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Browsing by Subject "Histone modification"

Now showing 1 - 2 of 2
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    Alu and LINE-1 are determinants for repressive mark type at genes and degree of gene expression level variation
    (2013-01) Gong, Wuming
    A fundamental unanswered question in biology is why the Alu transposable elements that constitute 11% of the human genome have amassed at varying levels in the vicinity of most genes and appear to have been selected against in non-gene regions while LINE-1 transposons that constitute 16% of the genome have accumulated around a minority of genes and are abundant in non-gene regions. Here we show that genes flanked by increasingly higher Alu concentrations display progressively less variation in expression level among humans and across human cell types while genes flanked by increasingly higher LINE-1 concentrations show progressively higher variation. Bayesian network modeling indicates that Alu elements promote H3K36me3 chromatin that fosters low gene expression variation while LINE-1 elements encourage H3K9me3 chromatin that procures high expression variation. Accordingly, genes in high Alu low LINE-1 environments produce H3K36me3 in their transcribed regions of at levels reflecting the levels of transcription while genes residing in progressively higher LINE-1 environments are increasingly likely to establish H3K9me3 in their transcribed regions, again at levels reflecting the levels of transcription. Further along these lines, silent genes occupied by repressive H3K36me3 across their regulatory regions reside primarily in high Alu low LINE-1 chromosomal environments, while occupation of silent genes by H3K9me3 is most prevalent in low Alu high LINE-1 environments, and genes silenced by H3K27me3 are concentrated in low Alu low LINE-1 environments. Genes residing in medium-high LINE-1 but extreme low Alu genes are exceptional as they tend to be occupied by an uncharacterized chromatin type. Finally, gene-distant regions are generally high LINE-1 low Alu, and here LINE-1 also promotes uncharacterized non-H3K9me3 chromatin that Alu opposes. Our findings indicate that local Alu and LINE-1 concentrations determine chromatin systems utilized by many genes.
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    Epigenetic and genetic control of imprinting at the Mez1 locus in maize.
    (2008-05) Haun, WIlliam John
    Genomic imprinting is the mono-allelic expression of gene based on its parent-of-origin and is important for normal progeny development in plants. The goal of this research was to better classify the epigenetic modifications at the Zea mays (maize) imprinted gene Mez1, while also investigating the phenotypic consequence of a loss-of-imprinting. The Mez1 gene in maize is imprinted in endosperm tissue, displaying expression solely from the maternal allele. A differentially methylated region (DMR) was identified in the 5' cis -proximal region of Mez1 in endosperm tissue. In this DMR, the paternal allele displays significantly higher levels of both CpG and CpNpG DNA methylation relative to the corresponding region of the maternal allele. The chromatin modifications of the maternal and paternal alleles of Mez1 and a second imprinted gene, ZmFie1, were studied using allele-specific chromatin immunoprecipitation (ChIP). HistoneH3 and HistoneH4 acetylation are maternally-enriched in endosperm tissue, while HistoneH3 Lysine27 tri-methylation (and to a lesser extent HistoneH3 Lysine27 di-methylation) show paternal allele enrichment. HistoneH3 Lysine9 di-methylation and HistoneH3 Lysine9 tri-methylation do not show parent-specific enrichment. These results suggest DNA methylation and histone modifications are involved in the epigenetic regulation of imprinting in plants. Numerous studies have focused on understanding the mechanism of imprinting, however relatively little is known about the phenotypic consequence of expressing the normally silent allele of an imprinted gene. Several different alleles containing Mu transposon insertions into the 5' cis -proximal region of Mez1 were characterized. Both maternal and paternal inheritance of mez1-mu alleles can result in a loss-of-imprinting. This suggests that Mu transposon insertions at the Mez1 locus can act by disrupting the production of a trans -acting factor or interfering with the cis -acting elements involved in imprinting. Interestingly, the mez1-mu insertions do not effect plant vegetative growth or seed development. These results suggest allelic communication is important between the two parental alleles of imprinted loci.