Rebecca A Mosher
- Associate Professor, Plant Sciences
- Assistant Professor, Applied BioSciences - GIDP
- Assistant Professor, Genetics - GIDP
- Ph.D. Genetics and Genomics
- Duke University, Durham, North Carolina, United States
- B.S. Biochemistry and Molecular and Cellular Biology
- The University of Arizona, Tucson, Arizona, United States
- Postdoctoral Fellow, The University of Cambridge (2008 - 2010)
- Postdoctoral Fellow, The Sainsbury Laboratory (2005 - 2008)
- The Bart Cardon Early Career Faculty Teaching Award
- CALS, Fall 2014
Epigenetics, plant reproductive development, small RNA, DNA methylation
Directed ResearchBIOC 392 (Fall 2016)
DissertationMCB 920 (Fall 2016)
DissertationPLS 920 (Fall 2016)
Lab Presentations & DiscussionMCB 696A (Fall 2016)
ResearchMCB 900 (Fall 2016)
ResearchPLS 900 (Fall 2016)
DissertationPLS 920 (Spring 2016)
Independent StudyPLS 499 (Spring 2016)
Introduction to ResearchMCB 795A (Spring 2016)
Lab Presentations & DiscussionMCB 696A (Spring 2016)
Plant Growth and PhysiologyMCB 360 (Spring 2016)
Plant Growth and PhysiologyPLS 360 (Spring 2016)
ResearchMCB 900 (Spring 2016)
ResearchPLS 900 (Spring 2016)
DissertationPLS 920 (Fall 2015)
Independent StudyPLS 499 (Fall 2015)
Lab Presentations & DiscussionMCB 696A (Fall 2015)
ResearchMCB 900 (Fall 2015)
ResearchPLS 900 (Fall 2015)
Directed RsrchMCB 492 (Spring 2015)
Master's ReportABS 909 (Spring 2015)
Plant Growth and PhysiologyMCB 360 (Spring 2015)
Plant Growth and PhysiologyPLS 360 (Spring 2015)
ResearchPLS 900 (Spring 2015)
Independent StudyPLS 399 (Fall 2014)
Introduction to ResearchMCB 795A (Fall 2014)
ResearchPLS 900 (Fall 2014)
Plant Growth and PhysiologyMCB 360 (Spring 2014)
Plant Growth and PhysiologyPLS 360 (Spring 2014)
ResearchPLS 900 (Spring 2014)
ResearchPLS 900 (Fall 2013)
- Mosher, R. (2011). Pol IV-dependent siRNAs in Plants. In Non-coding RNAs in Plants. Springer-Verla.More infoEditor(s): Erdmann, VA | Barciszewsk, J
- 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.More infoArgonaute (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.
- Gohlke, J., & Mosher, R. A. (2015). Exploiting mobile RNA silencing for crop improvement. American Journal of Botany (review article), 102(9), 1399-400. doi:10.3732/ajb.1500173
- Huang, Y., Kendall, T., Forsythe, E. S., Dorantes-Acosta, A., Li, S., Caballero-Pérez, J., Chen, X., Arteaga-Vázquez, M., Beilstein, M. A., & Mosher, R. A. (2015). Ancient Origin and Recent Innovations of RNA Polymerase IV and V. Molecular biology and evolution, 32(7), 1788-99. doi:10.1093/molbev/msv060More infoSmall RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highly in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.
- Matzke, M. A., & Mosher, R. A. (2014). RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Reviews Genetics (review article), 15(6), 394-408.More infoCorresponding authors: RAM and MAM
- Mosher, R. A. (2014). An Interview with Rebecca Mosher (review article). Trends in Plant Science.
- Huang, Y., Kendall, T., & Mosher, R. A. (2013). Pol IV-Dependent siRNA Production is Reduced in Brassica rapa. Biology, 2(4), 1210-1223.
- Mosher, R. A. (2012). Pinpointing a puzzling polymerase. Nature Structural and Molecular Biology, 19(9), 865-866.More infoPMID: 22955933;
- Mosher, R. A., & Mosher, R. A. (2012). Pinpointing a puzzling polymerase. Nature Structural & Molecular Biology (Review Article), 19(9).
- Mosher, R. A., Tan, E. H., Shin, J., Fischer, R. L., Pikaard, C. S., & Baulcombe, D. C. (2011). An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent sirnas. PLoS ONE, 6(10).More infoPMID: 22003406;PMCID: PMC3189211;Abstract: Background: Small RNAs generated by RNA polymerase IV (Pol IV) are the most abundant class of small RNAs in flowering plants. In Arabidopsis thaliana Pol IV-dependent short interfering (p4-si)RNAs are imprinted and accumulate specifically from maternal chromosomes in the developing seeds. Imprinted expression of protein-coding genes is controlled by differential DNA or histone methylation placed in gametes. To identify epigenetic factors required for maternal-specific expression of p4-siRNAs we analyzed the effect of a series of candidate mutations, including those required for genomic imprinting of protein-coding genes, on uniparental expression of a representative p4-siRNA locus. Results: Paternal alleles of imprinted genes are marked by DNA or histone methylation placed by DNA METHYLTRANSFERASE 1 or the Polycomb Repressive Complex 2. Here we demonstrate that repression of paternal p4-siRNA expression at locus 08002 is not controlled by either of these mechanisms. Similarly, loss of several chromatin modification enzymes, including a histone acetyltransferase, a histone methyltransferase, and two nucleosome remodeling proteins, does not affect maternal expression of locus 08002. Maternal alleles of imprinted genes are hypomethylated by DEMETER DNA glycosylase, yet expression of p4-siRNAs occurs irrespective of demethylation by DEMETER or related glycosylases. Conclusions: Differential DNA methylation and other chromatin modifications associated with epigenetic silencing are not required for maternal-specific expression of p4-siRNAs at locus 08002. These data indicate that there is an as yet unknown epigenetic mechanism causing maternal-specific p4-siRNA expression that is distinct from the well-characterized mechanisms associated with DNA methylation or the Polycomb Repressive Complex 2. © 2011 Mosher et al.
- Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., Young, S. K., Furuya, K., Guo, Y., Pidoux, A., Chen, H. M., Robbertse, B., Goldberg, J. M., Aoki, K., Bayne, E. H., , Berlin, A. M., et al. (2011). Comparative functional genomics of the fission yeasts. Science, 332(6032), 930-936.More infoPMID: 21511999;PMCID: PMC3131103;Abstract: The fission yeast clade - comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus - occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
- Mosher, R. A. (2010). Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm. New Phytologist, 186(2), 358-364.More infoPMID: 20074090;Abstract: Small RNAs recently emerged as ubiquitous regulators of gene expression. However, the most abundant class of small RNAs in flowering plants is poorly understood. Known as Pol IV-dependent (p4-)siRNAs, these small RNAs are associated with transcriptional gene silencing, transposable elements and heterochromatin formation. Recent research demonstrates that they are initially expressed in the maternal gametophyte and uniparentally expressed from maternal chromosomes in developing endosperm. This unique expression pattern links p4-siRNAs to double fertilization, parental genome interactions and imprinted gene expression. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).
- Mosher, R. A., & Melnyk, C. W. (2010). siRNAs and DNA methylation: seedy epigenetics. Trends in Plant Science, 15(4), 204-210.More infoPMID: 20129810;Abstract: To understand how DNA sequence is translated to phenotype we must understand the epigenetic features that regulate gene expression. Recent research illuminates the complex interactions between DNA methylation, small RNAs, silencing of transposable elements, and genomic imprinting in the Arabidopsis (Arabidopsis thaliana) seed. These studies suggest that transposable elements reactivated in specific cells of the gametophyte and seed might enhance silencing of transposable elements in the germline and embryo. By sacrificing genomic integrity these cells might make an epigenetic rather than genetic contribution to the progeny. This research could have implications for interspecies hybridization, the evolution of genomic imprinting, and epigenetic communication from plant to progeny. © 2010 Elsevier Ltd. All rights reserved.
- Djupedal, I., Kos-Braun, I. C., Mosher, R. A., Söderholm, N., Simmer, F., Hardcastle, T. J., Fender, A., Heidrich, N., Kagansky, A., Bayne, E., Gerhart, E., Baulcombe, D. C., Allshire, R. C., & Ekwall, K. (2009). Analysis of small RNA in fission yeast; Centromeric siRNAs are potentially generated through a structured RNA. EMBO Journal, 28(24), 3832-3844.More infoPMID: 19942857;PMCID: PMC2797062;Abstract: formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 5′-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1Δ cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. © 2009 European Molecular Biology Organization.
- Mosher, R. A., Melnyk, C. W., Kelly, K. A., Dunn, R. M., Studholme, D. J., & Baulcombe, D. C. (2009). Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature, 460(7252), 283-286.More infoPMID: 19494814;Abstract: Most eukaryotes produce small RNA (sRNA) mediators of gene silencing that bind to Argonaute proteins and guide them, by base pairing, to an RNA target. MicroRNAs (miRNAs) that normally target messenger RNAs for degradation or translational arrest are the best-understood class of sRNAs. However, in Arabidopsis thaliana flowers, miRNAs account for only 5% of the sRNA mass and less than 0.1% of the sequence complexity. The remaining sRNAs form a complex population of more than 100,000 different small interfering RNAs (siRNAs) transcribed from thousands of loci. The biogenesis of most of the siRNAs in Arabidopsis are dependent on RNA polymerase IV (PolIV), a homologue of DNA-dependent RNA polymerase II. A subset of these PolIV-dependent (p4)-siRNAs are involved in stress responses, and others are associated with epigenetic modifications to DNA or chromatin; however, the biological role is not known for most of them. Here we show that the predominant phase of p4-siRNA accumulation is initiated in the maternal gametophyte and continues during seed development. Expression of p4-siRNAs in developing endosperm is specifically from maternal chromosomes. Our results provide the first evidence for a link between genomic imprinting and RNA silencing in plants. © 2009 Macmillan Publishers Limited. All rights reserved.
- Mosher, R. A., & Baulcombe, D. C. (2008). Bacterial pathogens encode suppressors of RNA-mediated silencing.. Genome biology, 9(10), 237-.More infoPMID: 18947381;PMCID: PMC2760867;Abstract: Plant pathogenic bacteria encounter host defenses mediated by a variety of small RNAs. Bacterial suppressors of silencing that inhibit multiple steps of plant microRNA biogenesis and function have recently been identified.
- Mosher, R. A., Schwach, F., Studholme, D., & Baulcombe, D. C. (2008). PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proceedings of the National Academy of Sciences of the United States of America, 105(8), 3145-3150.More infoPMID: 18287047;PMCID: PMC2268599;Abstract: DNA-dependent RNA polymerase (Pol)IV in Arabidopsis exists in two isoforms (PolIVa and PolIVb), with NRPD1a and NRPD1b as their respective largest subunits. Both isoforms are implicated in production and activity of siRNAs and in RNA-directed DNA methylation (RdDM). Deep sequence analysis of siRNAs in WT Arabidopsis flowers and in nrpd1a and nrpd1b mutants identified >4,200 loci producing siRNAs in a PolIV-dependent manner, with PolIVb reinforcing siRNA production by PolIVa. Transposable element identity and pericentromeric localization are both features that predispose a locus for siRNA production via PolIV proteins and determine the extent to which siRNA production relies on PolIVb. Detailed analysis of DNA methylation at PolIV-dependent loci revealed unexpected deviations from the previously noted association of PolIVb-dependent siRNA production and RdDM. Notably, PolIVb functions independently in DNA methylation and siRNA generation. Additionally, we have uncovered siRNA-directed loss of DNA methylation, a process requiring both PolIV isoforms. From these findings, we infer that the role of PolIVb in siRNA production is secondary to a role in chromatin modification and is influenced by chromatin context. © 2008 by The National Academy of Sciences of the USA.
- 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.More infoPMID: 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.More infoPMID: 17447904;
- 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.More infoPMID: 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.
- Grover, J. W., Bomhoff, M., Davey, S., Gregory, B. D., Mosher, R. A., & Lyons, E. H. (2017, January). User-Friendly Whole Genome DNA Methylation Analysis With FlowGE. Plant and Animal Genomes Conference XXV, Invited seminar. San Diego, CA, USA.
- Grover, J. W., Gohlke, J., Chen, W., Kendall, T., & Mosher, R. A. (2017, January). Dynamic nucleocytoplasmic trafficking of ARGONAUTE 4 enables RNA-directed DNA methylation. Plant and Animal Genomes Conference XXV, Invited seminar. San Diego, CA, USA.
- Mosher, R. A. (2016, June). The Argonaute-binding platform of NRPE1 Evolves through Modulation of Intrinsically Disordered Repeats. Odd Pols 2016: International Conference on Transcription by RNA Polymerases I, III, IV, and V, Invited seminar. Ann Arbor, MI, USA.
- Mosher, R. A. (2015, December). RNA Polymerase V – the Evolution of an Argonaute-binding domain. Invited seminar at Department of Plant & Microbial Biology, The University of California Berkeley.
- Mosher, R. A. (2015, February). Polymerase IV and V: The Rise of Silencing in Plants. Keystone Symposium on RNA Silencing in Plants, invited plenary talk. Keystone, CO, USA.
- Mosher, R. A. (2015, May). RNA Polymerase IV and V: Understanding the Rise of Silencing in Plants.. Invited seminar at The John Innes Centre. Norwich, UK.
- Mosher, R. A. (2015, May). RNA Polymerase IV and V: Understanding the Rise of Silencing in Plants. Invited seminar at The University of Cambridge Department of Plant Sciences/The Sainsbury Laboratory Cambridge. Cambridge, UK.
- Mosher, R. A. (2014, Sept). RNA Polymerase IV and V: The Rise of Silencing in Plants. Congreso Nacional de Genetica, invited plenary speaker. Xalapa, Mexico.
- Mosher, R. A. (2012). Oral presentation. 1st International Symposium/ Course on Epigenetics and Developmental Biology. Xalapa, Mexico.
- Mosher, R. A. (2012). Research seminar. Bilateral Shennong Center Symposium. Tucson, AZ.
- Mosher, R. A. (2012). Research seminar. USDA Plant Gene Expression Center Seminar. Albany, CA: USDA Plant Gene Expression Center.
- Mosher, R. A. (2011). Oral presentation at the Cold Spring Harbor/Pioneer-DuPont Collaboration meeting. Cold Spring Harbor/Pioneer-DuPont Collaboration meeting. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
- Mosher, R. A. (2011). Oral presentation at the Gordon Conference on Epigenetics. Gordon Conference on Epigenetics. Easton, MA.
- Mosher, R. A. (2011). Oral presentation in a plenary session. International Conference on Arabidopsis Research. Madison, WI.
- Mosher, R. A. (2011). Postdoc Career Event. University of Cambridge Long Term Academic Careers Event.More infoInternet/intranet
- Mosher, R. A. (2011). Research seminar in the UC Riverside Botany & Plant Sciences Graduate Seminar (BPS 250). UC Riverside Botany & Plant Sciences Graduate Seminar. Riverside, CA.
- Trujillo, J. T., Beilstein, M. A., & Mosher, R. A. (2016, June). The Argonaute-binding platform of NRPE1 Evolves through Modulation of Intrinsically Disordered Repeats. Odd Pols 2016: International Conference on Transcription by RNA Polymerases I, III, IV, and V. Ann Arbor, MI, USA.
- Wang, Y., Tsukamoto, T., Liu, X., Noble, J., Harris, R. A., & Palanivelu, R. (2015, January). A growth-promoting role for Arabidopsis LORELEI, a maternally expressed imprinted gene, in early seed development. School of Plant Sciences Research Retreat. Tucson, Arizona: School of Plant Sciences.
- Wang, Y., Tsukamoto, T., Liu, X., Noble, J., Harris, R. A., & Palanivelu, R. (2015, July). A growth-promoting role for Arabidopsis LORELEI, a maternally expressed imprinted gene, in early seed development. 5th Annual meeting of Pollen Research Coordination Network. University of Minneapolis, Minnesota: Pollen RCN.
- Mosher, R. A. (2014, Oct). RNA Polymerase IV and V: The Rise of Silencing in Plants. Invited seminar at Duke University Department of Biology.
- Mosher, R. A. (2012, June). Cold Spring Harbor Symposium on Plant Biology. Not Provided in APROL. Cold Spring Harbor Laboratory.