Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
作者： Gordon R. McInroy , Dario Beraldi , Eun-Ang Raiber , Katarzyna Modrzynska , Pieter van Delft
DOI: 10.1371/JOURNAL.PONE.0152322
关键词: 5-Methylcytosine 、 DNA methylation 、 Context (language use) 、 Bisulfite 、 Genetics 、 Genomic library 、 Bisulfite sequencing 、 Genomics 、 Methylated DNA immunoprecipitation 、 Biology
摘要: Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in genome at single base resolution. However, associated chemical treatment causes strand scission, which depletes number sequenceable DNA fragments library and thus necessitates PCR amplification. The AT-rich nature generated from bisulfite adversely affects this amplification, resulting introduction major biases that can confound methylation analysis. Here, we report method enables more accurate analysis, by rebuilding bisulfite-damaged components library. This recovery after (ReBuilT) approach PCR-free low nanogram quantities genomic DNA. We apply ReBuilT first whole methylome analysis highly Plasmodium berghei. Side-by-side comparison to commercial protocol involving amplification demonstrates substantial improvement uniformity coverage reduction sequence context bias. Our will be widely applicable quantitative even technically challenging genomes, where limited sample available.
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sci-hub.se 参考文章(33)
Kenneth Eyring, Ivana V. Yang, Brent S. Pedersen, David A. Schwartz, Subhajyoti De, Fast and accurate alignment of long bisulfite-seq reads arXiv: Genomics. ,(2014)
Archna P. Gupta, Wai Hoe Chin, Lei Zhu, Sachel Mok, Yen-Hoon Luah, Eng-How Lim, Zbynek Bozdech, Dynamic Epigenetic Regulation of Gene Expression during the Life Cycle of Malaria Parasite Plasmodium falciparum PLoS Pathogens. ,vol. 9, pp. e1003170- ,(2013) , 10.1371/JOURNAL.PPAT.1003170
Robert K. Tran, Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, Steven Henikoff, DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. ,vol. 15, pp. 154- 159 ,(2005) , 10.1016/J.CUB.2005.01.008
M. Frommer, L. E. McDonald, D. S. Millar, C. M. Collis, F. Watt, G. W. Grigg, P. L. Molloy, C. L. Paul, A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 89, pp. 1827- 1831 ,(1992) , 10.1073/PNAS.89.5.1827
N. A. Malmquist, T. A. Moss, S. Mecheri, A. Scherf, M. J. Fuchter, Small-molecule histone methyltransferase inhibitors display rapid antimalarial activity against all blood stage forms in Plasmodium falciparum. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 109, pp. 16708- 16713 ,(2012) , 10.1073/PNAS.1205414109
Lexiang Ji, Takahiko Sasaki, Xiaoxiao Sun, Ping Ma, Zachary A. Lewis, Robert J. Schmitz, Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Frontiers in Genetics. ,vol. 5, pp. 341- 341 ,(2014) , 10.3389/FGENE.2014.00341
H. Sano, R. Sager, Tissue specificity and clustering of methylated cystosines in bovine satellite I DNA. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 79, pp. 3584- 3588 ,(1982) , 10.1073/PNAS.79.11.3584
Marcel Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet.journal. ,vol. 17, pp. 10- 12 ,(2011) , 10.14806/EJ.17.1.200
Kazuo Tanaka, Akimitsu Okamoto, Degradation of DNA by bisulfite treatment. Bioorganic & Medicinal Chemistry Letters. ,vol. 17, pp. 1912- 1915 ,(2007) , 10.1016/J.BMCL.2007.01.040
M. J. Booth, M. R. Branco, G. Ficz, D. Oxley, F. Krueger, W. Reik, S. Balasubramanian, Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution Science. ,vol. 336, pp. 934- 937 ,(2012) , 10.1126/SCIENCE.1220671