Available Technologies

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High throughput identification of transcriptome wide RNA-protein interactions

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

Technology Overview: 

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

Stage of Development: 

In vitro testing 

Intellectual Property: 

Reference Media: 

Desired Partnerships: 

  • License
  • Co-development

Patent Information:


Docket # Y6152

For Information, Contact:

Cortney Cavanaugh Licensing Officer, SEAS/SAS Licensing Group
University of Pennsylvania