PET diagram

Diagram of the PET sequencing strategy. PETs can be created via cloning based (left) and non-cloning based (right) techniques. Figure 1, Fullwood M J et al. Genome Res. 2009;19:521-532

Paired-end tags (PET), also known as paired-end ditags, are short sequences found at the 5' and 3' ends of a fragment of DNA.  Depending on the length of the PET sequences, each pair should, hypothetically, appear only once in a genome.  This is the basis for the PET strategy of DNA sequencing, which can be used to determine the sequence of DNA fragment of interest.  Once the 5' and 3' ends of that fragment are identified, they can be mapped on the genome of interest.  The resulting sequence of DNA between the two tags is the sequence of the original DNA fragment (1 , 2 ).

PET Sequencing ModificationsEdit

PET sequencing is being used in several different and creative ways.  Transcripts of whole genomes are being identified by using the cDNA of all expressed genes in a particular sample, a technique called RNA-PET (3 ).  Modified chromatin immunoprecipitation assays (ChIP-PET) and other chromatin interaction assays (ChIA-PET) have been developed to determine the sequences of DNA that interact with various transcription factors (1 , 4 ).

PET table

Table of PET sequencing applications. Box 1, Fullwood M J et al. Genome Res. 2009;19:521-532


1. Fullwood, MJ, et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009

2. Patrick, NG, et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods. 2005

3. Ruan, X and Ruan, Y. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012

4. Fullwood, MJ, et al. An Oestrogen Receptor alpha-bound Human Chromatin Interactome. Nature. 2009