Single Molecule, Real-Time Sequencing for base modification detection in eukaryotic organisms: Coprinopsis cinerea.

Author(s): Luong, Khai and Clark, Tyson A. and Boitano, Matthew and Song, Yi and Turner, Stephen W. and Korlach, Jonas and Chavez, Lukas and Pukkila, Patricia J. and Huang, Yun and Hench, Virginia K. and Pastor, William and Iyer, Lakshminarayan M. and Agarwal, Suneet and Iyer, L. Aravind and Rao, Anjana

Single Molecule Real-Time (SMRT) DNA sequencing provides a wealth of kinetic information beyond the extraction of the primary DNA sequence, and this kinetic information can provide for the direct detection of modified bases present in genomic DNA. This method has been demonstrated for base modification detection in prokaryotes at base and strand resolutions. In eukaryotes, the common base modifications known to exist are the cytosine variants including methyl, hydroxymethyl, formyl and carboxyl forms. Each of these modifications exhibits different signatures in SMRT kinetic data, allowing for unprecedented possibilities to differentiate between them in direct sequencing data. We present early results of directly sequencing different base modifications in eukaryotic genomic DNA using this method.

Organization: PacBio
Year: 2013

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