Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.
Michael J. Booth,Tobias William Barr Ost,Dario Beraldi,Neil M. Bell,Miguel R. Branco,Miguel R. Branco,Wolf Reik,Wolf Reik,Wolf Reik,Shankar Balasubramanian +9 more
TLDR
Xu et al. as discussed by the authors used bisulfite sequencing to locate 5mC and 5hmC marks at single-base resolution in genomic DNA, which can uncover the function of and interplay between the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcyte (5hmC), new techniques and advances in current technology are needed.Abstract:
To uncover the function of and interplay between the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), new techniques and advances in current technology are needed. To this end, we have developed oxidative bisulfite sequencing (oxBS-seq), which can quantitatively locate 5mC and 5hmC marks at single-base resolution in genomic DNA. In bisulfite sequencing (BS-seq), both 5mC and 5hmC are read as cytosines and thus cannot be discriminated; however, in oxBS-seq, specific oxidation of 5hmC to 5-formylcytosine (5fC) and conversion of the newly formed 5fC to uracil (under bisulfite conditions) means that 5hmC can be discriminated from 5mC. A positive readout of actual 5mC is gained from a single oxBS-seq run, and 5hmC levels are inferred by comparison with a BS-seq run. Here we describe an optimized second-generation protocol that can be completed in 2 d.read more
Citations
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Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression
Luisa Cimmino,Igor Dolgalev,Yubao Wang,Akihide Yoshimi,Gaëlle H. Martin,Jingjing Wang,Victor Ng,Bo Xia,Matthew T. Witkowski,Marisa Mitchell-Flack,Isabella Grillo,Sofia Bakogianni,Delphine Ndiaye-Lobry,Miguel Torres Martin,Maria Guillamot,Robert S. Banh,Mingjiang Xu,Maria E. Figueroa,Ross A. Dickins,Omar Abdel-Wahab,Christopher Y. Park,Aristotelis Tsirigos,Benjamin G. Neel,Iannis Aifantis +23 more
TL;DR: TET-mediated DNA oxidation induced by vitamin C treatment in leukemia cells enhances their sensitivity to PARP inhibition and could provide a safe and effective combination strategy to selectively target TET deficiency in cancer.
Journal ArticleDOI
Mapping DNA methylation with high-throughput nanopore sequencing
Arthur C Rand,Miten Jain,Jordan M. Eizenga,Audrey Musselman-Brown,Hugh E. Olsen,Mark Akeson,Benedict Paten +6 more
TL;DR: The results show that the model is sensitive enough to detect changes in genomic DNA methylation levels as a function of growth phase in Escherichia coli.
Journal ArticleDOI
Quantitative comparison of DNA methylation assays for biomarker development and clinical applications
Christoph Bock,Florian Halbritter,Francisco J. Carmona,Sascha Tierling,Paul Datlinger,Yassen Assenov,María Berdasco,Anke K. Bergmann,Keith Booher,Florance Busato,Mihaela Campan,Christina Dahl,Christina M. Dahmcke,Dinh Diep,Agustín F. Fernández,Clarissa Gerhäuser,Andrea Haake,Katharina Heilmann,Thomas Holcomb,Dianna Hussmann,Mitsuteru Ito,Ruth Kläver,Martin Kreutz,Marta Kulis,Virginia Lopez,Shalima S. Nair,Dirk S. Paul,Nongluk Plongthongkum,Wenija Qu,Ana C. Queirós,Frank Reinicke,Guido Sauter,Thorsten Schlomm,Aaron L. Statham,Clare Stirzaker,Ruslan Strogantsev,Rocío G. Urdinguio,Kimberly Walter,Dieter Weichenhan,Daniel J. Weisenberger,Stephan Beck,Susan J. Clark,Manel Esteller,Anne C. Ferguson-Smith,Mario F. Fraga,Per Guldberg,Lise Lotte Hansen,Peter W. Laird,José I. Martín-Subero,Anders O. H. Nygren,Ralf Peist,Christoph Plass,David S. Shames,Reiner Siebert,Xueguang Sun,Jörg Tost,Jörn Walter,Kun Zhan +57 more
TL;DR: The results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use are described, with amplicon bisulfite sequencing and bisulfITE pyrosequencing showing the best all-round performance.
Journal ArticleDOI
Profiling genome-wide DNA methylation.
TL;DR: This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples, and provides researchers useful guidance for the selection of a profiling method suited to specific research questions.
Journal ArticleDOI
Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis
Ruili Yang,Ruili Yang,Ruili Yang,Cunye Qu,Yu Zhou,Joanne E. Konkel,Shihong Shi,Yi Liu,Chider Chen,Chider Chen,Shiyu Liu,Dawei Liu,Yi-Bu Chen,Ebrahim Zandi,Wanjun Chen,Yanheng Zhou,Songtao Shi,Songtao Shi +17 more
TL;DR: Hydrogen sulfide promotes Tet1 and Tet2 expression, which are recruited to Foxp3 by TGF-β and IL-2 signaling to maintain Foxp 3 demethylation and Treg-cell-associated immune homeostasis.
References
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Journal ArticleDOI
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Mamta Tahiliani,Kian Peng Koh,Yinghua Shen,William A. Pastor,Hozefa S. Bandukwala,Yevgeny Brudno,Suneet Agarwal,Lakshminarayan M. Iyer,David R. Liu,L. Aravind,Anjana Rao +10 more
TL;DR: It is shown here that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro.
Journal ArticleDOI
Functions of DNA methylation: islands, start sites, gene bodies and beyond
TL;DR: Improved genome-scale mapping of methylation allows us to evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences.
Journal ArticleDOI
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Felix Krueger,Simon Andrews +1 more
TL;DR: Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed.
Journal ArticleDOI
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
Marianne Frommer,Louise E. McDonald,Douglas Spencer Millar,Christina M. Collis,Fujiko Watt,Geoffrey W. Grigg,Peter L. Molloy,Cheryl L. Paul +7 more
TL;DR: A genomic sequencing method is reported that provides positive identification of 5-methylcytosine residues and yields strand-specific sequences of individual molecules in genomic DNA, which suggests that the high methylation level of single-copy sequences in sperm may be locally modulated by binding of protein factors in germ-line cells.
Journal ArticleDOI
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
Shinsuke Ito,Li Shen,Qing Dai,Susan C. Wu,Leonard B. Collins,James A. Swenberg,Chuan He,Yi Zhang +7 more
TL;DR: This study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation, and identifies two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins.