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Estimate of "dark matter" RNA using single-molecule sequencing

Posted by pkapranov on 21 Jul 2011 at 02:04 GMT

Bravo Michael, John and Colleagues! To add to your findings we thought it important to bring everyone’s attention to a manuscript we published last year where we directly estimated the levels of “dark matter” RNAs in human cells and tissues using single-molecule sequencing of total RNA (http://www.ncbi.nlm.nih.g...). We reported the majority (up to ~2/3) of the mass of cellular RNA, after removing ribosomal and mitochondrial transcripts, corresponds to “dark matter” RNA population. This unique single molecule sequencing method for preparation of RNA does not rely on PCR amplification which can distort the cellular RNA profiles, thus differing significantly from all other RNAseq technologies. In addition, we found 100’s of very long (100’s of kbs) regions of abundant transcription in intergenic regions devoid of annotated transcripts; we termed these vlinc regions. Overall, we hope these works can finally put this long-raging debate about the complexity of the “dark matter” RNA and its relative cellular mass to rest. Our work, while not referred to by van Bakel et al and Clark et al, presents definitive information on the issues of selective expression and mass of these “dark matter” RNAs in normal and neoplastic cells.

Philipp Kapranov
Georges St. Laurent
Patrice Milos
Robert Arceci
John Thompson
Timothy Triche

Competing interests declared: I am a former employee and a consultant with Helicos BioSciences.