The RNA Transcript, June 7, 2021
Join the University of Michigan RNA research community!!
Congratulations to the winners of the 2021 Warren Alpert Prize: Dr. Lynne Maquat, University of Rochester, and Dr. Joan Steitz, Yale University and an Investigator of the Howard Hughes Medical Institute.  

The Warren Alpert Foundation Prize recognizes the research of scientists throughout the world and acknowledged the work of Maquat and Steitz as reshaping our understanding of the myriad of roles RNA plays in cell function and disease.
Tuesday, June 8, 3:00 pm ET | Harvard Medical School, Initiative for RNA Medicine
ZOOM, Password: 770277, Meeting ID: 963 4075 0975
“New Life for Old Drugs: Optimizing the Immune Response to mRNA Vaccines”
Ulrich von Andrian, M.D., Mallinckrodt Professor of Immunopathology at Harvard Medical School, Program Leader, Basic Immunology at Ragon Institute of MGH, MIT and Harvard
Director, HMS Center for Immune Imaging
Wednesday, June 9, 4:00 am ET (5:00 pm Korean time) | Institute for Basic Science and Seoul National University

Mini-Symposia series: Chengqi Yi (PKU), Gunter Meister (UR), Fan-Yan Wei (Tohoku), and Young-suk Lee (KAIST)
Friday, June 11, 12:00 pm ET | Ethical, Legal, and Social Implications of genetics and genomics - ELSI Friday Forum

"Ethical Challenges in Novel Gene Therapies for Sickle Cell Disease"
Liza-Marie Johnson, M.D., M.P.H., M.S.B., St. Jude's Children's Research Hospital
Melissa Creary, Ph.D., M.P.H., University of Michigan
Moderator: Pilar Ossorio, J.D., Ph.D., University of Wisconsin-Madison Law School

Panelists Melissa Creary and Liza Johnson will describe the current state of therapy for sickle cell disease, and some ethical issues that arise in the emerging use of gene transfer or gene editing for treating the disease. Dr. Johnson will focus on ethical issues identified by patients, and Dr. Creary will discuss some of the social and historical ethical challenges that relate to genetic interventions for sickle cell.
Monday, June 14, 9:00 am ET | U-M Bioinformatics, Dissertation defense

"Identification of Genes (MRNA or MicroRNA) and DNA Methylation Sites That May Underlie the Genetic Predisposition to Complex Diseases Using Multi-Omics and Meta-Analysis"
Li Guan, advisors: Laura Scott & Michael Boehnke
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
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.
Co-transcriptional splicing efficiencies differ within genes and between cell types, Karan BediBrian R MagnusonIshwarya NarayananMichelle PaulsenThomas E Wilson and Mats Ljungman, Published in Advance May 11, 2021, doi: 10.1261/rna.078662.120, RNA 2021.

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
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....
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