The RNA Transcript, September 20, 2021 |
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On National Postdoc Appreciation week,
we warmly thank our RNA postdocs and are pleased to feature
The objective of the RNA Student Postdoc council is to work collaboratively across disciplines, build a scientific community, and generate ideas and activities that advance RNA research and education across the University of Michigan.
The 2021-2022 RNA Council is a group of nine graduate students and five postdoctoral research fellows who drive collaboration and training development in a way that has a ‘trainee first’ focus. The Council was created at the recommendation of our Executive Committee. While the group has financial support from the Center, it has also secured ‘RNA Salon’ grants from The RNA Society. These grants provide additional funds to support new and exciting initiatives created by the RNA Council.
Last year, the council launched a series of videos that explain RNA techniques. Our first one is about Total RNA Extraction.
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2021–2022 RNA Student Postdoc Council Members
- Marissa Cloutier, Graduate Student, Human Genetics, Medical School
- Elizabeth Fogarty, Ph.D., Postdoctoral Research Fellow, MCDB, LSA
- Varun Gadkari, Ph.D., Postdoctoral Research Fellow, Chemistry, LSA
- Meredith Purchal, Graduate Student, Chemistry, Program in Chemical Biology, LSA
- Andreas Schmidt, Ph.D., Postdoctoral Research Fellow, Chemistry, LSA
- Melissa Seman, Graduate Student, Biological Chemistry, Cellular and Molecular Biology Program, Medical School
- Renke Tan, Graduate Student, Biological Chemistry, Medical School
- Elizabeth Tidwell, Graduate Student, BIophysics, LSA
- Lam Tran, Graduate Student, Biostatistics, School of Public Health
- Megan Trotter, Graduate Student, Human Genetics, Michigan Medicine
- Isha Verma, Ph.D., Postdoctoral Research Fellow, Neurology, Medical School
- Robb Welty, Ph.D., Postdoctoral Research Fellow, Chemistry, LSA
- Ciara Witt, Graduate Student, Chemistry, LSA
- Jiaqiang Zhu, Graduate Student, Biostatistics, Public Health
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Monday–Tuesday, September 20–22, 4:00 pm ET | RiboClub Annual Symposium
"Transcriptomics and cancer biology"
Keynote speakers:
Tom Cech, University of Colorado Boulder, USA
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Tuesday, September 21, 12:00-1:00 pm ET | University of Michigan, Biological Chemistry Seminar
"Base Editing-Performing Chemistry on the Genome"
Hosts: Nils Walter and Yan Zhang
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"A small RNA perspective on genomic conflict”
"Targeting RNA with small molecules: tools and tactics"
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Thursday, September 23, 11:00 am ET, West Lecture Hall in MSII | University of Michigan, Human Genetics Dissertation defense
"Leveraging New Technologies to Explore Regulatory and Structural Elements of the Human Genome"
Torrin McDonald, advisor: Alan Boyle
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Friday, September 24, 10:00-11:00, LSI Library and Zoom (Password: structure) | University of Michigan, Life Sciences Institute, U-M Structure Seminar
"Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites"
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Monday, October 4, 4:00 pm ET | University of Michigan Center for RNA Biomedicine, RNA Innovation Seminar Series
“Fluorescent nucleoside analogues with new properties”
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Thursday, October 7, 2:30 – 5:30 pm EST | The Warren Alpert Foundation and Harvard Medical School, 2021 Warren Alpert Foundation Prize Virtual Symposium
"Getting the Message: How Elucidation of Messenger RNA Formation Empowered RNA Therapeutics"
Symposium in honor of Lynne Maquat, Ph.D., and Joan Steitz, Ph.D., for the discovery of fundamental pathways and mechanisms that ensure accurate RNA splicing and quality control of gene expression involving RNA.
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For press releases and blog articles about your upcoming top journal publications, please
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Our members' publications are available through Altmetric. Five queries are currently available: "RNA," "microRNA," "Transcriptome," "Translation," and "Molecule." Please make sure to have at least one of these key words in your title or abstract. Below are recent highlights.
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Long Noncoding RNAs in Plants, Wierzbicki A T, Blevins T, Świeżewski S, Annual Review of Plant Biology, Vol. 72:245-271 (Volume publication date June 2021)
Abstract: Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics, Joshua D.Karslake, Eric D.Donarski, Sarah A.Shelby, Lucas M.Demey, Victor J.DiRita, Sarah L.Veatch, Julie S.Biteen, Methods, Volume 193, September 2021, Pages 16-26, https://doi.org/10.1016/j.ymeth.2020.03.008
Abstract: ... Here, we develop a method for the case of multiple interconverting species undergoing free diffusion and introduce a new approach to analyzing single-molecule trajectories: the Single-Molecule Analysis by Unsupervised Gibbs sampling (SMAUG) algorithm, which uses nonparametric Bayesian statistics to uncover the whole range of information contained within a single-particle trajectory dataset. Even in complex systems where multiple biological states lead to a number of observed mobility states, SMAUG provides the number of mobility states, the average diffusion coefficient of single molecules in that state, the fraction of single molecules in that state, the localization noise, and the probability of transitioning between two different states. In this paper, we provide the theoretical background for the SMAUG analysis and then we validate the method using realistic simulations of single-particle trajectory datasets as well as experiments on a controlled in vitro system. Finally, we demonstrate SMAUG on real experimental systems in both prokaryotes and eukaryotes to measure the motions of the regulatory protein TcpP in Vibrio cholerae and the dynamics of the B-cell receptor antigen response pathway in lymphocytes. Overall, SMAUG provides a mathematically rigorous approach to measuring the real-time dynamics of molecular interactions in living cells.
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Abstract: Non-coding transcription is an important determinant of heterochromatin formation. In Arabidopsis thaliana a specialized RNA polymerase V (Pol V) transcribes pervasively and produces long non-coding RNAs. These transcripts work with small interfering RNA to facilitate locus-specific establishment of RNA-directed DNA methylation (RdDM). Subsequent maintenance of RdDM is associated with elevated levels of Pol V transcription. However, the impact of DNA methylation on Pol V transcription remained unresolved. We found that DNA methylation strongly enhances Pol V transcription. The level of Pol V transcription is reduced in mutants defective in RdDM components working downstream of Pol V, indicating that RdDM is maintained by a mutual reinforcement of DNA methylation and Pol V transcription. Pol V transcription is affected only on loci that lose DNA methylation in all sequence contexts in a particular mutant, including mutants lacking maintenance DNA methyltransferases, which suggests that RdDM works in a complex crosstalk with other silencing pathways.
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Assistant Professor position in Dr. Melissa Harrison's lab, Department of Biomolecular Chemistry at the University of Wisconsin School of Medicine and Public Health.This is a broad search that seeks a colleague with a rigorous research program to build on the many strengths of the department, which include chromosome and RNA biology, gene expression, development, metabolism and cellular signaling. Approaches of interest include (but are not limited to) quantitative imaging and structural biology.
The deadline for applications is October 31 and must be submitted through jobs.hr.wisc.edu (PVL237912).
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