Biology subjects

Grover, J. W.

Publications and source records attributed to Grover, J. W..

5 recordsLinked to original sources

bioRxiv2021

Ovule siRNAs methylate and silence protein-coding genes in trans

24-nt small interfering siRNAs maintain asymmetric DNA methylation at thousands of euchromatic transposable elements in plant genomes in a process call RNA-directed DNA Methylation (RdDM). RdDM is dispensable for growth and development in Arabidopsis, but is required for reproduction in other plant species, such as Brassica rapa. 24-nt siRNAs are particularly abundant in maternal reproductive tissue, due largely to overwhelming expression from a small number of loci in the ovule and developing seed coat, termed siren loci. Recently it was shown that abundantly expressed 24-nt siRNAs produced in the tapetal tissue of anthers can methylate male meiocyte genes in trans (Long et al., 2021). Here we show that 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 the CLSY3 putative chromatin remodeller. This research describes a new mechanism whereby RdDM influences gene expression and sheds light on the role of RdDM during plant reproduction.

plant biology↗

bioRxiv2021

Repeated administration of 2-hydroxypropyl-β-cyclodextrin (HPβCD) attenuates the chronic inflammatory response to experimental stroke

Globally, more than 67 million people are living with the effects of ischemic stroke. Importantly, many stroke survivors develop a chronic inflammatory response that may contribute to cognitive impairment, a common and debilitating sequela of stroke that is insufficiently studied and currently untreatable. 2-hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) is an FDA-approved cyclic oligosaccharide that can solubilize and entrap lipophilic substances. The goal of the present study was to determine whether the repeated administration of HP{beta}CD curtails the chronic inflammatory response to stroke by reducing lipid accumulation within stroke infarcts in a distal middle cerebral artery occlusion mouse model of stroke. To achieve this goal, we subcutaneously injected young adult and aged male mice with vehicle or HP{beta}CD three times per week, with treatment beginning one week after stroke. We evaluated mice at 7 weeks following stroke using immunostaining, RNA sequencing, lipidomics, and behavioral analyses. Chronic stroke infarct and peri-infarct regions of HP{beta}CD-treated mice were characterized by an upregulation of genes involved in lipid metabolism and a downregulation of genes involved in innate and adaptive immunity, reactive astrogliosis, and chemotaxis. Correspondingly, HP{beta}CD reduced the accumulation of lipid droplets, T lymphocytes, B lymphocytes, and plasma cells in stroke infarcts. Repeated administration of HP{beta}CD also preserved NeuN immunoreactivity in the striatum and thalamus and c-Fos immunoreactivity in hippocampal regions. Additionally, HP{beta}CD improved recovery through the protection of hippocampal-dependent spatial working memory and reduction of impulsivity. These results indicate that systemic HP{beta}CD treatment following stroke attenuates chronic inflammation and secondary neurodegeneration and prevents post-stroke cognitive decline. Significance StatementDementia is a common and debilitating sequela of stroke. Currently, there are no available treatments for post-stroke dementia. Our study shows that lipid metabolism is disrupted in chronic stroke infarcts, which causes an accumulation of uncleared lipid debris and correlates with a chronic inflammatory response. To our knowledge, these substantial changes in lipid homeostasis have not been previously recognized or investigated in the context of ischemic stroke. We also provide a proof of principle that solubilizing and entrapping lipophilic substances using HP{beta}CD could be an effective strategy for treating chronic inflammation after stroke and other CNS injuries. We propose that using HP{beta}CD for the prevention of post-stroke dementia could improve recovery and increase long-term quality of life in stroke sufferers.

neuroscience↗

bioRxiv2020

Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa

BackgroundRNA directed DNA methylation (RdDM) initiates cytosine methylation in all contexts, and maintains asymmetric CHH methylation (where H is any base other than G). 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 whether embryo hypermethylation is autonomously regulated by the embryo itself or influenced by the maternal sporophyte. ResultsHere, we demonstrate that B. rapa embryos are hypermethylated in both euchromatin and heterochromatin and that this process requires RdDM. Contrary to current models, B. rapa embryo hypermethylation is not correlated with demethylation of the endosperm. We also show that maternal somatic RdDM is not sufficient for global embryo hypermethylation, and we find no compelling evidence for maternal somatic influence over embryo methylation at any locus. Decoupling of maternal and zygotic RdDM leads to successful seed development despite loss of embryo CHH hypermethylation. ConclusionsWe conclude that embryo CHH hypermethylation is conserved, autonomously controlled, and not required for embryo development. Furthermore, maternal somatic RdDM, while required for seed development, does not directly influence embryo methylation patterns.

plant biology↗

bioRxiv2019

Abundant expression of maternal siRNAs is a conserved feature of seed development

Small RNAs are abundant in plant reproductive tissues, especially 24-nt short interfering (si)RNAs. Most 24-nt siRNAs are dependent on RNA Pol IV and RDR2, and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa, 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 B. rapa 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. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/866806v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@68de55org.highwire.dtl.DTLVardef@dca8eaorg.highwire.dtl.DTLVardef@d5d489org.highwire.dtl.DTLVardef@74824a_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2017

CoGe LoadExp+: A web-based suite that integrates next-gen sequencing data analysis workflows and visualization

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 CoGes existing features, all analyses are available for visualization and additional downstream processing, and are available for export to CyVerses data management and analysis platforms. LoadExp+ provides easy-to-use functionality to manage genomics and epigenomics data throughout its entire lifecycle and facilitates greater accessibility of genomics analyses to researchers of all skill levels. LoadExp+ can be accessed at https://genomevolution.org.

bioinformatics↗