Cherry, Sara

Email Address
ORCID
Disciplines
Research Projects
Organizational Units
Position
Introduction
Research Interests

Filters

2012 - 20132
2
2
Reset filters

Settings

Search Results

Now showing 1 - 2 of 2
  • Publication
    Global Analysis of RNA Secondary Structure in Two Metazoans
    (2012-01-26) Li, Fan; Zheng, Qi; Ryvkin, Paul; Valladares, Otto; Murray, John I; Dragomir, Isabelle; Desai, Yaanik; Aiyer, Subhadra; Cherry, Sara; Wang, Li-San; Yang, Jamie; Gregory, Brian D; Bambina, Shelley; Sabin, Leah R; Lamitina, Todd; Rai, Arjun
    The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.
  • Publication
    Dicer-2 Processes Diverse Viral RNA Species
    (2013-02-12) Zheng, Qi; Sabin, Leah R; Thekkat, Pramod; Gregory, Brian D; Yang, Jamie; Hannon, Gregory J; Cherry, Sara; Tudor, Matthew
    RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double-stranded (ds)RNA precursors by Dicer and guide the RNA-induced silencing complex (RISC) to targets. Although principles governing small RNA sorting into RISC have been uncovered, the spectrum of RNA species that can be targeted by Dicer proteins, particularly the viral RNAs present during an infection, are poorly understood. Dicer-2 potently restricts viral infection in insects by generating virus-derived siRNAs from viral RNA. To better characterize the substrates of Dicer-2, we examined the virus-derived siRNAs produced during the Drosophila antiviral RNAi response to four different viruses using high-throughput sequencing. We found that each virus was uniquely targeted by the RNAi pathway; dicing substrates included dsRNA replication intermediates and intramolecular RNA stem loops. For instance, a putative intergenic RNA hairpin encoded by Rift Valley Fever virus generates abundant small RNAs in both Drosophila and mosquito cells, while repetitive sequences within the genomic termini of Vaccinia virus, which give rise to abundant small RNAs in Drosophila, were found to be transcribed in both insect and mammalian cells. Moreover, we provide evidence that the RNA species targeted by Dicer-2 can be modulated by the presence of a viral suppressor of RNAi. This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi.