Native Genomic Blotting: High-resolution Mapping of DNase I-hypersensitive Sites and Protein-DNA Interactions

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1988 Jan 1

PMID 3422413

Citations 11

Authors

U Pauli

S Chrysogelos

J Stein

G Stein

Affiliations

Soon will be listed here.

Abstract

DNase I-hypersensitive sites are observed in the promoter regions of actively expressed genes, potentially active genes, and genes that were once active. We have developed an approach that greatly increases the resolution for mapping these sites by electrophoresing genomic DNA on native polyacrylamide gels prior to electroblotting and hybridization. This improved method has been used to scan the promoter and coding region of a cell-cycle-dependent human histone H4 gene with an accuracy of +/-5-10 base pairs. Protein-DNA interactions can be seen in the autoradiograph as light areas and DNase I-hypersensitive sites as dark bands. Therefore, this method provides a rapid and relatively simple means to accurately localize protein-DNA interactions as well as DNase I-hypersensitive sites, thus directly displaying DNase I hypersensitivity and protein-DNA complexes on one autoradiograph. It also potentially allows the analysis of small changes in DNase I-hypersensitive sites under various biological conditions. With this technique rather large regions of DNA can be screened to determine areas that should be analyzed by more sophisticated methods, such as genomic sequencing or gel retardation assays.

Citing Articles

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Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S-phase transition.

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The abbreviated pluripotent cell cycle.

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The architectural organization of human stem cell cycle regulatory machinery.

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The homeodomain transcription factor CDP/cut interacts with the cell cycle regulatory element of histone H4 genes packaged into nucleosomes.

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