Population Epigenomics and Mechanisms of Epigenetic Inheritance
We are interested in determining how phenotypic plasticity and diversity are driven by natural and spontaneous epigenetic variation. Recent advances in genomic technologies are enabling acquisition of sequence-level data at an unprecedented rate and resolution. As a result, genomes for thousands of individuals are being analyzed to determine the total genetic variation present within a species and to determine the impact these variants have on phenotypic variation. Missing from these efforts is the identification of environmentally induced, spontaneous and natural epigenetic alleles (epialleles). We apply epigenomic approaches to populations to study the impact that epialleles have on life history traits and to understand their role in establishing responses to the environment. These epialleles are often associated with changes in their DNA methylation status making their identification possible. Systematically identifying these epialleles, understanding their patterns of heritability, their interaction with genetic variants and their specific roles in controlling gene expression is necessary for a comprehensive understanding of phenotypic variation.
Schmitz RJ*, Schultz MD*, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A†, McCosh RB, Chen H, Schork NJ, Ecker JR. (2013) Patterns of Population Epigenomic Diversity. Nature. Mar;495(7440):193-8.
Vollmers C*, Schmitz RJ*, Nathanson J, Yeo G, Ecker JR, Panda S. (2012) Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metabolism. Dec;16(6):833-45. PMCID: PMC3541940
Schultz MD*, Schmitz RJ*, Ecker JR. (2012) "Leveling" the playing field for analysis of single base resolution DNA methylomes. Trends in Genetics. Dec;28(12):583-5. PMCID: PMC3523709
Dowen RJ, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci. Jun;109(32):E2183-91. PMCID: PMC3420206
Schmitz RJ, Ecker JR. (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana.Trends in Plant Sciences. Mar;17(3):149-54.
Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA†, Lilbiger O, Schork NJ, Ecker JR. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science. Oct;334(6045):369-373. PMCID: PMC3210014
Schmitz RJ‡, Zhang X‡. (2011) High-throughput approaches for studying plant epigenomics. Current Opinions in Plant Biology. Apr;14:130-136. PMCID: PMC3112054
Schmitz RJ*, Tamada Y*, Doyle MR, Zhang X, Amasino RM. (2009) Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiology. Feb;149(2):1196-204.PMCID: PMC2633843
Schmitz RJ*, Sung S*, Amasino RM. (2008) Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana.Proc Natl Acad Sci. Jan;15:105(2):411-6. PMCID: PMC2206549