Rebecca A Mosher

Interests

Research

Epigenetics, plant reproductive development, small RNA, DNA methylation

Courses

Scholarly Contributions

Chapters

• Trujillo, J. T., & Mosher, R. A. (2017). Identification and Evolutionary Characterization of ARGONAUTE-Binding Platforms. In Plant Argonaute Proteins: Methods and Protocols(pp 257-266). Springer New York.
• Mosher, R. (2011). Pol IV-dependent siRNAs in Plants. In Non-coding RNAs in Plants. Springer-Verla.
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  Editor(s): Erdmann, VA | Barciszewsk, J

Journals/Publications

• Chow, H. T., & Mosher, R. A. (2023). Mapping a mutation causing pale yellow petals in. microPublication biology, 2023.
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  Petal color is an important trait for both ornamental purposes and also for attracting pollinators. Here, we report a mutation of R-o-18 with pale yellow petals that we retrieved from an EMS population and named ( ). Phenotypic segregation ratio of an F2 mapping population indicates the phenotype is controlled by a single recessive gene. Mapping data from the whole genome sequencing coupled with allele frequency analysis suggests the mutation is located in a ~2 Mbp interval on chromosome 2. The interval contains a putative esterase/lipase/thioesterase protein previously demonstrated to account for floral color in . We demonstrate that carries a G to A missense mutation causing an aspartate to asparagine substitution within the putative lysophospholipid acyltransferase domain.
• Chow, H. T., Kendall, T., & Mosher, R. A. (2023). A novel CLAVATA1 mutation causes multilocularity in. Plant direct, 7(1), e476.
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  Locules are the seed-bearing structure of fruits. Multiple locules are associated with increased fruit size and seed set, and therefore, control of locule number is an important agronomic trait. Locule number is controlled in part by the CLAVATA-WUSCHEL pathway. Disruption of either the CLAVATA1 receptor-like kinase or its ligand CLAVATA3 can cause larger floral meristems and an increased number of locules. In an EMS mutagenized population of , we identified a mutant allele that raises the number of locules from four to a range of from six to eight. Linkage mapping and genetic analysis support that the mutant phenotype is due to a missense mutation in a () homolog. In addition to increased locule number, additional internal gynoecia are formed in individuals, suggesting a failure to terminate floral meristem development, which results in decreased seed production.
• Dew-Budd, K. J., Chow, H. T., Kendall, T., David, B. C., Rozelle, J. A., Mosher, R. A., & Beilstein, M. A. (2023). Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. Plant physiology.
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  In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally-derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes in Arabidopsis (Arabidopsis thaliana), where the pathway has been most thoroughly studied. In contrast, Brassica rapa mutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in three additional members of the Brassicaceae family: Camelina sativa, Capsella rubella, and Capsella grandiflora. Among these three species, only mutations in the obligate outcrosser, C. grandiflora, displayed a seed production defect similar to Brassica rapa mutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
• Eckardt, N. A., Axtell, M. J., Barta, A., Chen, X., Gregory, B. D., Guo, H., Manavella, P. A., Mosher, R. A., & Meyers, B. C. (2023). Focus on RNA biology. The Plant cell, 35(6), 1617-1618.
• Hari Sundar G, V., Swetha, C., Basu, D., Pachamuthu, K., Raju, S., Chakraborty, T., Mosher, R. A., & Shivaprasad, P. V. (2023). Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. Genome research, 33(5), 715-728.
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  Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative heterochromatic marks in protein-coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein-coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger genome with distributed heterochromatin compared with Our results indicate the division of labor among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation but also in influencing chromatin boundaries.
• Burgess, D., Chow, H. T., Grover, J. W., Freeling, M., & Mosher, R. A. (2022). Ovule siRNAs methylate protein-coding genes in trans. The Plant cell, 34(10), 3647-3664.
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  Twenty-four-nucleotide (nt) small interfering RNAs (siRNAs) maintain asymmetric DNA methylation at thousands of euchromatic transposable elements in plant genomes in a process called RNA-directed DNA methylation (RdDM). RdDM is dispensable for growth and development in Arabidopsis thaliana, but is required for reproduction in other plants, such as Brassica rapa. The 24-nt siRNAs are abundant in maternal reproductive tissue, due largely to overwhelming expression from a few loci in the ovule and developing seed coat, termed siren loci. A recent study showed that 24-nt siRNAs produced in the anther tapetal tissue can methylate male meiocyte genes in trans. Here we show that in B. rapa, a similar process takes place in female tissue. siRNAs are produced from gene fragments embedded in some siren loci, and these siRNAs can trigger methylation in trans at related protein-coding genes. This trans-methylation is associated with silencing of some target genes and may be responsible for seed abortion in RdDM mutants. Furthermore, we demonstrate that a consensus sequence in at least two families of DNA transposons is associated with abundant siren expression, most likely through recruitment of CLASSY3, a putative chromatin remodeler. This research describes a mechanism whereby RdDM influences gene expression and sheds light on the role of RdDM during plant reproduction.
• Chakraborty, T., Payne, H., & Mosher, R. A. (2022). Expansion and contraction of small RNA and methylation machinery throughout plant evolution. Current opinion in plant biology, 69, 102260.
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  The revolution in sequencing has created a wealth of plant genomes that can be mined to understand the evolution of biological complexity. Complexity is often driven by gene duplication, which allows paralogs to specialize in an activity of the ancestral gene or acquire novel functions. Angiosperms encode a variety of gene silencing pathways that share related machinery for small RNA biosynthesis and function. Recent phylogenetic analysis of these gene families plots the expansion, specialization, and occasional contraction of this core machinery. This analysis reveals the ancient origin of RNA-directed DNA Methylation in early land plants, or possibly their algal ancestors, as well as ongoing duplications that evolve novel small RNA pathways.
• Chakraborty, T., Trujillo, J. T., Kendall, T., & Mosher, R. A. (2022). A null allele of the pol IV second subunit impacts stature and reproductive development in Oryza sativa. The Plant journal : for cell and molecular biology, 111(3), 748-755.
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  All eukaryotes possess three DNA-dependent RNA polymerases, Pols I-III, while land plants possess two additional polymerases, Pol IV and Pol V. Derived through duplication of Pol II subunits, Pol IV produces 24-nt short interfering RNAs that interact with Pol V transcripts to target de novo DNA methylation and silence transcription of transposons. Members of the grass family encode additional duplicated subunits of Pol IV and V, raising questions regarding the function of each paralog. In this study, we identify a null allele of the putative Pol IV second subunit, NRPD2, and demonstrate that NRPD2 is the sole subunit functioning with NRPD1 in small RNA production and CHH methylation in leaves. Homozygous nrpd2 mutants have neither gametophytic defects nor embryo lethality, although adult plants are dwarf and sterile.
• Schmitz, R. J., Marand, A. P., Zhang, X., Mosher, R. A., Turck, F., Chen, X., Axtell, M. J., Zhong, X., Brady, S. M., Megraw, M., & Meyers, B. C. (2022). Quality control and evaluation of plant epigenomics data. The Plant cell, 34(1), 503-513.
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  Epigenomics is the study of molecular signatures associated with discrete regions within genomes, many of which are important for a wide range of nuclear processes. The ability to profile the epigenomic landscape associated with genes, repetitive regions, transposons, transcription, differential expression, cis-regulatory elements, and 3D chromatin interactions has vastly improved our understanding of plant genomes. However, many epigenomic and single-cell genomic assays are challenging to perform in plants, leading to a wide range of data quality issues; thus, the data require rigorous evaluation prior to downstream analyses and interpretation. In this commentary, we provide considerations for the evaluation of plant epigenomics and single-cell genomics data quality with the aim of improving the quality and utility of studies using those data across diverse plant species.
• Chakraborty, T., Kendall, T., Grover, J. W., & Mosher, R. A. (2021). Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa. Genome biology, 22(1), 140.
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  RNA-directed DNA methylation (RdDM) initiates cytosine methylation in all contexts and maintains asymmetric CHH methylation. Mature plant embryos show one of the highest levels of CHH methylation, and it has been suggested that RdDM is responsible for this hypermethylation. Because loss of RdDM in Brassica rapa causes seed abortion, embryo methylation might play a role in seed development. RdDM is required in the maternal sporophyte, suggesting that small RNAs from the maternal sporophyte might translocate to the developing embryo, triggering DNA methylation that prevents seed abortion. This raises the question of whether embryo hypermethylation is autonomously regulated by the embryo itself or influenced by the maternal sporophyte.
• Mosher, R. A. (2021). Small RNAs on the move in male germ cells. Science (New York, N.Y.), 373(6550), 26-27.
• Sundar, V. H., Swetha, C., Basu, D., Pachamuthu, K., Chakraborty, T., Mosher, R., & Shivaprasad, P. V. (2021). Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. bioRxiv.
• Chakraborty, T., Kendall, T., Grover, J. W., & Mosher, R. A. (2020). Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa. BioRxiv.
• Chow, H. T., Chow, H. T., Chakraborty, T., & Mosher, R. A. (2020). RNA-directed DNA Methylation and sexual reproduction: expanding beyond the seed.. Current Opinion in Plant Biology, 54, 11-17. doi:10.1016/j.pbi.2019.11.006
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  Two trends are changing our understanding of RNA-directed DNA methylation. In model systems like Arabidopsis, tissue-specific analysis of DNA methylation is uncovering dynamic changes in methylation during sexual reproduction and unraveling the contribution of maternal and paternal epigenomes to the developing embryo. These studies indicate that RNA-directed DNA Methylation might be important for mediating balance between maternal and paternal contributions to the endosperm. At the same time, researchers are moving beyond Arabidopsis to illuminate the ancestral role of RdDM in non-flowering plants that lack an endosperm, suggesting that RdDM might play a broader role in sexual reproduction.
• Grover, J. W., Burgess, D., Kendall, T., Baten, A., Pokhrel, S., King, G. J., Meyers, B. C., Freeling, M., & Mosher, R. A. (2020). Abundant expression of maternal siRNAs is a conserved feature of seed development. Proceedings of the National Academy of Sciences of the United States of America, 117(26), 15305-15315.
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  Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In , RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.
• Chow, H. T., Chakraborty, T., & Mosher, R. A. (2019). RNA-directed DNA Methylation and sexual reproduction: expanding beyond the seed. Current opinion in plant biology, 54, 11-17.
• Kirkbride, R. C., Lu, J., Zhang, C., Mosher, R. A., Baulcombe, D. C., & Chen, Z. J. (2019). Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in. Proceedings of the National Academy of Sciences of the United States of America, 116(7), 2761-2766.
• Grover, J. W., Kendall, T., Baten, A., Burgess, D., Freeling, M., King, G. J., & Mosher, R. A. (2018). Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa. The Plant journal : for cell and molecular biology, 94(4), 575-582.
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  Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV-dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.
• Trujillo, J. T., Seetharam, A. S., Hufford, M. B., Beilstein, M. A., & Mosher, R. A. (2018). Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. Molecular biology and evolution, 35(10), 2454-2462.
• Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., Nakamura, Y., Berger, F., Adam, C., Aki, S. S., Althoff, F., Araki, T., Arteaga-Vazquez, M. A., Balasubrmanian, S., Barry, K., Bauer, D., Boehm, C. R., , Briginshaw, L., et al. (2017). Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell, 171(2), 287-304.e15.
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  The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.
• 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).
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  To make genomic and epigenomic analyses more widely available to the biological research community, we have created LoadExp+, a suite of bioinformatics workflows integrated with the web-based comparative genomics platform, CoGe. LoadExp+ allows users to perform transcriptomic (RNA-seq), epigenomic (bisulfite-seq), chromatin-binding (ChIP-seq), variant identification (SNPs), and population genetics analyses against any genome in CoGe, including genomes integrated by users themselves. Through LoadExp+'s integration with CoGe's existing features, all analyses are available for visualization and additional downstream processing, and are available for export to CyVerse's data management and analysis platforms. LoadExp+ provides easy-to-use functionality to manage genomics and epigenomics data throughout its entire lifecycle using a publicly available web-based platform and facilitates greater accessibility of genomics analyses to researchers of all skill levels. LoadExp+ can be accessed at https://genomevolution.org.
• Trujillo, J. T., & Mosher, R. A. (2017). Identification and Evolutionary Characterization of ARGONAUTE-Binding Platforms. Methods in molecular biology (Clifton, N.J.), 1640, 257-266.
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  ARGONAUTE (AGO) proteins are eukaryotic RNA silencing effectors that interact with their binding partners via short peptide motifs known as AGO hooks. AGO hooks tend to cluster in one region of the protein to create an AGO-binding platform. In addition to the presence of AGO hooks, AGO-binding platforms are intrinsically disordered, contain tandem repeat arrays, and have weak sequence conservation even between close relatives. These characteristics make it difficult to identify and perform evolutionary analysis of these regions. Because of their weak sequence conservation, only a few AGO-binding platforms are characterized, and the evolution of these regions is only poorly understood. In this chapter we describe modules developed for computational identification and evolutionary analysis of AGO-binding platforms, with particular emphasis on understanding evolution of the tandem repeat arrays.
• Wang, Y., Tsukamoto, T., Noble, J. A., Liu, X., Mosher, R. A., & Palanivelu, R. (2017). Arabidopsis LORELEI, a Maternally Expressed Imprinted Gene, Promotes Early Seed Development. Plant physiology, 175(2), 758-773.
• 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.
• 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/msv060
• 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.
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  Corresponding 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 & 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).
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  PMID: 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.
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  PMID: 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.
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  PMID: 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.
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  PMID: 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.
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  PMID: 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.
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  PMID: 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-.
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  PMID: 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.
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  PMID: 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.
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  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.
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  PMID: 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.
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  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.

Presentations

• Mosher, R. A. (2022, April). RNA-directed DNA Methylation: a maternal influence during seed development.. John Innes Centre seminar. Norwich, UK.
• Mosher, R. A. (2022, August). Modeling RNA-directed DNA Methylation
  . Find Your Inner Modeller IV conference, project presentation. Chicago, IL.
• Mosher, R. A. (2022, March). RNA-directed DNA Methylation: a maternal influence during seed development.. Imperial College London Department of Life Sciences seminar. virtual.
• Mosher, R. A. (2022, March). RNA-directed DNA Methylation: a maternal influence during seed development.. Iowa State University Department of Genetics, Development, and Cell Biology seminar. Ames, IA.
• Mosher, R. A. (2022, May). RNA-directed DNA Methylation: a maternal influence during seed development.. 23rd Penn State Symposium in Plant Biology. College Park, PA.
• Mosher, R. A. (2022, May). RNA-directed DNA Methylation: a maternal influence during seed development.. Oxford Department of Biology seminar. virtual.
• Mosher, R. A. (2020, January). Using orthologous mutations to understand the role of RNA-directed DNA Methylation during seed development. Oral presentation at the Plant and Animal Genomes Conference XXVIII (Comparative Genomics session).
• Mosher, R. A. (2019, August). Evolution of RNA Polymerases in Plants.. Invited presentation at the 3rd Annual Arizona RNA Salon Symposium.
• Mosher, R. A. (2019, August). Evolution of RNA Polymerases in plants: understanding duplication of multi-subunit complexes.. Invited seminar at Department of Genetics, University of Georgia; Athens, GA, USA.
• Mosher, R. A. (2019, January). Using Brassica rapa to understand epigenetic dynamics in the seed. Oral presentation at the Plant and Animal Genomes Conference XXVII (Brassica session).
• Mosher, R. A. (2019, June). Origin of “plant-specific” polymerases in Charophycean algae.. Oral presentation at "Algal model systems on the rise: Understanding and exploiting the algae to land plant transition" (SEB satellite meeting); Seville, Spain.
• Mosher, R. A. (2019, November). RNA-directed DNA Methylation during seed development.. Invited seminar at Plant Biology Graduate Seminar, University of California; Davis, CA, USA.
• Mosher, R. A. (2019, September). RNA-directed DNA methylation: evolution and roles in reproduction.. School of Plant Sciences Departmental Seminar.
• Mosher, R. A. (2019, September). Using parallel mutations to understand the role of RNA-directed DNA Methylation during seed development.. National Science Foundation Plant Genome Research Annual Meeting.
• Mosher, R. A. (2017, Sept). Using comparative genetics to understand the role of small RNAs during reproduction. Oral presentation at the Plant Genome Research Program annual PI meeting.
• Mosher, R. A. (2018, April). RNA-directed DNA methylation: evolution and roles in reproduction.. Invited seminar at Institut de Recherche pour le Développement (IRD); Montpellier, France.
  More info

  This interactive workshop is designed to help academics scientists of all levels recognize and counter impostor thoughts to improve their happiness and success in science.
• Mosher, R. A. (2018, October). Evolution of RNA Polymerases in plants: understanding duplication of multi-subunit complexes.. Invited seminar at School of Integrated Plant Sciences, Cornell University; Ithaca, NY, USA.
• Trujillo, J. T., & Mosher, R. A. (2018, June). Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. Gordon Conference on Plant Molecular Biology.
• 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. (2017, February). RNA-directed DNA methylation: mother knows best!. Invited seminar at The Center for Molecular Agriculture, Purdue University; West Lafayette, IN.
• Mosher, R. A. (2017, June). Pol IV-dependent siRNAs from maternal somatic tissue are required for seed development.. 28th International Conference on Arabidopsis Research.
• Mosher, R. A. (2017, June). RNA-directed DNA methylation: mother knows best!. Invited seminar at The Donald Danforth Plant Science Center; St. Louis, MO.
• Mosher, R. A. (2017, June). RNA-directed DNA methylation: mother knows best!. Invited seminar at The University of Missouri Interdisciplinary Plant Group; Columbia, MO.
• Mosher, R. A. (2017, October). Evolution of RNA Polymerases in plants: understanding duplication of multi-subunit complexes. Invited seminar at The Earlham Institute; Norwich, UK.
• Mosher, R. A. (2017, October). Overcoming the Impostor Phenomenon in Academic Science. Invited seminar at Sainsbury Laboratory Cambridge University, Cambridge, UK.
  More info

  This interactive workshop is designed to help academics scientists of all levels recognize and counter impostor thoughts to improve their happiness and success in science.
• Mosher, R. A. (2017, October). Overcoming the Impostor Phenomenon in Academic Science. Invited seminar at The Swedish University of Agricultural Sciences; Uppsala, Sweden.
  More info

  This interactive workshop is designed to help academics scientists of all levels recognize and counter impostor thoughts to improve their happiness and success in science.
• Mosher, R. A. (2017, October). RNA-directed DNA methylation: mother knows best!. Invited seminar at The Linnean Centre, Swedish University of Agricultural Sciences; Uppsala, Sweden.
• Mosher, R. A. (2017, September). RNA-directed DNA methylation: mother knows best!. Invited seminar at The Department of Crop Genetics, John Innes Centre; Norwich, UK.
• Mosher, R. A. (2017, September). Using comparative genetics to understand the role of small RNAs during reproduction.. National Science Foundation Plant Genome Research Annual Meeting.
• Mosher, R. A. (2017, September). Using Brassica rapa to understand epigenetic communication during seed development.. UK-China Brassica Symposium.
• Mosher, R. A. (2016, January). The Argonaute-binding platform of NRPE1 Evolves through Modulation of Intrinsically Disordered Repeats. Plant and Animal Genomes Conference XXIV, 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. (2015, May). RNA Polymerase IV and V: Understanding the Rise of Silencing in Plants. Invited seminar at The University of Edinburgh Institute of Evolutionary Biology. Edinburgh, UK.
• 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. (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.
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  Internet/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.

Poster Presentations

• Grover, J. W., & Mosher, R. A. (2019, January). Spatiotemporal Dynamics of Small RNA Accumulation During Seed Development in Brassica rapa. Plant and Animal Genomes Conference. San Diego, CA.
• Mosher, R. A. (2019, August). Evolution of DNA-dependent RNA polymerases in plants. American Society of Plant Biology Annual Meeting. San Jose, CA: ASBP.
• Beilstein, M. A., Harris, R. A., & Dew-Budd, K. (2018, July). Identifying the genomic factors that influence the impact of RNA-directed DNA during seed development. American Society of Plant Biologists Annual Meeting (ASPB 2018). Montreal, Canada: American Society of Plant Biologists.
• Chen, W., Gohlke, J., Grover, J. W., & Mosher, R. A. (2017, June). Stabilization of AGO4 by single-stranded siRNA in Arabidopsis thaliana. 28th International Conference on Arabidopsis Research.
• Grover, J. W., Dew-Budd, K., Beilstein, M. A., & Mosher, R. A. (2017, Sept). Deciphering the link between RNA-directed DNA Methylation and reproduction in Brassicaceae. National Science Foundation Plant Genome Research Program. Washington, DC: NSF.
• Grover, J. W., Dew-Budd, K., Beilstein, M. A., & Mosher, R. A. (2018, Sept). Deciphering the link between RNA-directed DNA Methylation and reproduction in Brassicaceae. National Science Foundation Plant Genome Research Program. Washington, DC: NSF.
• Trujillo, J. T., Beilstein, M. A., & Mosher, R. A. (2017, June). Understanding molecular variation in the RNA polymerase V Ago-binding platform. 28th International Conference on Arabidopsis Research.
• 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. (2016, March). A growth-promoting role for LORELEI, a maternally expressed imprinted gene, in early seed development in Arabidopsis. Plant Reproduction 2016. Tucson, Arizona: International Association of Sexual Plant Reproduction.
• 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. (2012, June). Cold Spring Harbor Symposium on Plant Biology. Not Provided in APROL. Cold Spring Harbor Laboratory.

Reviews

• Chow, H. T., & Mosher, R. A. (2023. Small RNA-mediated DNA methylation during plant reproduction(pp 1787-1800).
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  Reproductive tissues are a rich source of small RNAs, including several classes of short interfering (si)RNAs that are restricted to this stage of development. In addition to RNA polymerase IV-dependent 24-nt siRNAs that trigger canonical RNA-directed DNA methylation, abundant reproductive-specific siRNAs are produced from companion cells adjacent to the developing germ line or zygote and may move intercellularly before inducing methylation. In some cases, these siRNAs are produced via non-canonical biosynthesis mechanisms or from sequences with little similarity to transposons. While the precise role of these siRNAs and the methylation they trigger is unclear, they have been implicated in specifying a single megaspore mother cell, silencing transposons in the male germ line, mediating parental dosage conflict to ensure proper endosperm development, hypermethylation of mature embryos, and trans-chromosomal methylation in hybrids. In this review, we summarize the current knowledge of reproductive siRNAs, including their biosynthesis, transport, and function.

Others

• Mosher, R. A. (2017, September). Combatting the Impostor Syndrome in academic science – you probably are as smart as they think!. Plantae: The American Society of Plant Biologists Blog. https://plantae.org/blog/combatting-the-impostor-syndrome-in-academic-science-you-probably-are-as-smart-as-they-think/
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  In this invited blog post I describe Imposter Syndrome and discuss a few strategies to help academics overcome feelings of imposterism.
• Mosher, R. A., & Hunter, L. (2017, February). Rethinking Mentoring – Building Peer Communities for Accountability and Support. Lo Que Pasa. https://plantae.org/blog/combatting-the-impostor-syndrome-in-academic-science-you-probably-are-as-smart-as-they-think/
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  In this short piece in the Faculty-specific issue of Lo Que Pasa, Dr. Hunter and I describe the benefits of peer mentorship for professional development of faculty.