A multidimensional platform for the purification of non-coding RNA species

Yok Hian Chionh, Chia Hua Ho, Dumnoensun Pruksakorn, I. Ramesh Babu, Chee Sheng Ng, Fabian Hia, Megan E. McBee, Dan Su, Yan Ling Joy Pang, Chen Gu, Hongping Dong, Erin G. Prestwich, Pei Yong Shi, Peter Rainer Preiser, Sylvie Alonso, Peter C. Dedon

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22 Scopus citations

Abstract

A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.

Original languageEnglish (US)
Pages (from-to)e168
JournalNucleic acids research
Volume41
Issue number17
DOIs
StatePublished - Sep 1 2013
Externally publishedYes

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ASJC Scopus subject areas

  • Genetics

Cite this

Chionh, Y. H., Ho, C. H., Pruksakorn, D., Ramesh Babu, I., Ng, C. S., Hia, F., McBee, M. E., Su, D., Pang, Y. L. J., Gu, C., Dong, H., Prestwich, E. G., Shi, P. Y., Preiser, P. R., Alonso, S., & Dedon, P. C. (2013). A multidimensional platform for the purification of non-coding RNA species. Nucleic acids research, 41(17), e168. https://doi.org/10.1093/nar/gkt668