The Current and Future PETs

Yijun Ruan, PhD, Genome Institute of Singapore

Modern biological research is largely and will be continuously relying on our ability to sequence and characterize our genome and all other genomes. Rapid developments of new sequencing methods and strategies are evident in recent years. Our approach of making contribution is to improve tag-based sequencing strategy. In this effort, we first developed the paired-end ditagging (PET) strategy and devised the Gene Identification Signature (GIS-PET) analysis to precisely demarcate the boundaries of full-length transcripts (Ng et al. 2005 Nature Methods 2:105-111). Immediately afterward, we invented the ChIP-PET analysis (chromatin immuno-precipitation coupled with paired-end ditagging) for highly accurate, robust and unbiased genome-wide identification of transcription factor binding sites (Wei et al. 2006 Cell 124:207-219; Loh et al. 2006 Nature Genetics). These PET-based genomic analyses are further enhanced by incorporating the ‘short read’ but ‘high multiplex’ 454 pyrosequencing for multiplex sequencing of paired-end ditags (MS-PET) (Ng et al. 2006 Nucleic Acid Research 34:e84). To push the envelope, we are generating PETs derived from large genomic DNA fragments over 10kb to facilitate genome assemble and scan (GAS-PET), expand PET tags with a few hundred nucleotide sequences (Long PET) for better mapping alignment, and creating PETs reflecting chromatin interactions (CIA-PET). Currently, we are using the PET strategy to analyze genome rearrangement, identify fusion transcripts, map out transcription regulatory circuits, and explore the 3-dementional territories of chromosome folding and chromatin interactions.