Eric Richards

Professor
Eric Richards
ejr77@cornell.edu
Office/Lab: 305/310
Phone: 607-254-4676
Office/Lab: 305/310
Affiliations: Adjunct Professor, Department of Molecular Biology and Genetics / Cornell University
Graduate Fields: Genetics & Development; Genomics; Plant Biology
Research Areas: Epigenetics, Nuclear cell 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.

Internship Program | Projects & FacultyApply for an Internship
Cell Biology of the Plant Nucleus
2017.
Meier, I., Richards, Eric Jean, Evans, D. E.
Annual Review of Plant Biology.
68
:
139–172
A cross species exploration of nuclear morphology
2014.
Ahlers, B., Hughes, E., Richards, Eric Jean
FASEB JOURNAL.
28
:
Arabidopsis VIM Proteins Regulate Epigenetic Silencing by Modulating DNA Methylation and Histone Modification in Cooperation with MET1
2014.
Kim, J., Kim, J. H., Richards, Eric Jean, Chung, K. M., Woo, H. R.
Molecular Plant.
7
:
1470–1485
VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway
2014.
Shook, M. S., Richards, Eric Jean
Epigenetics.
9
:
980–986
Natural Epigenetic Variation in Arabidopsis
2013.
Richards, Eric Jean, Henkhaus, N., Anand, I. S.
Integrative and Comparative Biology.
53
:
E179–E179
Arabidopsis CROWDED NUCLEI (CRWN) proteins are required for nuclear size control and heterochromatin organization
2013.
Wang, H., Dittmer, T. A., Richards, Eric Jean
BMC Plant Biology.
13
:
200–200
DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)
2012.
Higo, H., Tahir, M., Takashima, K., Miura, A., Watanabe, K., Tagiri, A., Ugaki, M., Ishikawa, R., Ei…
Molecular genetics and genomics : MGG.
287
:
785–792
Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment
2012.
Berger, F., Cao, X., Chandler, V., Dennis, L., Martienssen, R., Meyers, B., Pikaard, C., Peacock, J.…
THE PLANT CELL ONLINE.
24
:
2257–2261
Natural epigenetic variation in plant species: a view from the field
2011.
Richards, Eric Jean
Current Opinion in Plant Biology.
14
:
204–209
The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species
2010.
Richards, Eric Jean, Richards, E. J.
Mobile DNA.
1
:
10–10
Gene Duplication and Hypermutation of the Pathogen Resistance Gene SNC1 in the Arabidopsis bal Variant
2009.
Yi, H., Richards, Eric Jean
Genetics.
183
:
1227–1234
Epigenetic variation and inheritance
2009.
Richards, Eric Jean, Woo, H. R., Travis, D., Rangwala, S.
FEBS JOURNAL.
276
:
7–7
Quantitative epigenetics: DNA sequence variation need not apply
2009.
Richards, Eric Jean
Genes & development.
23
:
1601–1605
Phenotypic instability of Arabidopsis alleles affecting a disease Resistance gene cluster
2008.
Yi, H., Richards, Eric Jean
BMC Plant Biology.
8
:
36–36
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, Eric Jean
PLoS Genetics.
4
:
e1000156–e1000156
Signaling silence – Breaking ground and spreading out
2008.
Hye, R. W., Richards, Eric Jean
Genes & development.
22
:
1719–1723
Population epigenetics
2008.
Richards, Eric Jean
Current Opinion in Genetics & Development.
18
:
221–226
Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana
2008.
Woo, H. R., Richards, Eric Jean
BMC Plant Biology.
8
:
92–92
Role of LINC proteins in plant nuclear morphology
2008.
Dittmer, T. A., Richards, Eric Jean
Plant Signaling and Behavior.
3
:
485–487
LITTLE NUCLEI Genes Affecting Nuclear Morphology in Arabidopsis thaliana
2007.
Dittmer, T. A., Stacey, N. J., Sugimoto-Shirasu, K., Richards, Eric Jean
THE PLANT CELL ONLINE.
19
:
2793–2803
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