scholarly journals The GLI gene encodes a nuclear protein which binds specific sequences in the human genome.

1990 ◽  
Vol 10 (2) ◽  
pp. 634-642 ◽  
Author(s):  
K W Kinzler ◽  
B Vogelstein
Keyword(s):  
Zinc Finger ◽  
Base Pair ◽  
Binding Sites ◽  
Protein Product ◽  
Variable Number ◽  
Binding Motifs ◽  
Dna Binding Motifs ◽  
Pair Sequence ◽  
Polymerase Chain

The GLI gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the GLI gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three GLI binding sites were identified by using a novel procedure in which total human DNA was bound to a GLI recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The GLI protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify GLI binding sites should be applicable to the characterization of other zinc finger proteins.

The GLI gene encodes a nuclear protein which binds specific sequences in the human genome

1990 ◽  
Vol 10 (2) ◽  
pp. 634-642
Author(s):  
K W Kinzler ◽  
B Vogelstein
Keyword(s):  
Zinc Finger ◽  
Base Pair ◽  
Binding Sites ◽  
Protein Product ◽  
Variable Number ◽  
Binding Motifs ◽  
Dna Binding Motifs ◽  
Pair Sequence ◽  
Polymerase Chain

The GLI gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the GLI gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three GLI binding sites were identified by using a novel procedure in which total human DNA was bound to a GLI recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The GLI protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify GLI binding sites should be applicable to the characterization of other zinc finger proteins.

scholarly journals Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Colin T. Waters ◽  
Stephen S. Gisselbrecht ◽  
Yuliya A. Sytnikova ◽  
Tiziana M. Cafarelli ◽  
David E. Hill ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Enhancer Activity ◽  
Epistatic Interactions ◽  
Binding Motifs ◽  
Transcriptional Enhancers ◽  
Significant Challenge ◽  
Dna Binding Sites ◽  
Dna Binding Motifs ◽  
Quantitative Changes

AbstractUnderstanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers. We measure quantitative changes in enhancer activity and discover a range of epistatic interactions among the motifs, both synergistic and alleviating. We find that understanding the regulatory consequences of TF binding motifs requires that they be investigated in combination across enhancer contexts.

scholarly journals Direct Molecular Characterization of Acid-Fast Bacilli Smear of Nontuberculosis Mycobacterium Species Causing Pulmonary Tuberculosis in Guna Yala Region, Panama

2021 ◽  
Author(s):  
Arístides López ◽  
Fermin Acosta ◽  
Dilcia Sambrano ◽  
Musharaf Tarajia ◽  
Sophia Navajas ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Tandem Repeats ◽  
Nontuberculous Mycobacteria ◽  
Restriction Analysis ◽  
Clinical Signs ◽  
Variable Number ◽  
Remote Areas ◽  
Laboratory Capacity ◽  
Polymerase Chain

Mycobacterium tuberculosis (MTB) stands out as the main causative agent of pulmonary tuberculosis (TB). However, nontuberculous mycobacteria (NTM) species also have the potential to infect and cause TB in susceptible individuals. The objective of this study was to identify NTM species that cause public health problems in remote areas. The study was carried out using 105 sputum smears obtained from patients from the Guna Yala Region of Panama with clinical signs suggestive of TB. DNA was extracted from sputum smears. Nontuberculous mycobacteria and MTB were characterized using polymerase chain reaction restriction analysis (hsp65, rpob) and an evaluation of 24-mycobacterial interspersed repetitive units–variable number of tandem repeats loci. Twenty-six Mycobacterium species were characterized; 19 (18%) were identified as MTB, and 7 (6.7%) were identified as NTM (four M. avium complex, two M. haemophilum, one M. tusciae). These results suggest that at least one in five cases of pulmonary TB among this population is caused by an NTM. Thus, identifying the bacteria causing pulmonary disease is key even in remote regions of the world where standard diagnosis and culture are not available. Strengthening the laboratory capacity within the Guna Yala Region is needed to identify NTM infections promptly.

scholarly journals Characterization of the salA, syrF, and syrG Regulatory Genes Located at the Right Border of the Syringomycin Gene Cluster of Pseudomonas syringae pv. syringae

2002 ◽  
Vol 15 (1) ◽  
pp. 43-53 ◽  
Author(s):  
Shi-En Lu ◽  
Brenda K. Scholz-Schroeder ◽  
Dennis C. Gross
Keyword(s):  
Gene Cluster ◽  
Pseudomonas Syringae ◽  
Binding Motifs ◽  
Right Border ◽  
Dna Binding Motifs ◽  
In Series ◽  
Regulatory Loci ◽  
The Right ◽  
The Relationship

Sequence analysis of the right border of the syr gene cluster of Pseudomonas syringae pv. syringae strain B301D revealed the presence of the salA gene 8,113 bp downstream of syrE. The predicted SalA protein of strain B301D differs by one amino acid from that of strain B728a. Two homologs of salA, designated syrF and syrG, were identified between syrE and salA. All three proteins contain helix-turn-helix DNA-binding motifs at their C termini and exhibit homology to regulatory proteins of the LuxR family. A salA mutant failed to produce syringomycin, whereas syrF and syrG mutants produced 12 and 50%, respectively, of syringomycin relative to the wild-type strain. The salA, syrF, and syrG mutants were significantly reduced in virulence, forming small, nonspreading lesions in immature cherry fruits. Translational fusions to the uidA gene were constructed to evaluate expression of syrB1 in regulatory mutant backgrounds and to determine the relationship among the three regulatory loci. Expression of a syrB1::uidA fusion required functional salA and syrF genes and, in series, the expression of a syrF::uidA fusion required a functional salA gene. These results demonstrate that salA is located upstream of syrF in the regulatory hierarchy controlling syringomycin production and virulence in P. syringae pv. syringae.

Artificial Nine Zinc-Finger Peptide with 30 Base Pair Binding Sites†

Biochemistry ◽  
1998 ◽  
Vol 37 (39) ◽  
pp. 13827-13834 ◽  
Author(s):  
Tatsuya Kamiuchi ◽  
Emiko Abe ◽  
Miki Imanishi ◽  
Tamaki Kaji ◽  
Makoto Nagaoka ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Base Pair ◽  
Binding Sites ◽  
Zinc Finger Peptide

scholarly journals The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Rita A Batista ◽  
Jordi Moreno-Romero ◽  
Yichun Qiu ◽  
Joram van Boven ◽  
Juan Santos-González ◽  
...  
Keyword(s):  
Binding Sites ◽  
Transcriptional Activity ◽  
Endosperm Development ◽  
Imprinted Genes ◽  
Mads Box ◽  
Binding Motifs ◽  
Molecular Domestication ◽  
Dna Binding Motifs ◽  
Carg Box ◽  
Eukaryotic Organisms

MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

scholarly journals Structural and functional characterization of the bacterial biofilm activator RemA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tamara Hoffmann ◽  
Devid Mrusek ◽  
Patricia Bedrunka ◽  
Fabiana Burchert ◽  
Christopher-Nils Mais ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Regulatory Protein ◽  
Bacterial Biofilm ◽  
Binding Motifs ◽  
Expression Of Genes ◽  
Dna Binding Motifs ◽  
Matrix Production ◽  
In Vivo Characterization

AbstractBacillus subtilis can form structurally complex biofilms on solid or liquid surfaces, which requires expression of genes for matrix production. The transcription of these genes is activated by regulatory protein RemA, which binds to poorly conserved, repetitive DNA regions but lacks obvious DNA-binding motifs or domains. Here, we present the structure of the RemA homologue from Geobacillus thermodenitrificans, showing a unique octameric ring with the potential to form a 16-meric superstructure. These results, together with further biochemical and in vivo characterization of B. subtilis RemA, suggests that the protein can wrap DNA around its ring-like structure through a LytTR-related domain.

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