Research in the Richards lab is broadly focused on epigenetics, the study of inherited information superimposed on the genetic sequence. Most of our efforts to date have concentrated on cytosine methylation, which is one of the most fundamental types of epigenetic information in eukaryotic cells. We are interested in both the regulation of cytosine methylation and the phenotypic consequences of variation in cytosine methylation patterns. Our work also extends to higher-order epigenetic information encoded in alternative chromatin packaging and the three-dimensional organization of the genetic material. Our studies take advantage of the genetic and genomic resources available in the model organism Arabidopsis thaliana.
Chromatin – DNA Methylation Interface
Our forward genetic screens for Arabidopsis variants with reduced cytosine methylation levels have led to two unexpected gene targets that encode proteins implicated in chromatin regulation. These findings underscore the interconnections between chromatin and DNA modification. The first gene discovered in our genetic screens, DDM1 (DECREASED DNA METHYLATION 1), encodes a SNF2 family nucleosome remodeling protein. Loss of DDM1 function leads to dramatic loss of cytosine methylation in heterochromatic repeats as well as a loss of histone modification marks characteristic of heterochromatin. Mammalian DDM1 orthologs appear to play an analogous role in the maintenance of heterochromatic epigenetic markers. How DDM1 facilitates deposition and retention of heterochromatic marks is poorly understood and one objective of our research program is to elucidate these mechanisms.
The second class of chromatin proteins uncovered by our genetic screens binds methylated cytosine residues via an SRA (SET- and RING-associated) domain. We are focusing on the VIM (VARIANT IN METHYLATION) protein family, a subclass of SRA domain methylcytosine-binding proteins required for maintenance of CpG methylation throughout the genome. Our goal is to understand how these proteins interpret cytosine methylation patterns and coordinate epigenetic regulation across the DNA methylation-chromatin interface.
Epigenetic Variation and Inheritance
In our initial characterization of Arabidopsis mutations that reduce DNA methylation we observed that the hypomethylated state of different genomic regions was inherited through meiosis independently of the mutations that caused the aberrant methylation. This simple genetic result led us to undertake a variety of studies to weigh the interaction between genetic and epigenetic variation. This work, in turn, has sparked a broader investigation of the prevalence and significance of epigenetic variation in plants within an agricultural, ecological, and evolutionary context.
The three-dimensional organization of eukaryotic nuclei is an important topic of study from both a cell biological and an epigenetic perspective. The determinants that specify nuclear architecture can affect the epigenetic state of different genomic compartments. We are striving to bridge our understanding of epigenetic codes at the level of DNA and chromatin modification with higher-order epigenetic information embedded in three-dimensional nuclear organization. We are beginning this long-term effort with a project centered around a group of nuclear coiled-coil proteins that we have called LINC (LITTLE NUCLEI) for the reduction in nuclear size and alteration in nuclear shape caused by combining loss-of-function mutations in LINC paralogs. LINC proteins are plant-specific but share some structural features reminiscent of animal lamins, which are the key constituent proteins of the nuclear lamina – a mesh-like cage that underlies the nuclear membrane in animal cells. In our LINC project, we are pursuing two different research questions: the first is aimed at understanding how LINC proteins control plant nuclear architecture, while the second explores the interaction between nuclear organization and epigenetics.
Shook, M.S., and Richards, E.J. 2014. VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway. Epigenetics. 9, 980–986 [Full Text ...]
Wang, H., Dittmer, T. A., and Richards, E. J . 2013. Arabidopsis CROWDED NUCLEI (CRWN) proteins are required for nuclear size control and heterochromatin organization. BMC Plant Biology. 13:200 [Full Text ...]
Berger, F., Cao, X.F., Chandler, V., Dennis, L., Martienssen, R., Meyers, B., Pikaard, C., Peacock, J., Richards, E., Wagner, D., Weigel, D., Colot, V., Deal, R., Dean, C., Ecker, J., Gehring, M., Gong, Z.Z., Gregory, B., Rodrigo, G., Gutierrez-Marcos, J., Hasebe, M., Hwang, I.D., Jacobsen, S., Kakutani, T., Li, J.Y., Michaels, S., Noh, Y.S., Provart, N., Vaughn, M. and Comm, E.P. 2012. Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environment. Plant Cell 24: 2257-2261 [Full Text ...]
Richards, E.J. 2011. Natural epigenetic variation in plant species: A view from the field. Curr Opin Plant Biol 14: 204-209 [Full Text ...]
Rangwala, S.H. and Richards, E.J. 2010. The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species. Mob DNA 1: 10 [Full Text ...]
Richards, E.J. 2009. Quantitative epigenetics: DNA sequence variation need not apply. Gene Dev 23: 1601-1605 [Full Text ...]
Woo, H.R., Dittmer, T.A., Richards, E.J. 2008. Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis. PLoS Genetics 4(8) [Full Text ...]
Woo, H.R., Pontes, O., Pikaard, C.S., and Richards, E.J. 2007. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev 21: 267-77 [Full Text ...]
Rangwala, S.H., and Richards, E.J. 2007. Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics 176: 151-60 [Full Text ...]
Dittmer, T.A., Stacey, N.J., Sugimoto-Shirasu, K., and Richards, E.J. 2007. LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana. Plant Cell 19: 2793-803 [Full Text ...]
Yi, H., and Richards, E.J. 2007. A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing. Plant Cell 19: 2929-39 [Full Text ...]
Rangwala, R, Elumalai, R., Vanier, C, Ozkan, H., Galbraith, D.W., and Richards, E.J. 2006. Meiotically-stable natural epialleles of Sadhu, a novel Arabidopsis retroposon. PLoS Genet 2: e36 [Full Text ...]
Kuo, H.-F., Olsen, K.M., and Richards, E.J. 2006. Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end. Genetics 173: 401-17 [Full Text ...]
Richards, E.J. 2006. Inherited epigenetic variation. Nat. Rev. Genet 7: 395-401 [Full Text ...]
Riddle, N.C., and Richards, E.J. 2005. Genetic variation in epigenetic inheritance of ribosomal gene methylation in Arabidopsis. Plant Journal 41: 524-32 [Full Text ...]
Kankel, M.W., Ramsey, D.E., Stokes, T.L., Flowers, S.K., Haag, J.R., Jeddeloh, J.A., Riddle, N.C., Verbsky, M.L., and Richards, E.J. 2003. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163: 1109-22 [Full Text ...]
Stokes, T.L., Kunkel, B.N., and Richards, E.J. 2002. Epigenetic variation in Arabidopsis disease resistance. Genes Dev 16: 171-82 [Full Text ...]
Stokes, T.L., and Richards, E.J. 2002. Induced instability of two Arabidopsis constitutive pathogen-response alleles. Proc. Natl. Acad. Sci. USA 99: 7792-6 [Full Text ...]
Riddle, N.C., and Richards, E.J. 2002. The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355-63 [Full Text ...]
Jeddeloh, J.A, Bender, J., and Richards, E.J. 1998. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev 12: 1714-25 [Full Text ...]
Kakutani, T., Jeddeloh, J.A., Flowers, S., Munakata, K., and Richards, E.J. 1996. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 93: 12406-11 [Full Text ...]
Vongs, A., Kakutani, T., Martienssen, R., and Richards, E.J. 1993. Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-8 [Full Text ...]
In The News
Speakers will include Dr. Frank Schroeder, postdocs Daniela Floss and Patricia Manosalva, Dr. Robert Granados and Dr. Maureen Hanson (from Cornell), and discussion of postgraduate training and education with Dr. David Stern and Dr. Eric Richards Read More
CRWN proteins alter nuclear organization, which affects plant viability Read More
Research in the Richards lab is broadly focused on epigenetics, the study of inherited information superimposed on nucleotide sequence. Our efforts have concentrated on the study cytosine methylation through use of both induced mutants and natural variants of Arabidopsis with altered levels of cytosine methylation. We are now striving to understand how epigenetic codes at the level of DNA and chromatin modification affect higher-order epigenetic information embedded in three-dimensional nuclear organization. One component of this work is the investigation in natural variation in nuclear morphology. Student interns will screen Arabidopsis thaliana natural strains for altered nuclear size and shape in a variety of cell types. Genetic control of nuclear morphology variation will be charted using inter-strain segregating families or recombinant inbred populations. This work has the advantage of being technically tractable for students in an intern setting, while providing exposure to transmission genetics, and plant anatomy and cell biology.