Relationship between nucleosome positioning and DNA methylation

Abstract

Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana using massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified 10-base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results indicate that nucleosome positioning influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA, indicating that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA polymerase II (Pol II) was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition.

Figure 1. Characterization of A. thaliana nucleosome data

a, A representative UCSC Browser screenshot of a gene, nucleosome reads found in the region, and the calculated nucleosome densities. b, A chromosomal view of nucleosome read counts and ChIP-seq read counts in 100kb tiles along chromosome 1 shows nucleosome enrichment in pericentromeric regions. c, An autocorrelation of positive stranded reads shows local peaks at positions 174 and 355 bases. d, AA and GC dinucleotide and CG methylation profiles show a 10 base periodicity over nucleosome-bound DNA, with DNA methylation profiles in phase with WW dinucleotide profiles, and out of phase with SS dinucleotide profiles.

Figure 2. DNA methylation profiles of nucleosome-bound DNA in Arabidopsis

The weighted average percent DNA methylation was calculated and plotted at each distance from nucleosome start sites (0). a, b, c, CG methylation (a), CHG methylation (b), and CHH methylation (c) each show a 10 base periodicity over nucleosome-bound DNA (1–147 bases). Fast Fourier Transforms (FFTs) can be used to deconstruct inherent frequencies in a complex signal. The FFTs calculated over the region of the nucleosome demonstrate this periodicity in CG (a), CHG (b), and CHH (b) contexts.

Figure 3. DNA methylation profiles of nucleosome-bound DNA in Human

The weighted average percent DNA methylation was calculated and plotted at each distance from nucleosome start sites (0). a, b, c, CG methylation (a), CHG methylation (b), and CHH methylation (c) each show a 10 base periodicity over nucleosome-bound DNA (1–147 bases). d, e, f, The FFTs calculated over the region of the nucleosome demonstrate this periodicity in CG (d), CHG (e), and CHH (f) contexts.

Figure 4. Nucleosome and PolII levels in Exons

We performed chromatin immunoprecipitation with an antibody against RNA polymerase II (Pol II), and hybridized the resulting DNA to a whole genome Affymetrix microarray. We normalized these data to randomly sheared genomic DNA to control for probe efficiencies. a, Nucleosomes are phased in exons. Exon size limits were selected such that the exon could house no more than 1, 2, 3, or 4 nucleosomes. Nucleosome midpoints are plotted over these intron-exon boundaries. b, Each exon was divided into 25 equal sized bins and the nucleosome midpoints, Pol II and CG methylation levels are plotted over the exon and flanking introns.