Diverse 5' ends of an RNA can be generated by alternative transcription start sites or through post-trancriptional modification, such as microRNA mediated RNA cleavage. These processes are increasingly being recognized as key regulators of gene activity, and identifiying the different 5' ends in a cell-type specific manner is necessary for understanding an RNA's function. However, due to technical limitations, 5' ends have generally only been mapped in RNA from whole tissues.
To address this problem, students in the Nodine group developed a novel sequencing technique and associated software to map 5' RNA ends from nanogram quantities of RNA. nanoPARE, which stands for Parallel Analysis of RNA Ends from low input RNA, integrates 5' end information with gene-body mRNA-Seq data to obtain 5' end information at single-nucleotide resolution from as little as 10 picograms of RNA, less than the amount generally found in a single cell. This method is expected to be widely applicable to researchers studying genomics, transcriptomics, and gene regulation as well as RNA biologists.
Schon MA, Kellner MJ, ..., Nodine MD (2018) NanoPARE: parallel analysis of RNA 5' ends from low-input RNA. Genome Res [epub].