Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing

Alexander S Tanas; Marina E Borisova; Ekaterina B Kuznetsova; Viktoria V Rudenko; Kristina O Karandasheva; Marina V Nemtsova; Vera L Izhevskaya; Olga A Simonova; Sergey S Larin; Dmitry V Zaletaev; Vladimir V Strelnikov

doi:10.2217/epi-2017-0031

Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing

Epigenomics. 2017 Jun;9(6):833-847. doi: 10.2217/epi-2017-0031. Epub 2017 May 10.

Authors

Alexander S Tanas^{1

2}, Marina E Borisova³, Ekaterina B Kuznetsova^{1

4}, Viktoria V Rudenko¹, Kristina O Karandasheva^{1

2}, Marina V Nemtsova^{1

5}, Vera L Izhevskaya¹, Olga A Simonova¹, Sergey S Larin^{6

7}, Dmitry V Zaletaev^{1

4}, Vladimir V Strelnikov^{1

2}

Affiliations

¹ Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia.
² Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, Russia.
³ Chromatin Biology and Proteomics Group, Institute of Molecular Biology, Mainz, Germany.
⁴ Human Molecular Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, Russia.
⁵ Medical Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, Russia.
⁶ Molecular Immunology Laboratory, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology & Immunology, Moscow, Russia.
⁷ Gene Therapy Laboratory, Institute of Gene Biology, Moscow, Russia.

PMID: 28488887
DOI: 10.2217/epi-2017-0031

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.

Keywords: DNA methylation; degraded DNA samples; reduced representation bisulfite sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Methylation*
Deoxyribonucleases, Type II Site-Specific / chemistry
High-Throughput Nucleotide Sequencing / economics
High-Throughput Nucleotide Sequencing / methods*
High-Throughput Nucleotide Sequencing / standards
Humans
MCF-7 Cells
Whole Genome Sequencing / economics
Whole Genome Sequencing / methods*
Whole Genome Sequencing / standards

Substances

CCCGGG-specific type II deoxyribonucleases
Deoxyribonucleases, Type II Site-Specific