Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana (2008)
Abstract Background DNA methylation is an important biochemical mark that silences repetitive sequences, such as transposons, and reinforces epigenetic gene expression states. An important class of...
Phenotypic instability of Arabidopsisalleles affecting a disease Resistancegene cluster (2008)
Abstract Background Three mutations in Arabidopsis thaliana strain Columbia – cpr1 , snc1 , and bal – map to the RPP5 locus, which contains a cluster of disease Resistance genes. The similar...
Signaling silence--breaking ground and spreading out (2008)
Woo, Hye Ryun, Richards, Eric J.
Among the persistent mysteries in epigenetics are the criteria by which specific regions of the genome are chosen for deposition of distinguishing chromatin marks. Once a particular region is...
VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization (2007)
Woo, Hye Ryun, Pontes, Olga, Pikaard, Craig S., Richards, Eric J.
Epigenetic regulation in eukaryotes is executed by a complex set of signaling interactions among small RNA species and chromatin marks, including histone modification and DNA methylation. We...
Meiotically Stable Natural Epialleles of Sadhu, a Novel Arabidopsis Retroposon (2006)
Sanjida H. Rangwala, Rangasamy Elumalai, Cheryl Vanier, Hakan Ozkan, David W. Galbraith, Eric J. Richards
Epigenetic variation is a potential source of genomic and phenotypic variation among different individuals in a population, and among different varieties within a species. We used a two-tiered...
Pandey, Ritu, Müller, Andreas, Napoli, Carolyn A., Selinger, David A., Pikaard, Craig S., Richards, Eric J., ...
Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and...
Characterization of an Arabidopsis thaliana DNA hypomethylation mutant (1995)
Kakutani, Tetsuji, Jeddeloh, Jeffrey A., Richards, Eric J.
We have recently isolated two Arabidopsis thaliana DNA hypomethylation mutations, identifying the DDM1 locus, that cause a 70% reduction in genomic 5- methylcytosine levels [1]. Here we describe...
Characterization of Arabidopisis thaliana telomeres isolated in yeast (1992)
Richards, Eric J., Chao, Steven, Vongs, Aurawan, Yang, Jin
In an effort to learn more about the genomic organization of chromosomal termini in plants we employed a functional complementation strategy to isolate Arabidopsis thaliana telomeres in the yeast,...
Richards, Eric J., Goodman, Howard M., Ausubel, Frederick M.
We describe the structure of an Arabidopsis thaliana genomic clone containing two classes of repetitive DNA elements derived from the centromere region of chromosome 1. One class Is comprised of...
Induced instability of two Arabidopsis constitutive pathogen-response alleles
Stokes, Trevor L., Richards, Eric J.
Paramutation is an example of a non-Mendelian-directed allelic interaction that results in the epigenetic alteration of one allele. We describe a paramutation-like interaction between two alleles,...
Pandey, Ritu, Müller, Andreas, Napoli, Carolyn A., Selinger, David A., Pikaard, Craig S., Richards, Eric J., ...
Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and...
The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis
Jeddeloh, Jeffrey A., Bender, Judith, Richards, Eric J.
To investigate the relationship between cytosine methylation and gene silencing in Arabidopsis, we constructed strains containing the ddm1 hypomethylation mutation and a methylated and silenced PAI2...
Epigenetic variation in Arabidopsis disease resistance
Stokes, Trevor L., Kunkel, Barbara N., Richards, Eric J.
Plant pathogen resistance is mediated by a large repertoire of resistance (R) genes, which are often clustered in the genome and show a high degree of genetic variation. Here, we show that an...
Meiotically Stable Natural Epialleles of Sadhu, a Novel Arabidopsis Retroposon
Rangwala, Sanjida H, Elumalai, Rangasamy, Vanier, Cheryl, Ozkan, Hakan, Galbraith, David W, Richards, Eric J
Epigenetic variation is a potential source of genomic and phenotypic variation among different individuals in a population, and among different varieties within a species. We used a two-tiered...
Kuo, Hui-Fen, Olsen, Kenneth M., Richards, Eric J.
We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric...
The control of natural variation in cytosine methylation in Arabidopsis.
Riddle, Nicole C, Richards, Eric J
We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA...
Arabidopsis MET1 cytosine methyltransferase mutants.
Kankel, Mark W, Ramsey, Douglas E, Stokes, Trevor L, Flowers, Susan K, Haag, Jeremy R, Jeddeloh, Jeffrey A, ...
We describe the isolation and characterization of two missense mutations in the cytosine-DNA-methyltransferase gene, MET1, from the flowering plant Arabidopsis thaliana. Both missense mutations,...
Induced instability of two Arabidopsis constitutive pathogen-response alleles
Stokes, Trevor L., Richards, Eric J.
Paramutation is an example of a non-Mendelian-directed allelic interaction that results in the epigenetic alteration of one allele. We describe a paramutation-like interaction between two alleles,...
Pandey, Ritu, Müller, Andreas, Napoli, Carolyn A., Selinger, David A., Pikaard, Craig S., Richards, Eric J., ...
Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and...
Epigenetic variation in Arabidopsis disease resistance
Stokes, Trevor L., Kunkel, Barbara N., Richards, Eric J.
Plant pathogen resistance is mediated by a large repertoire of resistance (R) genes, which are often clustered in the genome and show a high degree of genetic variation. Here, we show that an...
The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis
Jeddeloh, Jeffrey A., Bender, Judith, Richards, Eric J.
To investigate the relationship between cytosine methylation and gene silencing in Arabidopsis, we constructed strains containing the ddm1 hypomethylation mutation and a methylated and silenced PAI2...
Meiotically Stable Natural Epialleles of Sadhu, a Novel Arabidopsis Retroposon
Rangwala, Sanjida H, Elumalai, Rangasamy, Vanier, Cheryl, Ozkan, Hakan, Galbraith, David W, Richards, Eric J
Epigenetic variation is a potential source of genomic and phenotypic variation among different individuals in a population, and among different varieties within a species. We used a two-tiered...
Kuo, Hui-Fen, Olsen, Kenneth M., Richards, Eric J.
We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric...
The control of natural variation in cytosine methylation in Arabidopsis.
Riddle, Nicole C, Richards, Eric J
We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA...
Arabidopsis MET1 cytosine methyltransferase mutants.
Kankel, Mark W, Ramsey, Douglas E, Stokes, Trevor L, Flowers, Susan K, Haag, Jeremy R, Jeddeloh, Jeffrey A, ...
We describe the isolation and characterization of two missense mutations in the cytosine-DNA-methyltransferase gene, MET1, from the flowering plant Arabidopsis thaliana. Both missense mutations,...
VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization
Woo, Hye Ryun, Pontes, Olga, Pikaard, Craig S., Richards, Eric J.
Epigenetic regulation in eukaryotes is executed by a complex set of signaling interactions among small RNA species and chromatin marks, including histone modification and DNA methylation. We...
Differential Epigenetic Regulation Within an Arabidopsis Retroposon Family
Rangwala, Sanjida H., Richards, Eric J.
We previously reported a novel family of Arabidopsis thaliana nonautonomous retroposons, Sadhu, showing epigenetic variation in natural populations. Here, we show that transcripts corresponding to...
Woo, Hye Ryun, Dittmer, Travis A., Richards, Eric J.
Methylcytosine-binding proteins decipher the epigenetic information encoded by DNA methylation and provide a link between DNA methylation, modification of chromatin structure, and gene silencing....
Yi, Hankuil, Richards, Eric J.
The RPP5 (for recognition of Peronospora parasitica 5) locus in the Arabidopsis thaliana Columbia strain contains a cluster of paralogous disease Resistance (R) genes that play important roles in...
LITTLE NUCLEI Genes Affecting Nuclear Morphology in Arabidopsis thaliana[W]
Dittmer, Travis A., Stacey, Nicola J., Sugimoto-Shirasu, Keiko, Richards, Eric J.
Efforts to understand nuclear organization in plant cells have received little assistance from the better-studied animal nuclei, because plant proteomes do not contain recognizable counterparts to...
Role of LINC proteins in plant nuclear morphology
Dittmer, Travis A, Richards, Eric J
A common fate of post-mitotic interphase plant nuclei is morphological differentiation into an array of shapes and sizes. Development of nuclear morphology occurs in a cell-specific manner and is...
Signaling silence—breaking ground and spreading out
Woo, Hye Ryun, Richards, Eric J.
Among the persistent mysteries in epigenetics are the criteria by which specific regions of the genome are chosen for deposition of distinguishing chromatin marks. Once a particular region is...