CASE 6

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CASE 6Arabidopsis Epigenomics
Relationship between nucleosome positioning and
DNA methylation , Nature 466, 388392 (15 July
2010)

• 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.
• nucleosome positioning influences DNA methylation
  patterning throughout the genome and that DNA
• methyltransferases preferentially target
  nucleosome-bound DNA. We also bserved similar
  trends in human nucleosomal DNA,
• nucleosomes were highly enriched on exons,and
  preferentially positioned at intronexon and
  exonintron Boundaries as same as DNA ethylation

Material Arabidopsis and human embryonic stem
cell line HSF1 Methods Nucleosome-seq?ChIP-seq?C
hIP-chip? Bisulfite-seq?RNA-seq
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Fig 1 DNA methylation profiles of
nucleosome-bound DNA in Arabidopsis (left) and
human(right)
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Fig 2a Nucleosome and Pol II levels in exons.
Nucleosomes are phased in exons. Nucleosome
midpoints are plotted over these intronexon
boundaries.
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Fig 2b RNA Pol II levels in exons. 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.
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CASE 7The Honey Bee Epigenomes
The Honey Bee Epigenomes Differential
Methylation of Brain DNA in Queens and Workers.
PLoS BIOL. 2010, 8(11)112.
German Cancer Research CenterJames
Cook University
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The quantities of methylated CpGs in queen and
worker brain DNA are very similar, 69,064 and
68,222, respectively, with 54,312 mCpGs in common.
The mCGs in queens and workers exons of content
is much higher than the levels in the introns.
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The repeated elements, ALU, and mariners that
harbor none of DNA methylation in the bee genome,
certainly not in the brain.
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Table CpG o/e in methylated genes
Methylation status Low CpG o/e High CpG o/e P-value (Fisher exact test)
All genes Methylated 5,195 643 lt 10-200
All genes Non-Methylated 1,391 3,489
Caste-specific genes Methylated 356 52 6.6 x 10-66
Caste-specific genes Non-Methylated 69 215
Differentially methylated, compared to all genes Methylated 393 156 3.0 x 10-6
Differentially methylated, compared to all genes Non-Methylated 6,273 3,877
Differentially methylated compared to methylated genes Methylated 393 156 5.7 x 10-28
Differentially methylated compared to methylated genes Non-Methylated 4,823 561
High-CpG genes in A. mellifera generally are not
more prone to epigenetic modulation than low-CpG
genes.
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CASE 8Arabidopsis
Patterns of population epigenomic diversity.
NATURE. 2013, 495193200.
The Salk Institute for Biological Studies
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CG- and CHG-SMPs in transposable elements tend to
be faithfully methylated throughout this
population, whereas CHH-SMPs are largely
unmethylated.
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Binomial Test Results Binomial Test Results Binomial Test Results Binomial Test Results Binomial Test Results Binomial Test Results
Total Expected Proportion
Genes 31177 0.704230761
Transposons 13094 0.295769239

C-DMRs C-DMRs Overlapping Total C-DMRs Proportion Alternative P-value
Genes 2738 13484 0.203055473 Less 2.26E-132
Transposons 5101 13484 0.378300208 Greater 8.97E-94

CG-DMRs CG-DMRs Overlapping Total CG-DMRs Alternative P-value
Genes 30801 40286 0.764558407 Greater 4.65E-164
Transposons 2891 40286 0.071761902 Less lt2.2e-16
CG-DMRs were enriched in gene bodies and depleted
in transposons. C-DMRs showed enrichment in
transposons and depletion in genes.
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Total Variants lt1 MAF lt5 MAF lt10 MAF gt10 MAF Fraction lt.01 MAF Fraction lt.05 MAF Fraction lt.1 MAF Fraction gt.1 MAF
CG 5458839 3809595 4256162 4525635 933204 69.79 77.97 82.90 17.10
CHG 5904538 4904853 5230125 5388564 515974 83.07 88.58 91.26 8.74
CHH 27375518 23423366 24289807 24904055 2471463 85.56 88.73 90.97 9.03
SNPs 6606689 2726439 4693282 5384891 1221798 41.27 71.04 81.51 18.49