Qing Li, Jonathan I. Gent, Greg Zynda, Jawon Song, Irina Makarevitch, Cory D. Hirsch, Candice N. Hirsch, R. Kelly Dawe, Thelma F. Madzima, Karen M. McGinnis, Damon Lisch, Robert J. Schmitz, Matthew W. Vaughn, and Nathan M. Springer
Abstract
The maize genome is relatively large (∼2.3 Gb) and has a complex organization of interspersed genes and transposable elements, which necessitates frequent boundaries between different types of chromatin. The examination of maize genes and conserved noncoding sequences revealed that many of these are flanked by regions of elevated asymmetric CHH (where H is A, C, or T) methylation (termed mCHH islands). These mCHH islands are quite short (∼100 bp), are enriched near active genes, and often occur at the edge of the transposon that is located nearest to genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications revealed that mCHH islands mark the transition from heterochromatin-associated modifications to euchromatin-associated modifications. The presence of an mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of insertion/deletions in promoters often influences the presence and position of an mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities and are lost in mop1 and mop3 mutants, but the nearby genes rarely exhibit altered expression levels. Instead, loss of an mCHH island is often accompanied by additional loss of DNA methylation in CG and CHG contexts associated with heterochromatin in nearby transposons. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of nearby genes.
See: http://www.pnas.org/content/112/47.toc
PNAS November 24, 2015; vol. 112 no. 47: 14728–14733, doi: 10.1073/pnas.1514680112
Fig. 2. mCHH islands are often located at transposon edges close to highly expressed genes. (A) All of the 100-bp tiles with >25% mCHH levels in B73 seedling were annotated based on their location relative to genes or CNSs. (B) The level of mCHH was determined for the distal and proximal edge (100 bp) of TEs greater than 1 kb in length. These TEs were also split according to whether they were located on the same or opposite strand as the gene. (C) The percentage of genes with a 5′ end mCHH island is shown for genes that are not expressed (NE) or genes in each of the four expression quartiles (Q1–Q4) using RNA-seq data from the same tissue as the WGBS data, B73 seedling leaf. The small letter above each bar indicates whether there is a significant difference between the proportion of genes with mCHH island, with same letter indicating no difference and different letter indicating significant difference at P < 0.01 (prop.test in R) level.
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