A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes

Matthew E. Pipkin, Mathias G. Lichtenheld

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

The study of eukaryotic gene transcription depends on methods to discover distal cis-acting control sequences. Comparative bioinformatics is one powerful strategy to reveal these domains, but still requires conventional wet-bench techniques to elucidate their specificity and function. The DNase I hypersensitivity assay (DHA) is also a method to identify regulatory domains, but can also suggest their function. Technically however, the classical DHA is constrained to mapping gene loci in small increments of ∼20 kb. This limitation hinders efficient and comprehensive analysis of distal gene regions. Here, we report an improved method termed mega-DHA that extends the range of existing DHAs to facilitate assaying intervals that approach 100 kb. We demonstrate its feasibility for efficient analysis of single-copy genes within a large and complex genome by assaying 230 kb of the human ADAMTS14perforin paladin gene cluster in four experiments. The results identify distinct networks of regulatory domains specific to expression of perforin and its two neighboring genes.

Original languageEnglish (US)
Article numbere34
JournalNucleic acids research
Volume34
Issue number4
DOIs
StatePublished - Mar 2006

ASJC Scopus subject areas

  • Genetics

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