ring of nicotine. Analysis of the pAO1 open reading frames (ORF) resulted in identification of the gene encoding a demethylating γ-N-methylaminobutyrate oxidase (mabO). This gene was shown to form an operon with purU- and folD-like genes. Only in bacteria grown in the presence of nicotine could transcripts of the purU-mabO-folD operon be detected, demonstrating that this operon constitutes part of the pAO1 nicotine regulon. Its transcriptional start site was determined by primer extension analysis. Transcription of the operon was shown to be controlled by a new transcriptional regulator, PmfR, the product of a gene that is transcribed divergently from the purU, mabO, and folD genes. PmfR was purified, and electromobility shift assays and DNase I-nuclease digestion experiments were used to determine that its DNA binding site is located between −48 and −88 nucleotides upstream of the transcriptional start site of the operon. Disruption of pmfR by homologous recombination with a chloramphenicol resistance cassette demonstrated that PmfR acts in vivo as a transcriptional activator. Mutagenesis of the PmfR target DNA suggested that the sequence GTTT-14 bp-AAAC is the core binding site of the regulator upstream of the −35 promoter region of the purU-mabO-folD operon.

scholarly journals The chromatin remodeler Ino80 mediates RNAPII pausing site determination

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Youngseo Cheon ◽  
Sungwook Han ◽  
Taemook Kim ◽  
Daehee Hwang ◽  
Daeyoup Lee
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Start Site ◽  
Regulation Of Gene Expression ◽  
Embryonic Stem ◽  
Start Site ◽  
Chromatin Remodeler ◽  
Close Relationship ◽  
Early Transcription ◽  
Different Characteristics

Abstract Background Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive. Results Here, we report highly confined RNAPII enrichments downstream of the transcriptional start site in Saccharomyces cerevisiae using PRO-seq experiments. This non-uniform distribution of RNAPII exhibits both similar and different characteristics with promoter-proximal pausing in Schizosaccharomyces pombe and metazoans. Interestingly, we find that Ino80p knockdown causes a significant upstream transition of promoter-proximal RNAPII for a subset of genes, relocating RNAPII from the main pausing site to the alternative pausing site. The proper positioning of RNAPII is largely dependent on nucleosome context. We reveal that the alternative pausing site is closely associated with the + 1 nucleosome, and nucleosome architecture around the main pausing site of these genes is highly phased. In addition, Ino80p knockdown results in an increase in fuzziness and a decrease in stability of the + 1 nucleosome. Furthermore, the loss of INO80 also leads to the shift of promoter-proximal RNAPII toward the alternative pausing site in mouse embryonic stem cells. Conclusions Based on our collective results, we hypothesize that the highly conserved chromatin remodeler Ino80p is essential in establishing intact RNAPII pausing during early transcription elongation in various organisms, from budding yeast to mouse.

Sign in / Sign up

Export Citation Format

Share Document