Protocol

The Myc Gene

Volume 1012 of the series Methods in Molecular Biology pp 117-133

Date:

Chromatin Immunoprecipitation Assays for Myc and N-Myc

  • Bonnie L. BarrilleauxAffiliated withDepartment of Cell Biology and Human Anatomy, Institute of Pediatric Regenerative Medicine, University of California Davis School of Medicine, Shriners Hospital For Children Northern California
  • , Rebecca CottermanAffiliated withDepartment of Cell Biology and Human Anatomy, Institute of Pediatric Regenerative Medicine, University of California Davis School of Medicine, Shriners Hospital For Children Northern California
  • , Paul S. KnoepflerAffiliated withDepartment of Cell Biology and Human Anatomy, Institute of Pediatric Regenerative Medicine, University of California Davis School of Medicine, Shriners Hospital For Children Northern California

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Abstract

Myc and N-Myc have widespread impacts on the chromatin state within cells, both in a gene-specific and genome-wide manner. Our laboratory uses functional genomic methods including chromatin immunoprecipitation (ChIP), ChIP-chip, and, more recently, ChIP-seq to analyze the binding and genomic location of Myc. In this chapter, we describe an effective ChIP protocol using specific validated antibodies to Myc and N-Myc. We discuss the application of this protocol to several types of stem and cancer cells, with a focus on aspects of sample preparation prior to library preparation that are critical for successful Myc ChIP assays. Key variables are discussed and include the starting quantity of cells or tissue, lysis and sonication conditions, the quantity and quality of antibody used, and the identification of reliable target genes for ChIP validation.

Key words

ChIP-seq Chromatin immunoprecipitation Myc N-Myc Epigenetics Histone modifications