The RNA Transcript, June 14, 2021
Happy Juneteenth!
TODAY, Monday, June 14, 4:00 pm ET | U-M Center for RNA Biomedicine, RNA Innovation Seminar, featuring Rising Scholars
“CCR5 as a model to examine reporter assays in evaluating translational phenomena”
Yousuf Khan, Ph.D. candidate, Knight-Hennessy Scholar, NSF fellow, Stanford University
“Intersection between RNA methylation and TDP43-mediated toxicity in ALS”
Mike McMillan, Ph.D. Candidate, Cellular and Molecular Biology, University of Michigan
The Center for Scientific Review (CSR) for the National Institutes of Health in the United States is inviting early career RNA researchers to apply to their Early Career Reviewer Program. This program provides junior faculty a valuable opportunity to learn about the NIH grant review process and to contribute to the evaluation and review of successful (and unsuccessful) grant applications. 

If you are a full-time faculty member at the Assistant Professor level (or equivalent), you are encouraged to consider this program as it provides an outstanding professional development opportunity - you will meet and work with your senior colleagues, gain experience with a grant review process, and significantly improve your own grant-writing (and research-evaluating) skills. 

For more information and to apply, please visit the NIH Early Career Reviewer Program website here.

One of the challenges of becoming an expert is to keep exploring broadly while being highly focused. Alyssa English, Ph.D., a postdoctoral fellow in Dr. Stephanie Moon’s lab, has found that by extensively studying basic science and rigorously applying the scientific method, she has acquired a strong foundation that allows her to tackle many different research areas. What she has learned from studying cellular processes in yeast will eventually serve her in disease research and keep the door open to many professional options. “My foundational training has prepared me very well to eventually pursue a career in industry,” she said.

In 2020, English joined the Moon lab to study the processes underlying severe neurological diseases. To answer fundamental biological questions, she now studies EIF2AK2, a gene that codes for protein kinase R (PKR), a major player in the integrated stress response which is a pathway that regulates transcription and translation in response to different stress signals such as pathogens. In particular, PKR responds to the presence of double-stranded RNA from viruses by inhibiting global translation. This prevents the cell from translating viral genes and, as a result, prevents further viral infection. .... READ MORE

Wednesday, June 16, 4:00 pm ET | RNA Collaborative Seminar Series, hosted by Yale Center for RNA Science and Medicine

“Revealing New Functions for Ancient RNA Modifying Enzymes in Health and Disease”
"Mechanisms of Posttranscriptional Regulation During the Maternal to Zygotic Transition"
Moderator: Jessie Mohsen
Thursday, June 17, 12:00 pm EST | University of Michigan CEW and International Institute

"Juneteenth Seminar: Pursuit of My Dreams for a Quarter of a Century"
Joseph Francisco, Professor of Earth and Environmental Science and Professor of Chemistry at the University of Pennsylvania 
Friday, June 18, 7:00 am–12:30 pm US ET | 14th Berlin Summer Meeting

“Innovative RNA: From Basic Discoveries to Future Medicine” 
Speakers: Narry Kim (Seoul National U, South Korea), Cynthia Sharma (U Würzburg, Germany), David Liu (Harvard U, US), Mano Manoharan (Alnylam, US), Jennifer Petter (Arrakis, US), Oliver Rausch (Storm Therapeutics, UK) and Matthew Disney (Scripps Research, US)
Tuesday, June 22, 1:00–4:30 pm ET | U-M Single Cell Spatial Analysis Program

"Single Cell Spatial Analysis Program Kick Off Symposium"
Featuring Keynote Speaker Dr. Tzumin Lee, Group Leader, Janelia Research Campus, HHMI
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.
ELOF1 is a transcription-coupled DNA repair factor that promotes DNA damage-induced RNAPII ubiquitylation, Yana van der Weegen, Klaas de Lint, Diana van den Heuvel, Yuka Nakazawa, Ishwarya V. Narayanan, Noud Klaassen, Annelotte P. Wondergem, Marta San Martin Alonso, Shivani Rampersad, Yuichiro Hara, Kana Kato, Mayuko Shimada, Sylvie M. Noordermeer, Mats Ljungman, Tomoo Ogi, Rob M.F. Wolthuis, and Martijn S. Luijsterburg, Nature Cell Biology, 23:595-607, 2021,

Summary: Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. The binding of the TCR-specific repair factor CSB triggers DNA damage-induced ubiquitylation of RNA polymerase II (RNAPII) at a single lysine (K1268) by the CRL4CSA ubiquitin ligase. However, how the CRL4CSA ligase is specifically directed toward the K1268 site is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to the K1268 site, revealing ELOF1 as a specificity factor that positions CRL4CSA for optimal RNAPII ubiquitylation. Furthermore, drug-genetic interaction screening reveals an unanticipated compensatory TCR pathway in which ELOF1 together with known factors DOT1L and HIRA protect CSB-deficient cells from collisions between transcription and replication machineries. Our study provides a genetic framework of the transcription stress response and reveals key insights into the molecular mechanism of TCR.
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.
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