Development of chimeric read amplification into a robust method for profiling targets of specific microRNAs and global amplification of all microRNA:mRNA pairings transcriptome-wide

PROJECT SUMMARYPost-transcriptional regulation by microRNAs is fundamental for cellular homeostasis. MicroRNAs are small non-coding RNAs that fine tune gene expression by base pairing to complementary sequences in target messenger RNA (mRNA) molecules. A single microRNA can have multiple targets allowing for coordinated regulation of mRNA networks. The importance of microRNA regulation is evidenced not only by their evolutionary conservation but also by the involvement of microRNAs in nearly every biological process including proliferation, inflammation, development, and metabolism. Misregulation of individual microRNAs or global microRNA processing has important consequences for development, physiology, and disease. Aberrant microRNA expression has been linked to many diseases ranging from cancer to cardiac failure, and microRNAs have become attractive targets and tools for therapeutic approaches. Precise target identification of microRNAs is essential to understand their functional role. Current methods to identify microRNA targets are limited, as they have high false-positive rates, are unable to definitively distinguish direct from indirect microRNA-target interactions or are unable to profile low-abundance microRNAs. To this end we have applied our previously developed enhanced crosslinking and immunoprecipitation (eCLIP) technology to develop a specialized alternative, chimeric-eCLIP, to unambiguously identify microRNA targets in a transcriptome-wide manner. Chimeric-eCLIP is based on AGO2 eCLIP and includes a ligation step where microRNA and mRNA fragments are ligated to each other forming chimeric RNA molecules that can then be sequenced. Direct targets of individual microRNAs are easily identifiable from chimeric-eCLIP data using microRNA:mRNA chimeric reads. The work proposed here will expand the previously developed chimeric-eCLIP technology to include microRNA- and gene-specific read enrichment methods, and a user-friendly analysis package resulting in a robust and versatile chimeric-eCLIP kit for wide-spread use by academic and biotechnology industries, as outlined in the following aims:1. Expand direct profiling of microRNA targets with probe-based chimeric-eCLIP2. Refine software tools for analysis of chimeric-eCLIP data to strengthen key customer-facing features3. Conduct expanded beta testing and finalize commercialization of the all-inclusive chimeric-eCLIP kit Eclipse Bio is an ideal candidate to perform the aims described above due to our expertise in genomics, RNA processing, and computational biology. The above aims will enable robust microRNA target mapping to be performed using a standard method by all biomedical researchers and will allow for rigorous validation of microRNA specificity. The ability to properly assess therapeutic microRNA-like molecules will provide significant benefit to researchers studying microRNA regulation and companies developing RNA therapies.