Title

A Comparative Analysis of Shotgun-Cloning and Tagged-Random Amplification-Cloning of Chromatin Immunoprecipitation-Isolated Genome Fragments

Document Type

Journal Article

Publisher

Academic Press Inc Elsevier Science

Faculty

Computing, Health and Science

School

Exercise, Biomedical and Health Science

RAS ID

5248

Comments

This article was originally published as: White, R. B., & Ziman, M. R. (2006). A comparative analysis of shotgun-cloning and tagged-random amplification-cloning of chromatin immunoprecipitation-isolated genome fragments. Biochemical and Biophysical Research Communications, 346(2), 479-483. Original article available here

Abstract

The cloning of transcription factor antibody-immunoprecipitated genomic fragments from chromatin immunoprecipitation (ChIP) experiments is a technically challenging procedure, especially when the input genomic DNA is isolated from whole tissues (in vivo) rather than cultured cells. Here we adapt a technique known as Tagged-Random PCR (T-PCR) to amplify ChIP-immunoprecipitated DNA from mouse embryonic tissue prior to cloning. Importantly, we then compare this technique with tandem shotgun-cloning experiments in terms of its capacity to identify target genes. We find that T-PCR dramatically increases the efficiency of cloning ChIP fragments without distortion of the relative location of cloned fragments to putative target genes. Thus, T-PCR is a simple procedure which greatly enhances the efficiency of cloning tissue-derived ChIP fragments.

DOI

10.1016/j.bbrc.2006.05.145

 

Link to publisher version (DOI)

10.1016/j.bbrc.2006.05.145