Transcriptome Subtractive Hybridization and its Reliability Validated by an E. coli Model  

Yijing Ma , Zhiping Hong , Qin Wu , Xinling Yao
School of Life Science, Ningxia University, Yinchuan, 750021, P.R., China
School of Life Science, Ningxia University
School of Life Science, Ningxia University
School of Life Science, Ningxia University
Author    Correspondence author
Bioscience Methods, 2011, Vol. 2, No. 6   doi: 10.5376/bm.2011.02.0006
Received: 22 Nov., 2011    Accepted: 28 Dec., 2011    Published: 30 Dec., 2011
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This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Ma et al., 2011, Transcriptome Subtractive Hybridization and its Reliability Validated by an E. coli Model, Bioscience Methods, Vol.2 No.6 (doi:10.5376/bm.2011.02.0006)


In the application of subtractive hybridization methods to identify differentially expressed genes, It is no doubt that would increase the efficiency of subtractive hybridization method by simplifying experimental procedures and reducing experimental time-consuming.

In this study, we reported a modified method, called transcriptome subtractive hybridization (abbr. TSH). In order to cover different types of RNA as much as possible and reduce the experimental procedure, TSH in the protocol neither uses restriction endonuclease for adopter ligation, nor use oligo-d (T) for the reverse transcription reaction. Instead, tester RNA directly hybridizes with driver single strand cDNA, then the hybrid of RNA/cDNA was digested by HaeIII, residual targeting tester RNA was enriched by reverse transcription PCR amplification. As a result, the experimental protocol was simplified to reduce experimental time-consuming.

To validate use reliability of the TSH, TSH was employed to identify cell-specific expressing ESTs in both E. coli JM109 with and without a recombinant plasmid. The results showed that the non-target RNA finally eliminated through direct hybridization and digestion of RNA/cDNA hybrids. Six reference genes within the recombinant plasmid were detected as expected in the tester library constructed from the JM109 RNA with the recombinant plasmid.

Obviously, the verified results showed that the TSH, a modified protocol, would be a reliable and effective method, which can be applied to identify differential gene expression between the two cell types.

Transcriptome subtractive hybridization; Differential expression; Reliability; An E. coli model
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