Dominant genomic structures: Detection and potential signal functions in the interferon-beta domain

Eukaryotic genomes are divided into chromatin domains, which are thought to represent independent regulatory units. Typically, these domains are flanked by bordering elements that insulate the transcription unit from outside influences. Borders also demarcate the range of action for enhancer-like el...

Full description

Saved in:
Bibliographic Details
Published in:Gene 2005-12, Vol.364, p.79-89
Main Authors: Klar, Martin, Stellamanns, Eric, AK, Prashanth, Gluch, Angela, Bode, Juergen
Format: Article
Language:English
Subjects:
Algorithms
Animals
Base Sequence
Binding Sites
Chromatin - genetics
Chromatin - ultrastructure
Chromatin domain
DNA Primers
DNAse I hypersensitive sites
Gene induction
Genes, Dominant
Genome
Humans
Interferon-beta - genetics
Interferon-β
Mice
Models, Genetic
Molecular Sequence Data
Plasmids
Polymerase Chain Reaction
Scaffold/matrix attachment region (S/MAR)
Signal Transduction - genetics
Stress-induced duplex destabilization (SIDD)
Yin-Yang 1 (YY1)
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Eukaryotic genomes are divided into chromatin domains, which are thought to represent independent regulatory units. Typically, these domains are flanked by bordering elements that insulate the transcription unit from outside influences. Borders also demarcate the range of action for enhancer-like elements within the domain as they are formed around dominant genomic structures such as DNAse I hypersensitive sites (HS). Here we describe an efficient strategy to localize these elements. Our procedure is based on a computational method and predictions are verified by classical in vivo and in vitro procedures. Exemplified by the interferon-β (IFN-β) domain it proves its potential to provide novel insights into remote control principles of transcription. Sites with secondary-structure forming potential are localized by the analysis of stress-induced duplex destabilization (SIDD) properties and the associating factors are characterized by electrophoretic mobility shift assays (EMSA). These studies reveal far upstream factor binding sites within the IFN-β domains of both humans and mice. A prominent example is YY1, a transcription factor that not only recognizes a core consensus motif, ATGG, but, in addition, the structural context, which is evident from characteristic imprints in the respective SIDD-profiles.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2005.07.023