ChIPping away at gene regulation

Abstract

The coordinated regulation of gene expression in higher eukaryotes is complex and poorly understood. Recent technological advances have allowed the first insights into these networks on a genome-wide scale. These investigations have identified transcription factor target sites in the genome and successfully predicted cooperative interactions with other factors. However, a detailed understanding of the processes that coordinate gene expression remains elusive. Here, we highlight the advances that have been made using current methods, and the need for new technologies to address the gaps in our knowledge and to map these complex pathways further.

Figure 1

Overview of chromatin immunoprecipitation strategies. (A) Summary of chromatin immunoprecipitation (ChIP) methodology. (B) Formaldehyde crosslinking chemistry. (C) Example of gel-electrophoresis analysis of chromatin before and after sonication. (D) Summary of DNA-fragment enrichment by ChIP, showing the large number of low-abundance non-specific DNA fragments and high-abundance specific ChIP-enriched DNA fragments. (E) Analysis of androgen receptor (AR) ChIP enrichment by real-time quantitative PCR for the Kallikrein (KLK)2 and KLK3 promoters. Values shown are relative to input material and β-actin control PCR. (F) Example of AR ChIP-chip data showing enrichment of the KLK2 promoter region in the androgen (+R1881) versus control (+Vehicle) treated conditions. Genomic positions are shown above ChIP-chip data ‘tracks' from the androgen (+R1881) and control (+Vehicle) conditions. The level of enrichment is shown by the height of the vertical bars. The location of the gene encoding KLK2 relative to the array probes is shown on the bottom line by a rectangle and the arrow indicates the direction of transcription.

Charles E. Massie

Ian G. Mills