3′ terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing

Background: Post-transcriptional 3' end processing is a key component of RNA regulation. The abundant and essential RNA subunit of RNase MRP has been proposed to function in three distinct cellular compartments and therefore may utilize this mode of regulation. Here we employ 3' RACE coupled with high-throughput sequencing to characterize the 3' terminal sequences of human MRP RNA and other noncoding RNAs that form RNP complexes. Results: The 3' terminal sequence of MRP RNA from HEK293T cells has a distinctive distribution of genomically encoded termini ( including an assortment of U residues) with a portion of these selectively tagged by oligo( A) tails. This profile contrasts with the relatively homogenous 3' terminus of an in vitro transcribed MRP RNA control and the differing 3' terminal profiles of U3 snoRNA, RNase P RNA, and telomerase RNA (hTR). Conclusions: 3' RACE coupled with deep sequencing provides a valuable framework for the functional characterization of 3' terminal sequences of noncoding RNAs.