Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published May 2014 | Supplemental Material + Published
Journal Article Open

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

Abstract

Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: Its location and function have not been established. We have used a novel and highly sensitive genomewide cytosine methylation assay to detect and map genome methylation in stage 5 Drosophila embryos. The methylation we observe with this method is highly localized and strand asymmetrical, limited to regions covering ∼1% of the genome, dynamic in early embryogenesis, and concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. Gene body methylation is associated with lower expression, and many genes containing methylated regions have developmental or transcriptional functions. The only known DNA methyltransferase in Drosophila is the DNMT2 homolog MT2, but lines deficient for MT2 retain genomic methylation, implying the presence of a novel methyltransferase. The association of methylation with a lower expression of specific developmental genes at stage 5 raises the possibility that it participates in controlling gene expression during the maternal-zygotic transition.

Additional Information

© 2014 Takayama et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. Received June 21, 2013. Accepted February 18, 2014. We thank Mark Biggin and Xiaoyong Li for the Canton-S Drosophila melanogaster DNA; Gunther Reuter and Frank Lyko for the Mt2 mutant strains and DNA; Sarah Siegrist for fly stocks, husbandry and other resources, and technical help and discussions. This work was supported by the NIH grants HL084474 (D.B.), ES016581 (D.I.K.M.), CA115768 (D.I.K.M.). J.D. was a Scholar of the California Institute of Regenerative Medicine. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author contributions: D.I.K.M. conceived the study; J.D. designed and performed the MeDIP-bisulfite deep sequencing experiments; S.T. performed the fly husbandry, obtained unfertilized oocytes, and carried out bisulfite PCR experiments; S.J.H. constructed the bisulfite-PCR sequencing libraries; S.T., G.M., and D.B. designed and performed bioinformatic analyses; A.R. and L.P. carried out the association between methylation and gene expression; D.I.K.M. and D.B. wrote the paper. Data access: Sequencing data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE34425. Bisulfite sequencing data have been submitted to the NCBI Sequence Read Archive (SRA; http://www.ncbi.nlm.nih.gov/sra) under accession nos. SRR1191286, SRR1191445, SRR1191486, SRR1191487, SRR1191684, and SRR1191728.

Attached Files

Published - Genome_Res.-2014-Takayama-821-30.pdf

Supplemental Material - Supplemental_Material.pdf

Supplemental Material - Supplemental_primers.xls

Files

Genome_Res.-2014-Takayama-821-30.pdf
Files (9.3 MB)
Name Size Download all
md5:c7dbb392945925c7dc657ba4a37c798d
1.8 MB Preview Download
md5:16cbf4046bd195433ae9b6b39e308359
31.7 kB Download
md5:f82adf8b3b6a385560c3651ae3f41bee
7.4 MB Preview Download

Additional details

Created:
August 20, 2023
Modified:
October 24, 2023