The RNA Transcript, June 28, 2021
Apologies for the error in the previous email. This webinar will take place this coming Wednesday, June 30, 4:00–5:00 pm ET, RNA Collaborative Seminar Series webinar, hosted by the U-M Center for RNA Biomedicine
“Dynamic multivalent interactions drive mammalian RNA regulation”
Sethu Pitchiaya, Ph.D., Urology, Medical School, University of Michigan

Dr. Pitchiaya is the June 2021 RNA Society spotlight member!
"Characterizing cellular RNA-protein interaction networks with chemical probes"
Chase Weidmann, Ph.D., Biological Chemistry, Medical School, University of Michigan

Moderator: Nils G. Walter
The RNA Collaborative Seminar Series, launched in April 2020 at the initiative of the University of Michigan (U-M) Center for RNA Biomedicine, is a consortium of 21 partners who share their latest RNA research through webinars hosted by each partner on a rotating basis. To further engage with the community, the Collaborative is now on Discord, a social media platform. Join us on Discord to further share and discuss RNA topics, for free!
A warm thank you to LSA Technology Services!
As we are hosting our last seminar of the academic year with the RNA Collaborative Seminar Series this Wednesday, June 30th, we want to give special thanks to the infallible support we have received from LSA Technology Services.

Like all of us, we were quite baffled by the pandemic-necessitated social distancing and the necessity to quickly implement virtual events. The LSA Technology Services team, especially Chris Taylor, Rob Feeley and Keith Kuras, has proven invaluable to educate us on the best tools and tips to run successful virtual events. “Live events can be stressful, and it was such a relief to know that they were with us every step of the way. They fixed issues before I even noticed them, I almost felt like they were our guardian angels!” said Martina Jerant, Center for RNA Biomedicine Manager.

The pool is open, enjoy the summer!!!
For press releases and blog articles about your upcoming top journal publications,
contact Elisabeth Paymal.

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.
Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases

Abstract: ... Herein, we performed a comprehensive transcriptome analysis to define the mRNAs that are associated with almost all aaRSs present in S. cerevisiae cytosol. .... Gene Ontology analyses for aaRSs with a considerable number of target mRNAs discovered an enrichment for pathways of amino acid metabolism and of ribosome biosynthesis. Furthermore, sequence and structure motif analysis revealed for some aaRSs an enrichment for motifs that resemble the anticodon stem loop of cognate tRNAs. These data suggest that aaRSs coordinate mRNA expression in response to amino acid availability and may utilize RNA elements that mimic their canonical tRNA binding partners.
Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses 

Sleep loss drives brain region- and cell type-specific alterations in ribosome-associated transcripts involved in synaptic plasticity and cellular timekeeping
Carlos Puentes-Mestril, James Delorme, Lijing Wang, Marcus Donnelly, Donald Popke, Sha Jiang and Sara J. Aton, Journal of Neuroscience, 17 May 2021, JN-RM-1883-20; DOI:

Significance Statement: Sleep loss-driven changes in transcript and protein abundance have been used as a means to better understand the function of sleep for the brain. Here we use translating ribosome affinity purification (TRAP) to characterize changes in abundance of ribosome-associated transcripts in excitatory and inhibitory neurons in mouse hippocampus and neocortex after a brief period of sleep or sleep loss. We show that these changes are not uniform, but are generally more pronounced in excitatory neurons than inhibitory neurons, and more pronounced in neocortex than in hippocampus.
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.
Positions for Postdoctoral Research Scientist-Neuroscience Pain Research-FDE
Eli Lilly and Company  Indianapolis, IN
Your work will contribute to the development of approaches for treating chronic pain with novel RNA-based modalities. MORE INFORMATION
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