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Ongoing research using cell transplantation and viral-mediated gene therapy has been making progress to restore vision by retinal repair, but targeted delivery and complete cellular integration remain challenging. An alternative approach is to induce endogenous Muller glia (MG) to regenerate lost neurons and photoreceptors, as occurs spontaneously in teleost fish and amphibians. Extracellular vesicles (EVs) can transfer protein and RNA cargo between cells serving as a novel means of cell-cell communication. We conducted an in vivo screen in zebrafish to identify sources of EVs that could induce MG to dedifferentiate and generate proliferating progenitor cells after intravitreal injection into otherwise undamaged zebrafish eyes. Small EVs (sEVs) from C6 glioma cells were the most consistent at inducing MG-derived proliferating cells. Ascl1a expression increased after intravitreal injection of C6 sEVs and knockdown of ascl1a inhibited the induction of proliferation. Proteomic and RNAseq analyses of EV cargo content were performed to begin to identify key factors that might target EVs to MG and initiate retina regeneration.

Proper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth., Wang et al. perform RNA-Seq on pineapple floral samples and also use previously published RNA-Seq datasets to generate tissue- and stage-specific transcriptomic profiles. The authors use weighted gene co-expression network analysis to identify gene networks, bringing insight to underlying pineapple reproductive organ growth.

Long noncoding RNAs (lncRNAs) have been identified in many mammals and plants and are known to play crucial roles in multiple biological processes. Pineapple is an important tropical fruit and a good model for studying the plant evolutionary adaptation to the dry environment and the crassulacean acid metabolism (CAM) photosynthesis strategy; however, the lncRNAs involved in CAM pathway remain poorly characterized. Here, we analyzed the available RNA-seq data sets derived from 26 pineapple leaf samples at 13 time points and identified 2,888 leaf lncRNAs, including 2,046 long intergenic noncoding RNAs (lincRNAs) and 842 long noncoding natural antisense transcripts (lncNATs). Pineapple leaf lncRNAs are expressed in a highly tissue-specific manner. Co-expression analysis of leaf lncRNA and mRNA revealed that leaf lncRNAs are preferentially associated with photosynthesis genes. We further identified leaf lncRNAs that potentially function as competing endogenous RNAs (ceRNAs) of two CAM photosynthesis pathway genes, PPCK and PEPC, and revealed their diurnal expression pattern in leaves. Moreover, we found that 48% of lncRNAs exhibit diurnal expression patterns in leaves, suggesting their important roles in CAM. This study conducted a comprehensive genome-wide analysis of leaf lncRNAs and identified their role in gene expression regulation of the CAM photosynthesis pathway in pineapple.

Background and Objective: High-grade serous ovarian cancers (HGSOC) retaining functional homologous recombination (HR) have poorer clinical outcomes and show relative resistance to DNA-damaging poly ADP ribose polymerase inhibitors (PARPi). We have shown that epigenetic drugs such as histone deacetylase inhibitors (HDACi) sensitize ovarian cancer cells to PARPi, in part through reduction of HR efficiency. However, these studies were conducted in immunocompromised mouse models, and drug effects on immune cell populations could not be fully examined. In this study, we will identify novel mechanisms of antitumor effects of combined HDACi/PARPi treatment by transcriptome analysis, and test drug effects in an established immune competent mouse model of ovarian cancer. Methods: HR-proficient SKOV-3 ovarian cancer cells were treated with vehicle (CON), PARPi olaparib (OLA; 10μM), HDACi panobinostat (PANO; 50nM) or OLA/PANO for 12h, and RNA-seq analysis performed. Differentially expressed genes between treatment groups were detected by DESeq2, based on fold change >1.5 and the corrected P value (FDR) Results: Functional group analysis of RNA-seq data showed significant enrichment of genes involved in cell proliferation, apoptosis, and DNA damage and repair with OLA/PANO treatment compared to CON or OLA alone. For a panel of 37 HR pathway genes, OLA/PANO treatment significantly reduced expression of 20 genes (e.g., BRCA1, BRCA2, WEE1). Examples of other significantly enriched functional pathways were cytokine secretion, inflammatory response genes, T cell activation (e.g., CD274/PD-L1, TNFSF9) and immune cell recruitment (e.g., IL-8, CXCL3). Consistent with these RNA-seq data, combined OLA/PANO treatment significantly reduced ID8-luc tumor burden and cell growth, and increased apoptosis and DNA damage, compared to CON or either drug alone. Moreover, there was increased infiltration of CD8+ T cells into OLA/PANO tumors, indicative of enhanced antitumor immunity. Conclusions: We have confirmed mechanisms such as reduced HR and identified a novel role for T-cell recruitment for OLA/PANO treatment of ovarian tumors. These findings support expanding the use of PARPi in HR-proficient HGSOC through rational combinations with HDACi and have the potential to benefit a substantial number of women with this devastating disease. Citation Format: Andrew J. Wilson, Xiaozhuan Dai, Qi Liu, Scott Hiebert, Marta Crispens, Dineo Khabele. Combination panobinostat and olaparib treatment promotes DNA damage and antitumor immunity in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A32.

Significance In flowering plants, the female germ line begins as a single cell known as the megaspore mother cell (MMC) in each ovule. The mechanisms that restrict MMC fate to a single cell remain largely unknown. We show that the Arabidopsis cytochrome P450 gene KLU acts through the chromatin remodeling complex SWR1 to promote WRKY28 expression in ovule primordia. We show that WRKY28 is expressed in a few somatic cells surrounding the MMC and is required to inhibit these cells from acquiring the MMC-like cell fate. Consistent with non–cell-autonomous KLU activity, KLU -expressing cells and WRKY28 -expressing cells are neither identical nor adjacently positioned. Our study demonstrates that cell–cell interactions involving only somatic cells in ovule primordia ensure the specification of a single MMC.

RNA structure plays a crucial role in gene maturation, regulation and function. Determining the form and frequency of RNA folds is essential for a better understanding of how RNA exerts its functions. Low-throughput studies have focused on RNA primary sequences and expression levels, but with an emphasis on relatively small numbers of transcripts. However, with the recent advent of high-throughput technologies, it is realistic to begin analyzing RNA secondary structures on a genome-wide scale. Here, we review genome-wide RNA secondary structure profiles as well as advances in computational structure predictions. We further discuss the novel characteristics of RNA secondary structure across messenger RNAs. Probing RNA secondary structure by high-throughput sequencing will enable us to build atlases of RNA secondary structures, an important step in helping us to understand the versatility of RNA functions in diverse cellular processes.

A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. We review progress in understanding the biogenesis and regulatory mechanisms of lncRNAs. We describe diverse computational and high throughput technologies for identifying and studying lncRNAs. We discuss the current knowledge of functional elements embedded in lncRNAs as well as insights into the lncRNA-based regulatory network in animals. We also describe genome-wide studies of large amount of lncRNAs in plants, as well as knowledge of selected plant lncRNAs with a focus on biotic/abiotic stress-responsive lncRNAs.

Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at +1 nucleosome and maintaining high gene accessibility at −1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed +1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcriptional control.