Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

Hana Yi, Yong Joon Cho, Sungho Won, Jong Eun Lee, Hyung Jin Yu, Sujin Kim, Gary P. Schroth, Shujun Luo, Jongsik Chun

Research output: Contribution to journalArticlepeer-review

92 Citations (Scopus)


Next-generation sequencing has great potential for application in bacterial transcriptomics. However, unlike eukaryotes, bacteria have no clear mechanism to select mRNAs over rRNAs; therefore, rRNA removal is a critical step in sequencing-based transcriptomics. Duplex-specific nuclease (DSN) is an enzyme that, at high temperatures, degrades duplex DNA in preference to single-stranded DNA. DSN treatment has been successfully used to normalize the relative transcript abundance in mRNA-enriched cDNA libraries from eukaryotic organisms. In this study, we demonstrate the utility of this method to remove rRNA from prokaryotic total RNA. We evaluated the efficacy of DSN to remove rRNA by comparing it with the conventional subtractive hybridization (Hyb) method. Illumina deep sequencing was performed to obtain transcriptomes from Escherichia coli grown under four growth conditions. The results clearly showed that our DSN treatment was more efficient at removing rRNA than the Hyb method was, while preserving the original relative abundance of mRNA species in bacterial cells. Therefore, we propose that, for bacterial mRNA-seq experiments, DSN treatment should be preferred to Hyb-based methods.

Original languageEnglish
JournalNucleic acids research
Issue number20
Publication statusPublished - 2011 Nov
Externally publishedYes

Bibliographical note

Funding Information:
Priority Research Centers Program (grant number 2010-0094020); National Research Foundation grant (2011-0016498) through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology, Republic of Korea. Funding for open access charge: National Science Foundation.

ASJC Scopus subject areas

  • Genetics


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