Alexander S Tanas1,2, Marina E Borisova3, Ekaterina B Kuznetsova1,4, Viktoria V Rudenko1, Kristina O Karandasheva1,2, Marina V Nemtsova1,5, Vera L Izhevskaya1, Olga A Simonova1, Sergey S Larin6,7, Dmitry V Zaletaev1,4, Vladimir V Strelnikov1,2. 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.
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.
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.
Entities:
Keywords:
DNA methylation; degraded DNA samples; reduced representation bisulfite sequencing
Authors: Daniel E Martin-Herranz; António J M Ribeiro; Felix Krueger; Janet M Thornton; Wolf Reik; Thomas M Stubbs Journal: Nucleic Acids Res Date: 2017-11-16 Impact factor: 16.971
Authors: Vladimir V Strelnikov; Ekaterina B Kuznetsova; Alexander S Tanas; Viktoria V Rudenko; Alexey I Kalinkin; Elena V Poddubskaya; Tatiana V Kekeeva; Galina G Chesnokova; Ivan D Trotsenko; Sergey S Larin; Sergey I Kutsev; Dmitry V Zaletaev; Marina V Nemtsova; Olga A Simonova Journal: Sci Rep Date: 2021-01-26 Impact factor: 4.379
Authors: Olga A Simonova; Ekaterina B Kuznetsova; Alexander S Tanas; Viktoria V Rudenko; Elena V Poddubskaya; Tatiana V Kekeeva; Ivan D Trotsenko; Sergey S Larin; Sergei I Kutsev; Dmitry V Zaletaev; Marina V Nemtsova; Vladimir V Strelnikov Journal: Biomedicines Date: 2020-05-10