Grover, J. W., Bomhoff, M., Davey, S., Gregory, B. D., Mosher, R. A., & Lyons, E. (2017). CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization. Plant Direct, 1(2).
BIO5 Collaborators
Eric H Lyons, Rebecca A Mosher
Preuss, S. B., Costa-Nunes, P., Tucker, S., Pontes, O., Lawrence, R. J., Mosher, R., Kasschau, K. D., Carrington, J. C., Baulcombe, D. C., Viegas, W., & Pikaard, C. S. (2008). Multimegabase Silencing in Nucleolar Dominance Involves siRNA-Directed DNA Methylation and Specific Methylcytosine-Binding Proteins. Molecular Cell, 32(5), 673-684.
PMID: 19061642;PMCID: PMC2741319;Abstract:
In genetic hybrids, the silencing of nucleolar rRNA genes inherited from one progenitor is the epigenetic phenomenon known as nucleolar dominance. An RNAi knockdown screen identified the Arabidopsis de novo cytosine methyltransferase, DRM2, and the methylcytosine binding domain proteins, MBD6 and MBD10, as activities required for nucleolar dominance. MBD10 localizes throughout the nucleus, but MBD6 preferentially associates with silenced rRNA genes and does so in a DRM2-dependent manner. DRM2 methylation is thought to be guided by siRNAs whose biogenesis requires RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Consistent with this hypothesis, knockdown of DCL3 or RDR2 disrupts nucleolar dominance. Collectively, these results indicate that in addition to directing the silencing of retrotransposons and noncoding repeats, siRNAs specify de novo cytosine methylation patterns that are recognized by MBD6 and MBD10 in the large-scale silencing of rRNA gene loci. © 2008 Elsevier Inc. All rights reserved.
Searle, I. R., Mosher, R. A., Melnyk, C. W., & Baulcombe, D. C. (2007). Small RNAs hit the big time: Meetings. New Phytologist, 174(3), 479-482.
Mosher, R. A., Durrant, W. E., Wang, D., Song, J., & Dong, X. (2006). A comprehensive structure-function analysis of Arabidopsis SNI1 defines essential regions and transcriptional repressor activity. Plant Cell, 18(7), 1750-1765.
PMID: 16766691;PMCID: PMC1488919;Abstract:
The expression of systemic acquired resistance (SAR) in plants involves the upregulation of many Pathogenesis-Related (PR) genes, which work in concert to confer resistance to a broad spectrum of pathogens. Because SAR is a costly process, SAR-associated transcription must be tightly regulated. Arabidopsis thaliana SNM (for Suppressor of NPR1, Inducible) is a negative regulator of SAR required to dampen the basal expression of PR genes. Whole genome transcriptional profiling showed that in the sni1 mutant, Nonexpresser of PR genes (NPR1)-dependent benzothiadiazole S-methylester-responsive genes were specifically derepressed. Interestingly, SNM also repressed transcription when expressed in yeast, suggesting that it functions as an active transcriptional repressor through a highly conserved mechanism. Chromatin immunoprecipitation indicated that histone modification may be involved in SNI1-mediated repression. Sequence comparison with orthologs in other plant species and a saturating NAAIRS-scanning mutagenesis of SNM identified regions in SNM that are required for its activity. The structural similarity of SNM to Armadillo repeat proteins implies that SNM may form a scaffold for interaction with proteins that modulate transcription. © 2006 American Society of Plant Biologists.
Trujillo, J. T., Beilstein, M. A., & Mosher, R. A. (2016). The Argonaute-binding platform of NRPE1 evolves through modulation of intrinsically disordered repeats. The New Phytologist, 212(4), 1094-1105.
Argonaute (Ago) proteins are important effectors in RNA silencing pathways, but they must interact with other machinery to trigger silencing. Ago hooks have emerged as a conserved motif responsible for interaction with Ago proteins, but little is known about the sequence surrounding Ago hooks that must restrict or enable interaction with specific Argonautes. Here we investigated the evolutionary dynamics of an Ago-binding platform in NRPE1, the largest subunit of RNA polymerase V. We compared NRPE1 sequences from > 50 species, including dense sampling of two plant lineages. This study demonstrates that the Ago-binding platform of NRPE1 retains Ago hooks, intrinsic disorder, and repetitive character while being highly labile at the sequence level. We reveal that loss of sequence conservation is the result of relaxed selection and frequent expansions and contractions of tandem repeat arrays. These factors allow a complete restructuring of the Ago-binding platform over 50-60 million yr. This evolutionary pattern is also detected in a second Ago-binding platform, suggesting it is a general mechanism. The presence of labile repeat arrays in all analyzed NRPE1 Ago-binding platforms indicates that selection maintains repetitive character, potentially to retain the ability to rapidly restructure the Ago-binding platform.
