Methylation of histone H3 Lys 4 in coding regions of active genes

Abstract

Posttranslational modifications of histone tails regulate chromatin structure and transcription. Here we present global analyses of histone acetylation and histone H3 Lys 4 methylation patterns in yeast. We observe a significant correlation between acetylation of histones H3 and H4 in promoter regions and transcriptional activity. In contrast, we find that dimethylation of histone H3 Lys 4 in coding regions correlates with transcriptional activity. The histone methyltransferase Set1 is required to maintain expression of these active, promoter-acetylated, and coding region-methylated genes. Global comparisons reveal that genomic regions deacetylated by the yeast enzymes Rpd3 and Hda1 overlap extensively with Lys 4 hypo- but not hypermethylated regions. In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, we conclude that Set1 facilitates transcription, in part, by protecting active coding regions from deacetylation.

Figure 1

An in-depth analysis of histone acetylation and methylation patterns at telomeres confirms and extends prior studies. Histone acetylation (H3 and H4) and methylation (H3 Lys 4) is plotted with respect to distance from the end of the chromosome and smoothed with a Lowess algorithm. Each curve represents data from ∼1,100 microarray elements corresponding to ends of the 16 yeast chromosomes. The Cy5:Cy3 ratios for telomere-proximal elements are significantly below the genome average (represented by the zero on the y axis), indicating that histones at telomeres are hypoacetylated and Lys 4 is hypomethylated.

Figure 2

Transcriptional activity correlates with histone acetylation in promoters and coding regions, but with histone H3 Lys 4 dimethylation in coding regions. Correlations between transcriptional activity and acetylation and methylation status of corresponding promoters and coding regions were calculated from chIP microarray data sets and expression data. Error bars represent 95% confidence intervals determined by bootstrap analysis. Because these correlations are not perfect, we anticipate that the modification status of certain genes will differ from genomewide trends.

Figure 3

(A) The ability of chIP microarray analysis to reflect relative levels of acetylation and methylation in promoters and coding regions was verified by conventional chIP experiments. SUB2 is a transcriptionally active gene that is, according to chIP microarray analysis, hypermethylated in its coding region and hyperacetylated in its promoter. Conventional chIP and quantitative PCR (shown) confirms that the SUB2 coding region is enriched 4.1-fold in a Lys 4 dimethyl chIP (with respect to the SUB2 promoter), and that the SUB2 promoter is enriched 2.8-fold in an H3 acetyl chIP (with respect to the SUB2 coding region). (B) Like SUB2, MNN9 and YHM2 are active genes found by chIP microarray analysis to be coding region-hypermethylated at Lys 4. Conventional chIP verifies both findings. The coding region of the transcriptionally active gene MNN9 is enriched 2.4-fold in the Lys 4 dimethyl chIP, relative to its promoter. Similarly, the coding region of the transcriptionally active YHM2 gene is enriched 2.0-fold relative to its promoter. These findings also verify the ability of chIP microarray to resolve between promoters and coding regions. (C) Although the rDNA locus may exhibit some degree of Lys 4 methylation, this locus is Lys 4 hypomethylated relative to the active SUB2 gene.

Figure 4

Chromatin regions methylated at histone H3 Lys 4 are not deacetylated by Rpd3 or Hda1. Lists of H3 Lys 4 hypomethylated and hypermethylated chromatin regions were collated from chIP microarray analyses, and compared with lists of chromatin regions deacetylated by Rpd3 or Hda1. There is extensive overlap between deacetylated regions and hypomethylated regions. In contrast, there is essentially no overlap between deacetylated regions and hypermethylated regions. These findings and those presented in Fig. 2 are consistent with a model in which methylation of histone H3 Lys 4 protects active coding regions from deacetylation.