Abstract
Across Eukaryota, DNA modifications play an important role in regulation of gene expression. While 5-methylcytosine (5mC) has been explored in depth, other modifications such as 6-methyladenine (6 mA) have historically been overlooked, in part due to technical difficulties in collecting/analyzing these data. However, recent technological advances have enabled exploration of these marks with much greater detail and on a larger scale. In this chapter, we discuss multiple methods for identifying and analyzing both 5mC and 6 mA across fungi.
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References
Zemach A, McDaniel IE, Silva P et al (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science (New York, NY) 328:916–919
Fu Y, Luo G-Z, Chen K et al (2015) N6-Methyldeoxyadenosine marks active transcription start sites in chlamydomonas. Cell 161:879–892
Zhang G, Huang H, Liu D et al (2015) N6-methyladenine DNA modification in Drosophila. Cell 161:893–906
Greer EL, Blanco MA, Gu L et al (2015) DNA methylation on N6-adenine in C. elegans. Cell 161:868–878
Mondo SJ, Dannebaum RO, Kuo RC et al (2017) Widespread adenine N6-methylation of active genes in fungi. Nat Genet 49(6):964–968
Krueger F, Kreck B, Franke A et al (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9:145–151
Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M et al (2013) Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc 8:176–189
Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27:1571–1572
Robinson JT, Thorvaldsdóttir H, Winckler W et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26
Dominissini D, Moshitch-Moshkovitz S, Schwartz S et al (2012) Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485:201–206
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, arXiv:1303.3997 [q-bio]
Zhang Y, Liu T, Meyer CA et al (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137
Acknowledgments
The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.
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Mondo, S.J., Kuo, R.C., Singan, V.R. (2018). Fungal Epigenomics: Detection and Analysis. In: de Vries, R., Tsang, A., Grigoriev, I. (eds) Fungal Genomics. Methods in Molecular Biology, vol 1775. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7804-5_14
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DOI: https://doi.org/10.1007/978-1-4939-7804-5_14
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