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Transcriptome-wide RNA-protein interactions

Description:

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

 

Inventor

Brian Gregory, Assistant Professor of Biology 

 

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. 

 

Advantages

•       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

 

Applications

•       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

USSN 9,097,708

 

Reference Media

Penn News highlight on Gregory lab.

Gosai SJ et al.  Molecular Cell, 2015.  57, p. 376-388.

Silverman IM et al.  Methods, 2015, 71:76-85.

Silverman IM et al.  Genome Biology, 2014, 15(R3)

 

Desired partnerships

•  License

Co-development

 

 

Download PDF

 

Docket #  Y6152 


Patent Information:
For Information, Contact:
Joshua Jeanson
Associate Director, SEAS/SAS Licensing Group
University of Pennsylvania
jeanson@upenn.edu
Inventors:
Brian Gregory
Keywords: