Mary Gehring

The goal of our laboratory is to understand how epigenome dynamics modulate plant growth and development. Epigenetics refers to heritable information that influences genome function but is not encoded in the DNA sequence itself. Cytosine DNA methylation is an epigenetic mark essential for transposable element silencing, genome stability, and genomic imprinting in a diverse array of organisms. Perturbations of DNA methylation patterns can lead to changes in gene expression programs and result in severe developmental defects. However, in both flowering plants and mammals, programmed changes in DNA methylation patterns are essential for gamete specification and the development of viable offspring. We use genetic, genomic, and molecular biology approaches to study aspects of epigenomic reprogramming during development, particularly the reproductive phase of the plant life cycle, primarily in the model plant Arabidopsis thaliana. We focus on the interplay among repetitive sequences, DNA methylation, and chromatin structure in these dynamic processes.

Interplay between DNA methylation and demethylation

DNA methylation patterns are a product of antagonistic methylation and demethylation activities. In plants, enzymatic DNA demethylation is mediated by DNA glycosylases that remove 5-methylcytosine via base excision repair. We are studying how the glycosylases are regulated at the transcriptional level and seek to understand how they find their specific targets among a vast sea of methylated cytosines.

Epigenome dynamics from gametogenesis through seed maturity

Seeds represent the next generation in plants and consist of three genetically distinct components: the maternally derived seed coat and the two products of fertilization, the diploid embryo and the triploid endosperm. The endosperm nourishes the embryo during seed development and is the caloric foundation of the human diet. Recent insights into genome-wide methylation changes that occur as a programmed part of gamete and seed development represent a first step in understanding the contribution of epigenomic dynamics to successful plant reproduction. The cell that is the female progenitor of the endosperm undergoes genome-wide active DNA demethylation before fertilization, with the largest changes in DNA methylation taking place at repetitive sequences that are normally targeted by RNA-directed DNA methylation in other tissues. Major questions about the functional consequences of DNA demethylation in relation to chromatin structure and transcription remain. Furthermore, the temporal and spatial dynamics of epigenomic reprogramming in relation to development are unknown. We are pursuing an understanding of seeds at the epigenomic level from gamete differentiation to seed maturity by integrating data from genome-wide DNA methylation, RNA, and chromatin profiling. A diverse array of genetic and genomic tools makes A. thaliana a powerful model system to understand the basic mechanisms of epigenomic reprogramming in the context of a whole organism.

The evolution of imprinted genes and their role in seed development

For some loci, DNA demethylation establishes gene imprinting in the endosperm, an epigenetic phenomenon found in flowering plants and animals whereby alleles of a gene are expressed differently depending on whether they are inherited from the male or female parent. Several known imprinted genes are essential for seed development. Our genome-wide DNA methylation profiling and subsequent RNA-seq analysis has identified many new imprinted genes. The function of most of these genes is unknown, but many encode putative transcription factors and chromatin-related proteins and thus could be important for directing the endosperm developmental program. We seek to understand the function of these genes during seed development, the molecular mechanism of their imprinting, and whether imprinting of these genes is conserved within the species and in related species. Transposable elements vary as lineages diverge, and DNA methylation and small RNAs have been shown to be polymorphic within A. thaliana. Our finding that DNA demethylation occurs at repeated sequences that correspond to remnants of transposable elements (TEs) suggested that the set of imprinted genes could vary within the species. We have recently defined a set of variably imprinted genes within A. thaliana and shown that this variation is correlated with intraspecific DNA methylation polymorphisms at proximal TEs. We are also defining the imprintome in the related outcrossing species A. lyrata to test evolutionary theories on the origins and function of imprinting.

Williams BP, Pignatta D, Henikoff S, Gehring M. “Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat.” PLoS Genetics 11: e1005142 (2015).

Erdmann RM, Souza AL, Clish CB, Gehring M. “5-hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA.” G3: Genes Genomes Genetics 5: 1-8 (2014).

Pignatta D, Erdmann RM, Scheer E, Picard CL, Bell GW, Gehring M. “Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.” eLife 3: 03198 (2014).

Gehring M, Missirian V, Henikoff S. "Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds." PLoS One 6: e23687 (2011).

Gehring M, Bubb KL, Henikoff S. “Extensive demethylation of repetitive elements during seed development underlies gene imprinting.” Science 324: 1447-1451 (2009).

Gehring M, Reik W, Henikoff S. “DNA demethylation by DNA repair.” Trends Genet 25: 82-90 (2009).

Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.” Nat Genet. 39: 61-69 (2007).

Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL. “DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation.” Cell. 124: 495-506 (2006).