“Precision Mapping” – High Resolution Mapping Using ChIP-exo
Presented by: Bryce Alves Ph.D., Research Scientist at Active Motif
Abstract: Transcriptional regulation is a complex mechanism that involves changes in epigenetic modifications, transcription factors and cofactors, and chromatin structure. Loss of controlled transcription is often found in various human diseases, such as what is seen in cancer. Gaining accurate insight into the mechanisms regulating or mis-regulating gene expression is crucial to understanding a diseases’ initiation and progression. Historically, ChIP-sequencing (ChIP-seq) and ChIP-chip are the commonly utilized methods to analyze DNA/protein interactions across the genome. However, ChIP-seq and ChIP-chip methods have limited resolution when identifying a transcription factor binding site.
To overcome these limitations of ChIP-seq and ChIP-chip, the laboratory of Frank Pugh developed ChIP-exonuclease (ChIP-exo), a modified ChIP-seq approach for high resolution mapping of transcription factor binding sites genome-wide. ChIP-exo has been shown to outperform ChIP-seq by decreasing the number of reads mapping outside of peaks and increasing the spatial resolution of DNA binding protein maps to more accurately define sequences representing protein/DNA binding motifs.We have developed an optimized and streamlined Illumina-based ChIP-exo protocol capable of precisely mapping the binding sites of multiple transcription factors in the human and mouse genomes. The results generated from the AM ChIP-exo experiments have increased resolution of the TF binding site with lengths usually ranging between 45 and 80 base pairs in contrast to the historic 200 to 450bp seen with ChIP-seq. The Active Motif’s ChIP-exo assay enables researchers to obtain genome-wide protein binding profiles at near base-pair resolution in mammalian cells, further enhancing our ability to identify and understand the impact of mutations or SNPs in transcription factor binding sites.