Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells

Elaine Delvaux, Diego Mastroeni, Jennifer Nolz, Paul Coleman

Research output: Contribution to journalArticle

Abstract

We describe a novel method for assessing the "open" or "closed" state of chromatin at selected locations within the genome. This method combines the use of Benzonase, which can digest DNA in the presence of actin, with quantitative polymerase chain reaction to define digested regions. We demonstrate the application of this method in brain homogenates and laser captured cells. We also demonstrate application to selected sites within more than 1 gene and multiple sites within 1 gene. We demonstrate the validity of the method by treating cells with valproate, known to render chromatin more permissive, and by comparison with classical digestion with DNase I in an in vitro preparation. Although we demonstrate the use of this method in brain tissue, we also recognize its applicability to other tissue types.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalNeuroepigenetics
Volume6
DOIs
StatePublished - Jun 1 2016

Keywords

  • Benzonase
  • Chromatin
  • QPCR

ASJC Scopus subject areas

  • Biochemistry
  • Developmental Neuroscience
  • Cognitive Neuroscience
  • Cellular and Molecular Neuroscience
  • Biological Psychiatry

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