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Open Access Highly Accessed Research article

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

Katherine C Goldfarb1 and Thomas R Cech12*

Author Affiliations

1 Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, CO, USA

2 Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA

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BMC Molecular Biology 2013, 14:23  doi:10.1186/1471-2199-14-23

Published: 21 September 2013

Abstract

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.

Keywords:
RNase MRP RNA; 3′ RACE deep sequencing; Oligo(U); Oligo(A); Telomerase RNA