Eric Richards

Professor, Vice President for Research
Eric Richards
ejr77@cornell.edu
Office/Lab: 305/310
Phone: 607-254-4676
Office/Lab: 327/326
Email: gbm7@cornell.edu
Office Phone: 607-254-1208
Lab Phone: 607-220-9610
Graduate Fields: Plant Pathology & Plant-Microbe Biology; Plant Biology
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.

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.

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VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway
2014
Author(s):Shook, M.S., and Richards, E.J.
Epigenetics
9,
980–986
View
Natural epigenetic variation in plant species: A view from the field
2011
Author(s):Richards, E.J.
Curr. Opin. Plant Biol.
14,
204-209
View
The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species
2010
Author(s):Rangwala, S.H., and Richards, E.J.
Mob. DNA
1,
10
View
Quantitative epigenetics: DNA sequence variation need not apply
2009
Author(s):Richards, E.J.
Genes Dev.
23,
1601-1605
View
Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis
2008
Author(s):Woo, H.R., Dittmer, T.A., Richards, E.J.
PLoS Genetics
4(8),
e1000156
View
VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization
2007
Author(s):Woo, H.R., Pontes, O., Pikaard, C.S., and Richards, E.J.
Genes Dev.
21,
267-277
View
Differential epigenetic regulation within an Arabidopsis retroposon family
2007
Author(s):Rangwala, S.H., and Richards, E.J.
Genetics
176,
151-160
View
LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana
2007
Author(s):Dittmer, T.A., Stacey, N.J., Sugimoto-Shirasu, K., and Richards, E.J.
Plant Cell
19,
2793-2803
View
A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing
2007
Author(s):Yi, H., and Richards, E.J.
Plant Cell
19,
2929-2939
View
Meiotically-stable natural epialleles of Sadhu, a novel Arabidopsis retroposon
2006
Author(s):Rangwala, R., Elumalai, R., Vanier, C., Ozkan, H., Galbraith, D.W., and Richards, E.J.
PLoS Genetics
2,
e36
View
Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end
2006
Author(s):Kuo, H.-F., Olsen, K.M., and Richards, E.J.
Genetics
173,
401-417
View
Inherited epigenetic variation
2006
Author(s):Richards, E.J.
Nature Reviews Genetics td>
, 395-401,
395-401
View
Genetic variation in epigenetic inheritance of ribosomal gene methylation in Arabidopsis
2005
Author(s):Riddle, N.C., and Richards, E.J.
Plant J.
41,,
524-532
View
Arabidopsis MET1 cytosine methyltransferase mutants
2003
Author(s):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
View
Epigenetic variation in Arabidopsis disease resistance
2002
Author(s):Stokes, T.L., Kunkel, B.N., and Richards, E.J.
Genes Dev.
16,
171-182
View
Induced instability of two Arabidopsis constitutive pathogen-response alleles
2002
Author(s):Stokes, T.L., and Richards, E.J.
P. Natl. Acad. Sci. U S A
99,
7792-7796
View
The control of natural variation in cytosine methylation in Arabidopsis
2002
Author(s):Riddle, N.C., and Richards, E.J.
Genetics
162,
355-363
View
The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis
1998
Author(s):Jeddeloh, J.A, Bender, J., and Richards, E.J.
Genes Dev.
12,
1714-1725
View
Developmental abnormalities and epimutations associated with DNA hypomethylation mutations
1996
Author(s):Kakutani, T., Jeddeloh, J.A., Flowers, S., Munakata, K., and Richards, E.J.
P. Natl. Acad. Sci. U S A
93,
12406-12411
View
Arabidopsis thaliana DNA methylation mutants
1993
Author(s):Vongs, A., Kakutani, T., Martienssen, R., and Richards, E.J.
Science
, 1926-1928,
1926-1928
View
Methods and Compositions for Determining Methylation Profiles
Eric Richards
Technology Area:Enabling Technology
US Patent/Application(s): 7,186,512
DNA methylation gene from plants
Eric Richards
Technology Area:Enabling Technology
US Patent/Application(s): 6,153,741
Publication: Nat Genet 1999
Artificial Chromosome Vector
Eric Richards
Technology Area:Enabling Technology
US Patent/Application(s): 5,270,201
Publication: Cell 1988

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