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Eric Richards
 &emdash;  Professor, Vice President for Research

Eric Richards
Office/Lab: 125/120
Affiliations:
  • Adjunct Professor, Department of Molecular Biology and Genetics
  • Cornell University
Graduate Fields: Genetics & Development; Genomics; Plant Biology
Research Areas:

Publications

  • VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway 2014

    Shook, M.S., and Richards, E.J.
    Epigenetics 9,  980–986
    Full text...
  • Arabidopsis CROWDED NUCLEI (CRWN) proteins are required for nuclear size control and heterochromatin organization 2013

    Wang, H., Dittmer, T. A., and Richards, E. J.
    BMC Plant Biology 13,  200
    Full text...
  • Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environment 2012

    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.
    Plant Cell 24,  2257-2261
    Full text...
  • Natural epigenetic variation in plant species: A view from the field 2011

    Richards, E.J.
    Curr. Opin. Plant Biol. 14,  204-209
    Full text...
  • The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species 2010

    Rangwala, S.H., and Richards, E.J.
    Mob. DNA 1,  10
    Full text...
  • Quantitative epigenetics: DNA sequence variation need not apply 2009

    Richards, E.J.
    Genes Dev. 23,  1601-1605
    Full text...
  • Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis 2008

    Woo, H.R., Dittmer, T.A., Richards, E.J.
    PLoS Genetics 4(8),  e1000156
    Full text...
  • VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization 2007

    Woo, H.R., Pontes, O., Pikaard, C.S., and Richards, E.J.
    Genes Dev. 21,  267-277
    Full text...
  • Differential epigenetic regulation within an Arabidopsis retroposon family 2007

    Rangwala, S.H., and Richards, E.J.
    Genetics 176,  151-160
    Full text...
  • LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana 2007

    Dittmer, T.A., Stacey, N.J., Sugimoto-Shirasu, K., and Richards, E.J.
    Plant Cell 19,  2793-2803
    Full text...
  • A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing 2007

    Yi, H., and Richards, E.J.
    Plant Cell 19,  2929-2939
    Full text...
  • Meiotically-stable natural epialleles of Sadhu, a novel Arabidopsis retroposon 2006

    Rangwala, R., Elumalai, R., Vanier, C., Ozkan, H., Galbraith, D.W., and Richards, E.J.
    PLoS Genetics 2,  e36
    Full text...
  • Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end 2006

    Kuo, H.-F., Olsen, K.M., and Richards, E.J.
    Genetics 173,  401-417
    Full text...
  • Inherited epigenetic variation 2006

    Richards, E.J.
    Nature Reviews Genetics , 395-401,  395-401
    Full text...
  • Genetic variation in epigenetic inheritance of ribosomal gene methylation in Arabidopsis 2005

    Riddle, N.C., and Richards, E.J.
    Plant J. 41,,  524-532
    Full text...
  • Arabidopsis MET1 cytosine methyltransferase mutants 2003

    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.
    Genetics 163,  1109-1122
    Full text...
  • Epigenetic variation in Arabidopsis disease resistance 2002

    Stokes, T.L., Kunkel, B.N., and Richards, E.J.
    Genes Dev. 16,  171-182
    Full text...
  • Induced instability of two Arabidopsis constitutive pathogen-response alleles 2002

    Stokes, T.L., and Richards, E.J.
    P. Natl. Acad. Sci. U S A 99,  7792-7796
    Full text...
  • The control of natural variation in cytosine methylation in Arabidopsis 2002

    Riddle, N.C., and Richards, E.J.
    Genetics 162,  355-363
    Full text...
  • The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis 1998

    Jeddeloh, J.A, Bender, J., and Richards, E.J.
    Genes Dev. 12,  1714-1725
    Full text...
  • Developmental abnormalities and epimutations associated with DNA hypomethylation mutations 1996

    Kakutani, T., Jeddeloh, J.A., Flowers, S., Munakata, K., and Richards, E.J.
    P. Natl. Acad. Sci. U S A 93,  12406-12411
    Full text...
  • Arabidopsis thaliana DNA methylation mutants 1993

    Vongs, A., Kakutani, T., Martienssen, R., and Richards, E.J.
    Science , 1926-1928,  1926-1928
    Full text...

Intern Projects

The interface between epigenetics and nuclear cell biology in plants

The three-dimensional structure of the nucleus affects gene expression and other activities of the eukaryotic genome.  We apply genetics, genomics, cell biology and biochemical approaches to study how the organization and dynamics of the nuclear organelle affect genome function.

Click the links to return to the Intern FacultyInternship Program,  Apply for an Internship pages on the BTI website.

Interns

Patents

    • Technology Area: Enabling Technology
    • Title: Methods and Compositions for Determining Methylation Profiles
    • US Patent/Application(s): 7,186,512
    • Publication: None
    • Technology Area: Enabling Technology
    • Title: DNA methylation gene from plants
    • US Patent/Application(s): 6,153,741
    • Publication: Nat Genet 1999
    • Technology Area: Enabling Technology
    • Title: Artificial Chromosome Vector
    • US Patent/Application(s): 5,270,201
    • Publication: Cell 1988

Research Utilization

Plant Epigenetics

Epigenetics encompasses regulatory mechanisms (e.g., cytosine methylation, chromatin protein modification, changes in chromatin packaging, and RNA interference) that alter the information content of the genome without changing nucleotide sequences. Differential epigenetic states associated with gene expression changes can be propagated at high fidelity through cell division, and in some cases, from parents to offspring. Consequently, epigenetics represents an independent form of inheritance, one that allows a single genotype to specify different phenotypes.

Epigenetic phenomena are widespread and have enormous impacts in agriculture. For example, transgene instability due to epigenetic silencing is a major concern in agricultural biotechnology, and epigenetic research is being applied to avoid silencing through better transgene design, identification of favorable insertion sites, and modification of host epigenetic systems. Research in the Richards lab has highlighted the importance of inherited “epimutations,” which can mimic stable Mendelian traits but are caused by differential DNA methylation and associated epigenetic marks. The generation, selection and manipulation of stable epigenetic alleles in agricultural breeding programs remain an underexplored frontier.

Plants serve as powerful experimental platforms for dissecting and elucidating epigenetic pathways and the ways that aberrations in these pathways can lead to epimutations. They are remarkably tolerant of epigenetic perturbation, providing the opportunity to identify and manipulate epigenetic modifiers while maintaining viability. Two of the epigenetic modifier proteins studied in the Richards lab, the nucleosome remodeler DDM1 and the VIM family of methylcytosine-binding proteins, are required for epigenomic stability in plants. Further, DDM1 and VIM1 have human orthologs that have been implicated in cell cycle control and tumorigenesis. Our work in plants to elucidate the mechanisms through which these proteins operate is being applied to understand the role that these proteins play in epigenetic phenomena, including transgene silencing and control of higher order chromatin organization.

Collaboration and Consulting Opportunities

  • The role of epigenetics in position effect and transgene expression stability
  • Inherited epigenetic variation in breeding programs

Collaborations and Consulting

In the News

Research Overview

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.

Nuclear Architecture

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.