RNAase-mediated protein footprint sequencing to reveal protein binding sites on transcriptome-wide scale

The Gregory Lab has developed a high-throughput, ribonuclease-mediated protein sequencing approach termed Protein Interaction Profile sequencing (PIP-seq). PIP-seq identifies RNA-protein interaction sites within both unprocessed and mature RNAs in a predominantly unbiased manner and on a transcriptome-wide scale. Multiple cross-linking techniques capture both direct and indirect RNA-protein interactions. 

PIP-seq has revealed that both single- and double-stranded RNases uncover distinct but overlapping sets of RNA-protein interaction sites. This is a reproducible sequencing approach capable of revealing known and unknown RNA-protein interactions. The researchers have applied PIP-seq to both the human and plant transcriptomes, identified RNA-binding protein motifs, and uncovered a significant enrichment for disease-associated polymorphisms within RNA-binding protein interaction sites. 

• Apply with cell culture, tissue, or whole organisms
• Captures large multiprotein complexes of RNA architecture
• Independent of incorporation of unnatural nucleotides or UV cross-linking methods

• Uncover transcriptome regulatory processes by global assessment of RNA-protein interactions
• Gene expression studies to identify single nucleotide polymorphisms associated with disease variants