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Epigenomics Volume 9, 2017 - Issue 6
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Research Article

Rapid and Affordable Genome-Wide Bisulfite DNA Sequencing by XmaI-Reduced Representation Bisulfite Sequencing

Alexander S Tanas1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, Russia;2 Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, RussiaView further author information
,
Marina E Borisova3 Chromatin Biology and Proteomics Group, Institute of Molecular Biology, Mainz, GermanyView further author information
,
Ekaterina B Kuznetsova1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, Russia;4 Human Molecular Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, RussiaView further author information
,
Viktoria V Rudenko1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, RussiaView further author information
,
Kristina O Karandasheva1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, Russia;2 Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, RussiaView further author information
,
Marina V Nemtsova1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, Russia;5 Medical Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, RussiaView further author information
,
Vera L Izhevskaya1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, RussiaView further author information
,
Olga A Simonova1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, RussiaView further author information
,
Sergey S Larin6 Molecular Immunology Laboratory, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology & Immunology,Moscow, Russia;7 Gene Therapy Laboratory, Institute of Gene Biology, Moscow, RussiaView further author information
,
Dmitry V Zaletaev1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, Russia;4 Human Molecular Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, RussiaView further author information
&
Vladimir V Strelnikov1 Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow115478, Russia;2 Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, RussiaCorrespondence[email protected]
View further author information
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Pages 833-847 | Received 25 Feb 2017, Accepted 30 Mar 2017, Published online: 10 May 2017
 
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Abstract

Aim: To develop a reduced representation bisulfite sequencing (RRBS) approach for rapid and affordable genome-wide DNA methylation analysis. Methods: We have selected restriction endonuclease XmaI to produce RRBS library fragments. After digestion and partial fill-in DNA fragments were ligated to barcoded adapters, bisulfite converted, size-selected, and sequenced on the Ion Torrent Personal Genome Machine. XmaI-RRBS results were compared with the previously published RRBS data. Results: We have developed an XmaI-RRBS method for rapid and affordable genome-wide DNA methylation analysis, with library preparation taking only 4 days and sequencing possible within 4 h. We have also addressed several challenges in order to further improve the RRBS technology. XmaI-RRBS may be performed on degraded DNA samples and is compatible with the bench-top next-generation sequencing machines.

Financial & competing interests disclosure

This research was supported by the Russian Foundation for Basic Research (grant 14–04–01606 A), VV Rudenko is a Fellow of the Russian Federation Presidential Young Scientist Fellowship. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

This research was supported by the Russian Foundation for Basic Research (grant 14–04–01606 A), VV Rudenko is a Fellow of the Russian Federation Presidential Young Scientist Fellowship. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.

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