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

Research output: Contribution to journalArticle

21 Citations (Scopus)

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)
JournalNucleic Acids Research
Volume41
Issue number17
DOIs
StatePublished - Sep 2013
Externally publishedYes

Fingerprint

Untranslated RNA
Ribonucleosides
Viral Genome
RNA
Long Noncoding RNA
Plasmodium
Reticulocytes
Viral RNA
Epigenomics
Bacteria

ASJC Scopus subject areas

  • Genetics

Cite this

Chionh, Y. H., Ho, C. H., Pruksakorn, D., Ramesh Babu, I., Ng, C. S., Hia, F., ... Dedon, P. C. (2013). A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Research, 41(17). https://doi.org/10.1093/nar/gkt668

A multidimensional platform for the purification of non-coding RNA species. / Chionh, Yok Hian; Ho, Chia Hua; Pruksakorn, Dumnoensun; Ramesh Babu, I.; Ng, Chee Sheng; Hia, Fabian; McBee, Megan E.; Su, Dan; Pang, Yan Ling Joy; Gu, Chen; Dong, Hongping; Prestwich, Erin G.; Shi, Pei-Yong; Preiser, Peter Rainer; Alonso, Sylvie; Dedon, Peter C.

In: Nucleic Acids Research, Vol. 41, No. 17, 09.2013.

Research output: Contribution to journalArticle

Chionh, YH, Ho, CH, Pruksakorn, D, Ramesh Babu, I, Ng, CS, Hia, F, McBee, ME, Su, D, Pang, YLJ, Gu, C, Dong, H, Prestwich, EG, Shi, P-Y, Preiser, PR, Alonso, S & Dedon, PC 2013, 'A multidimensional platform for the purification of non-coding RNA species', Nucleic Acids Research, vol. 41, no. 17. https://doi.org/10.1093/nar/gkt668
Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F et al. A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Research. 2013 Sep;41(17). https://doi.org/10.1093/nar/gkt668
Chionh, Yok Hian ; Ho, Chia Hua ; Pruksakorn, Dumnoensun ; Ramesh Babu, I. ; Ng, Chee Sheng ; Hia, Fabian ; McBee, Megan E. ; Su, Dan ; Pang, Yan Ling Joy ; Gu, Chen ; Dong, Hongping ; Prestwich, Erin G. ; Shi, Pei-Yong ; Preiser, Peter Rainer ; Alonso, Sylvie ; Dedon, Peter C. / A multidimensional platform for the purification of non-coding RNA species. In: Nucleic Acids Research. 2013 ; Vol. 41, No. 17.
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