Rebecca A Mosher

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.

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).

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.

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.