Unit

UNIT 21.10 Identifying Chromosomal Targets of DNA-Binding Proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE)

  1. Jonghwan Kim,
  2. Vishwanath R. Iyer

Published Online: 1 NOV 2005

DOI: 10.1002/0471142727.mb2110s72

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Kim, J. and Iyer, V. R. 2005. Identifying Chromosomal Targets of DNA-Binding Proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE). Current Protocols in Molecular Biology. 72:21.10:21.10.1–21.10.16.

Author Information

  1. University of Texas at Austin, Austin, Texas

Publication History

  1. Published Online: 1 NOV 2005
  2. Published Print: OCT 2005

Abstract

Sequence Tag Analysis of Genomic Enrichment (STAGE) is a method for experimentally identifying the in vivo chromosomal targets of DNA-binding proteins in any sequenced genome. STAGE generates 21-bp tags derived from DNA isolated by chromatin immunoprecipitation (ChIP; unit 21.3). Concatamers of tags are cloned and sequenced to yield a STAGE library. Tags in the library represent DNA fragments that were occupied by the DNA-binding protein, and mapping these tag sequences to the genome identifies the binding loci of the DNA-binding protein in vivo. STAGE can be applied to any sequenced genome to identify targets of DNA-binding proteins without requiring extensive microarray resources.

Keywords:

  • Chromatin immunoprecipitation (ChIP);
  • DNA-protein interaction;
  • Serial analysis of gene expression (SAGE);
  • Sequence tag analysis of genomic enrichment (STAGE);
  • Tags