The RNA Transcript, May 24, 2021
In memoriam: Charles R. Doering, Ph.D.
With great sadness we join the entire University of Michigan community in mourning Charles R. Doering, Ph.D., and expressing our deepest condolences to his colleagues, friends and loved ones.

Charles (Charlie) Doering was the Nicholas D. Kazarinoff Collegiate Professor of Complex Systems, Mathematics and Physics and was the Director of the Center for the Study of Complex Systems. He was a member of the U-M Center for RNA Biomedicine Strategic Advisory Board.

May 25–June 5 | The 26th Annual Meeting of the RNA Society

The program includes four keynote lectures to be given by:
  • Jennifer Doudna (HHMI, University of California Berkeley, USA)
  • Xiang-dong Fu (University of California San Diego, USA)
  • Sarah-Woodson (Johns Hopkins University, USA)
  • Irene Bozzoni (Istituto Italiano di Tecnologia, Italy)
Tuesday, May 25, 12:30 pm ET | U-M Cellular & Molecular Biology, Dissertation defense

"Using Intrahost Genetic Diversity to Understand Rna Virus Evolution and Transmission"
Andrew Valesano, advisor: Adam Lauring
Wednesday, June 2, 9:00 am ET | RNA Collaborative Seminar Series, hosted by European Molecular Biology Laboratory (EMBL)

"An evolutionarily conserved structure-to-function axis governs the functional mechanism of the regulatory lncRNA MEG3"

"Mechanistic dissection of SPEN function during X chromosome inactivation"

Moderator: Marco Marcia, Ph.D.
For press releases and blog articles about your upcoming top journal publications,

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.
A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair, Diana van den Heuvel, Cornelia G. Spruijt, Román González-Prieto, Angela Kragten, Michelle T. Paulsen, Di Zhou, Haoyu Wu, Katja Apelt, Yana van der Weegen, Kevin Yang, Madelon Dijk, Lucia Daxinger, Jurgen A. Marteijn, Alfred C.O. Vertegaal, Mats Ljungman, Michiel Vermeulen, and Martijn S. Luijsterburg, Nature Communications, 12:1342, 2021. PMC7910549

Abstract: Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. .... Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.

Subject terms: Nucleotide excision repair, Protein-protein interaction networks, Transcription
SARS-CoV-2 Total and Subgenomic RNA Viral Load in Hospitalized Patients 

Background: Previous studies demonstrated that SARS-CoV-2 RNA can be detected for weeks after infection. The significance of this finding is unclear and, in most patients, does not represent active infection. Detection of subgenomic RNA has been proposed to represent productive infection and may be a useful marker for monitoring infectivity.
RNA Ensembles from Solvent Accessibility Data: Application to the SAM-I Riboswitch Aptamer Domain, Jingru Xie and Aaron T. Frank, J. Phys. Chem. B 2021, 125, 14, 3486–3493, April 5, 2021

Abstract: Riboswitches are regulatory ribonucleic acid (RNA) elements that act as ligand-dependent conformational switches that recognize their cognate ligand via a binding pocket located in their aptamer domain. In the apo form, the aptamer domain is dynamic, requiring an ensemble representation of its structure. Here, as a proof-of-concept, we used solvent accessibility information to construct a pair of dynamical ensembles of the aptamer domain of the well-studied S-adenosylmethionine (SAM) class-I riboswitch in the absence (−SAM) and presence (+SAM) of SAM....
Job Opportunities
The Phil Zamore Lab at UMass Medical School is looking for motivated and ambitious researchers to join our team! Research in our lab focuses on molecular explanations for biological pathways guided by small RNAs and DNAs loaded into Argonaute proteins, including small interfering RNAs (siRNAs), microRNAs (miRNAs), and PIWI-interacting RNAs (piRNAs). Our flyer can be found here.

To apply, please email your CV to
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