Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

ABSTRACT: Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are numerous differences in the distribution of H3K27me3 among tissues. In contrast, we found the distribution of H3K27me3 among the two genetic backgrounds to be quite similar. The tissue-specific patterns of H3K27me3 are often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. Many maize genes with important developmental roles, including numerous genes encoding putative transcription factors, are modified with H3K27me3 in at least one of the tissues that were profiled. A comparison of the H3K27me3 targets in rice, maize, and Arabidopsis provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole genome duplication. Genomic profiling of H3K27me3 in loss-of-function mutant stocks for Mez2 and Mez3, two of the three putative H3K27me3 methyltranferases present in the maize genome, suggests partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 requires Mez2 and/or Mez3 and there was limited evidence for functional consequences of H3K27me3 at these targets. This study provides a catalogue of 6,337 genes that are marked by H3K27me3 in five maize tissues. B73 tissues for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels. histone modification mutants for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels. Mo17 tissues for h3k27 analysis: Samples contain antibody pulldown (IP) and control genomic DNA (input) channels.

ORGANISM(S): Zea mays

SUBMITTER: Steve Eichten

PROVIDER: E-GEOD-39456 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Transposable elements have the potential to act as controlling elements to influence the expression of genes. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of the transposable element and influence the chromatin state of neighboring low-copy sequences. This would allow transposable elements to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I transposable elements (retrotransposons) that are present in moderate to high copy numbers and many are found in regions near genes which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into flanking DNA around each family of retrotransposons through profiling of DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some LTR families exhibit enrichment of heterochromatic marks within 800-1200 base pairs of the insertion site while other families have very little evidence for spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the adjacent heterochromatin results from spreading of silencing rather than insertion-site preferences. Genes that are located near elements that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of LTR retrotransposon families may act as controlling elements influencing neighboring sequences while the majority of elements have little effect on flanking sequences Transposable elements comprise a substantial portion of many eukaryotic genomes. These mobile fragments of DNA can result in mutations through insertions into genes but may also affect the regulation of genes they insert near. There is evidence that the majority of transposable elements are epigenetically silenced and in some cases this silencing may affect neighboring sequences. However, evolutionary theory would predict that there would be selective pressures for transposable elements to limit their effects on neighboring genes. The maize genome has a complex organization with many genes flanked by retrotransposons. We profiled the spread of heterochromatin from the retrotransposons into nearby low copy sequences for 150 high copy retrotransposon families. While the manymajority of retrotransposons exhibit little to no spreading of heterochromatin there are a small number ofsome retrotransposon families that influence the chromatin state of surrounding regions. The families may represent bad “neighbors” that spread heterochromatin and influence nearby genes. 6 total samples: 3 replicates of B73 H3k9 and 3 replicates of Mo17 H3k9 3 total samples: mop1 mutant, b73.zmet2 (zmet2.m1 mutant in B73 background) and mo17.zmet2 (zmet2.m1 mutant in Mo17 background)

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Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

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