The RNA Transcript, August 29, 2022 |
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Diet Induced Microglial Activation and its Role in Hippocampal Dysfunction in Obesity
Monday, Sep 7, 2022
1:00 - 2:00 PM
HYBRID TBA
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Monitoring and Targeting Metastasis through Circulating Tumor Cells: from Molecular Profiling to Natural Killer Cell-Based Therapeutics
Monday, Sep 7, 2022
1:30 - 2:30 PM
NCRC, BUILDING-10 G065
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RNA Collaborative Seminar - host: UMassMed, RNA Therapeutics Institute
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Wednesday, Sep 7, 2022
4:00 - 5:00 PM
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Why do animals need two Argonaute families with different catalytic properties?
Structural basis for accurate and efficient microRNA biogenesis by Dicer
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The RiboClub Annual Meeting aims at encouraging the exchange of ideas and stimulates collaborations between RNA biologists around the world. The meeting covers different topics related to the chemistry, structure and biology of RNA with emphasis on upcoming and debatable biological questions.
September 18 – 22, 2022
Quebec, Canada
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The symposium aims to highlight success stories from the drug discovery community at Michigan, share best practices, and provide opportunities for networking. A poster session for graduate students and trainees will occur midday.
Mon, Sep 21, 2022
9:00 a.m. - 4:00 p.m.
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U-M Bioinnovations in Brain Cancer |
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Sep 30 – Oct 1, 2022
Ann Arbor, MI
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Midwest Oligonucleotide Therapeutics Symposium |
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The Midwest Symposium on Oligonucleotide Therapeutics is a grassroots meeting in Indianapolis supported by an Oligonucleotide Therapeutics Society (OTS) Local Delivery Grant.
October 8 – 9, 2022
Indianapolis, IN
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25th anniversary screening of GATTACA with Panel Discussion |
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Co-sponsored by Neurology, Human Genetics and the Center for RNA Biomedicine
Mon, Oct 10, 2022
6:30 - 9:00 p.m.
Michigan Theatre
Ann Arbor, MI
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RNA Society of North Carolina Symposium |
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The symposium will feature world-class speakers, talks from submitted abstracts, and many great opportunities for networking. Abstract deadlines are Sept 16th (to be considered for talks) and Sept 26th for posters.
October 13–14, 2022
Durham, NC
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Rustbelt RNA Meeting 2022 |
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October 14–15, 2022
Cleveland OH
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Our members' publications are available through Altmetrics. Queries are currently available: CRISPR, microRNA, molecule, RNA, RNA therapeutics, transcriptome, and translation. Below are recent highlights.
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Mateescu, B., Jones, J. C., Alexander, R. P., Alsop, E., An, J. Y., Asghari, M., Boomgarden, A., Bouchareychas, L., Cayota, A., Chang, H. C., Charest, A., Chiu, D. T., Coffey, R. J., Das, S., De Hoff, P., deMello, A., D'Souza-Schorey, C., Elashoff, D., Eliato, K. R., Franklin, J. L., … Tewari, M. (2022). Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research. iScience, 25(8), 104653. https://doi.org/10.1016/j.isci.2022.104653
Abstract
The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013-2018), Phase 2 of the program (ERCC2, 2019-2023) aims to fill critical gaps in knowledge and technology to enable rigorous and reproducible methods for separation and characterization of both bulk populations of exRNA carriers and single EVs. ERCC2 investigators are also developing new bioinformatic pipelines to promote data integration through the exRNA atlas database. ERCC2 has established several Working Groups (Resource Sharing, Reagent Development, Data Analysis and Coordination, Technology Development, nomenclature, and Scientific Outreach) to promote collaboration between ERCC2 members and the broader scientific community. We expect that ERCC2's current and future achievements will significantly improve our understanding of exRNA biology and the development of accurate and efficient exRNA-based diagnostic, prognostic, and theranostic biomarker assays.
Keywords: Biochemistry; Biological sciences; Cell biology; Molecular biology..
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Palomar, V. M., Jaksich, S., Fujii, S., Kuciński, J., & Wierzbicki, A. T. (2022). High-resolution map of plastid-encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression. The Plant journal : for cell and molecular biology, 111(4), 1139–1151. https://doi.org/10.1111/tpj.15882
Abstract
Plastids contain their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplast DNA using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq). We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with levels of RNA accumulation, which demonstrates the impact of PEP on chloroplast gene expression. Presented data are available through a publicly available Plastid Genome Visualization Tool (Plavisto) at https://plavisto.mcdb.lsa.umich.edu/.
Keywords: RNA polymerase; plastid; sigma factor; transcription.
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McLean, E. K., Nye, T. M., Lowder, F. C., & Simmons, L. A. (2022). The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria. Annual review of microbiology, 10.1146/annurev-micro-102521-014450. Advance online publication. https://doi.org/10.1146/annurev-micro-102521-014450
Abstract
During the essential processes of DNA replication and transcription, RNA-DNA hybrid intermediates are formed that pose significant risks to genome integrity when left unresolved. To manage RNA-DNA hybrids, all cells rely on RNase H family enzymes that specifically cleave the RNA portion of the many different types of hybrids that form in vivo. Recent experimental advances have provided new insight into how RNA-DNA hybrids form and the consequences to genome integrity that ensue when persistent hybrids remain unresolved. Here we review the types of RNA-DNA hybrids, including R-loops, RNA primers, and ribonucleotide misincorporations, that form during DNA replication and transcription and discuss how each type of hybrid can contribute to genome instability in bacteria. Further, we discuss how bacterial RNase HI, HII, and HIII and bacterial FEN enzymes contribute to genome maintenance through the resolution of hybrids. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022.
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Liu, Y., Munsayac, A., Hall, I., & Keane, S. C. (2022). Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA. Journal of molecular biology, 167688. Advance online publication. https://doi.org/10.1016/j.jmb.2022.167688
Abstract
The miR-17 ∼ 92a polycistron, also known as oncomiR-1, is commonly overexpressed in multiple cancers and has several oncogenic properties. OncomiR-1 encodes six constituent microRNAs (miRs), each enzymatically processed with different efficiencies. However, the structural mechanism that regulates this differential processing remains unclear. Chemical probing of oncomiR-1 revealed that the Drosha cleavage sites of pri-miR-92a are sequestered in a four-way junction. NPSL2, an independent stem loop element, is positioned just upstream of pri-miR-92a and sequesters a crucial part of the sequence that constitutes the basal helix of pri-miR-92a. Disruption of the NPSL2 hairpin structure could promote the formation of a pri-miR-92a structure that is primed for processing by Drosha. Thus, NPSL2 is predicted to function as a structural switch, regulating pri-miR-92a processing. Here, we determined the solution structure of NPSL2 using solution NMR spectroscopy. This is the first high-resolution structure of an oncomiR-1 element. NPSL2 adopts a hairpin structure with a large, but highly structured, apical and internal loops. The 10-bp apical loop contains a pH-sensitive A+·C mismatch. Additionally, several adenosines within the apical and internal loops have elevated pKa values. The protonation of these adenosines can stabilize the NPSL2 structure through electrostatic interactions. Our study provides fundamental insights into the secondary and tertiary structure of an important RNA hairpin proposed to regulate miR biogenesis.
Keywords: NMR spectroscopy; RNA structure; Thermal denaturation; microRNA.
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