DNA microarray technologies for measuring protein–DNA interactions

• Published in: Current opinion in biotechnology Vol. 17; no. 4; pp. 422 - 430
• Main Author: Bulyk, Martha L
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.08.2006
• Subjects: Animals; Chromatin Immunoprecipitation - methods; Cross-Linking Reagents - chemistry; DNA - analysis; DNA - chemistry; DNA - metabolism; DNA-Binding Proteins - analysis; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Humans; Oligonucleotide Array Sequence Analysis - methods; Protein Binding
• ISSN: 0958-1669; 1879-0429
• DOI: 10.1016/j.copbio.2006.06.015

DNA-binding proteins have key roles in many cellular processes, including transcriptional regulation and replication. Microarray-based technologies permit the high-throughput identification of binding sites and enable the functional roles of these binding proteins to be elucidated. In particular, microarray readout either of chromatin immunoprecipitated DNA-bound proteins (ChIP-chip) or of DNA adenine methyltransferase fusion proteins (DamID) enables the identification of in vivo genomic target sites of proteins. A complementary approach to analyse the in vitro binding of proteins directly to double-stranded DNA microarrays (protein binding microarrays; PBMs), permits rapid characterization of their DNA binding site sequence specificities. Recent advances in DNA microarray synthesis technologies have facilitated the definition of DNA-binding sites at much higher resolution and coverage, and advances in these and emerging technologies will further increase the efficiencies of these exciting new approaches.