Periodic Reporting for period 3 - MaintainMeth (Quantitative analysis of DNA methylation maintenance within chromatin)
Reporting period: 2020-04-01 to 2021-06-30
My laboratory’s recent work with DDM1 – an ancient protein conserved between plants and animals that can move nucleosomes – and linker histone H1, which binds to nucleosomes and the intervening ‘linker’ DNA, has allowed us to formulate a hypothesis wherein movement of nucleosomes by DDM1 dislodges H1 and allows methyltransferases to access the DNA. My laboratory also discovered that DNA methylation influences nucleosome placement, thereby demonstrating that the interaction between DNA methylation and nucleosomes is bidirectional, and providing a possible mechanism through which DNA methylation can reguate gene activity.
Our goal is to deeply understand the connected processes of maintenance methylation and nucleosome placement, and how these affect gene function. This will be achieved through interconnected research strands: elucidation of how DNA methylation is maintained within chromatin, determination of how DNA methylation interacts with nucleosomes and H1 in vivo, and understanding of the functional consequences of DNA methylation within genes.
DNA methylation and histone H1 are known to mediate transcriptional silencing of genes and transposable elements, but how they interact has been unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. We showed that H1 is enriched in methylated sequences, including genes, of Arabidopsis, yet this enrichment is independent of DNA methylation. We found that loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, we showed that H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. We also found that hypomethylation of genes activates antisense transcription, which is modestly enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes.