Zinc-finger domains of the transcriptional repressor KLF15 bind multiple sites in rhodopsin and IRBP promoters including the CRS-1 and G-rich repressor elements

doi:10.1186/1471-2199-6-15

BMC Molecular Biology
Volume 6

Viewing options:

Abstract
Full text
PDF (2.2MB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Otteson DC
Lai H
Liu Y
Zack DJ

on PubMed

Otteson DC
Lai H
Liu Y
Zack DJ
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research article

Zinc-finger domains of the transcriptional repressor KLF15 bind multiple sites in rhodopsin and IRBP promoters including the CRS-1 and G-rich repressor elements

Deborah C Otteson¹^,2^,4 , Hong Lai²^,5 , Yuhui Liu² and Donald J Zack¹^,2^,3

¹Guerrieri Center for Genetic Engineering and Molecular Ophthalmology at the Wilmer Eye Institute, Johns Hopkins University School of Medicine; 600 North Wolfe Street; Baltimore, MD 21287 USA

²Department of Ophthalmology, Johns Hopkins University School of Medicine; 600 North Wolfe Street; Baltimore, MD 21287 USA

³Departments of Neuroscience, and Molecular Biology and Genetics; Johns Hopkins University School of Medicine; 600 North Wolfe Street; Baltimore, MD 21287 USA

⁴College of Optometry, University of Houston; Houston, TX 77204 USA

⁵Department of Genetics, Stanford University School of Medicine; Stanford, CA 94305 USA

author email corresponding author email

BMC Molecular Biology 2005, 6:15doi:10.1186/1471-2199-6-15


Published:	17 June 2005

Additional files

Additional File 1:

Supplemental Data Files (Otteson SupplementalData.doc) containing full results of analysis of KFL15 binding sites using Target Explorer. Included in this data set are: 1. Sequences from bovine rhodopsin and IRBP promoters protected by KLF15-gst fusion proteins in DNAseI footprint analysis used as "training set" for Target Explorer. 2. List of top matrices for KLF15_9bpsite_otteson binding site. (sorted by information content): Assume 9 bp binding site and 60% AT/40% GC in genome. 3. Analysis to determine cutoff score for identification of KLF15 binding sites. Sequences and scores for bRho29, hRho29 and bRho29-mutations oligonucleotides used in competitive EMSA. Lists of putative binding sites in these oligos identified using Matrices 1–4: cut-off score = 1 indicating good and poor competitors. 4. List of top matrices for KLF15: Assume unknown binding site length and 60% T/40% GC in genome. 5. Analysis to determine cutoff score for identification of KLF15 binding sites assuming unknown binding site length. Sequences and scores for bRho29, hRho29 and bRho29-mutations oligonucleotides used in competitive EMSA. Lists of putative binding sites in these oligos identified using Matrices 1–4: cut-off score = 1 indicating good and poor competitors. 6. Identification of potential KLF15 binding sites in rhodopsin and IRBP promoters using matrix 2 with 9 bp binding site (cut-off score 4.87). Promoter sequences analyzed. Predicted binding sites

Format: DOC Size: 436KB Download file

This file can be viewed with: Microsoft Word Viewer