The RNA Transcript, February 28, 2022
Box lunch provided for all registered attendees

due tomorrow, Tues, 3/1
U-M Center for RNA Biomedicine Seminar, co-hosts: DCMB and Pediatric Oncology
"Translating the cancer genome: dark matter proteins"
Boston Children’s Cancer and Blood Disorders Center
Harvard Medical School

TODAY Monday, February 28, 2022
4:00 pm - 5:00 pm
BSRB, ABC Seminar rooms (hybrid)
U-M BRCF Advanced Genomics Core Seminar
Introduction to RNA-Seq Technology and Applications
Dipesh Risal, Proteogenomics

Thursday, March 3, 2022
1:00 pm - 2:00 pm
RNA Collaborative Seminar, Host: European Molecular Biology Laboratory (EMBL)
----Wednesday, March 9, 2022
----10:00 am - 11:00 am
"Liquid or Solid - Do material properties of RNP granules matter in vivo?"


"Molecular insights into the remodelling of roX lncRNA during Drosophila dosage compensation"
U-M BRCF Advanced Genomics Core Seminar
Correlated Expression of Protein and RNA Using Bulk and Single-Cell Proteogenomics
Dipesh Risal, Proteogenomics

Thursday, March 10, 2022
12:00 pm - 1:00 pm
Abstract Submission Deadlines
Funding Opportunities
Pfizer is seeking proposals for the advancement of RNA therapeutics and the development of the next generation of RNA medicines
Submissions invited for novel target concepts and therapeutic strategies amenable to RNA based approaches (mRNA, circular RNA, gene editing), in the following areas of interest:
  • Cellular reprogramming:
  • Cancer vaccines
  • Infectious Disease Vaccines
  • Chronic or Rare Kidney Disease (Focal Segmental Glomerulosclerosis, IgA Nephropathy, Alport Syndrome, or Autosomal Dominant Polycystic Kidney Disease)
  • Rare Liver Diseases and Rare Neuromuscular Diseases
  • Repeat Expansion Diseases (e.g. Huntington’s disease, Friedreich’s ataxia, ALS, myotonic dystrophy)
  • Preference given to targets not amenable to small or large molecule intervention

For more information about submission process and areas of interest go to pfizercti.com or email John.Androsavich@pfizer.com
Postdoctoral position is available in the group “RNA biogenesis, architecture and interactions” led by Carine Tisné in the Institute of Physico-chemical Biology (IBPC) in Paris, to work on RNA-mediated gene expression regulation.

Deadline March 27
RNAs are heavily co- or post-transcriptionally modified, with the largest diversity of modifications found in tRNAs. Given the widespread presence of post-transcriptional RNA modifications in all classes of RNAs and in all domains of life and their dynamics, RNA functions must have evolved under the influences of RNA modifications. Many RNA modifications or the respective enzymes are associated with human disease, especially cancer. We want to elucidate how RNA maturation control or influence RNA functions. A multi-disciplinary approach involving biochemical, biophysical and cellular experiments will be used to address these questions of RNA biology. The ultimate goal of the project is to advance our understanding of RNA-based regulation, by means of biochemical reconstitution and structural characterization of protein/RNA complexes. Candidates will hold or about to be awarded a PhD in Biochemistry, Biophysics or Molecular Biology and must have a proven track record of research achievements. Previous experience in the analysis of multi-protein complexes and protein/RNA interactions, as well as familiarity with biophysical techniques such as cryo-electron microscopy and single-particle analysis would be an advantage. This position may lead to a submission to the CNRS national competition for a permanent position.

Our members' publications are available through Altmetrics. Queries are currently available: CRISPR, microRNA, molecule, RNA, RNA therapeutics, transcriptome, and translation. Below are recent highlights.
Molecular Determinants in tRNA D-arm Required for Inhibition of HIV-1 Gag Membrane Binding, Sumner, C., Kotani, O., Liu, S., Musier-Forsyth, K., Sato, H., & Ono, A. (2022). Molecular Determinants in tRNA D-arm Required for Inhibition of HIV-1 Gag Membrane Binding. Journal of molecular biology, 434(2), 167390. doi.org/10.1016/j.jmb.2021.167390

Plasma-membrane-specific localization of Gag, an essential step in HIV-1 particle assembly, is regulated by the interaction of the Gag MA domain with PI(4,5)P2 and tRNA-mediated inhibition of non-specific or premature membrane binding. Different tRNAs inhibit PI(4,5)P2-independent membrane binding to varying degrees in vitro; however, the structural determinants for this difference remain unknown. Here we demonstrate that membrane binding of full-length Gag synthesized in vitro using reticulocyte lysates is inhibited when RNAs that contain the anticodon arm of tRNAPro, but not that of tRNALys3, are added exogenously. In contrast, in the context of a liposome binding assay in which the effects of tRNAs on purified MA were tested, full-length tRNALys3 showed greater inhibition of MA membrane binding than full-length tRNAPro. While transplantation of the D loop sequence of tRNALys3 into tRNAPro resulted in a modest increase in the inhibitory effect relative to WT tRNAPro, replacing the entire D arm sequence with that of tRNALys3 was necessary to confer the full inhibitory effects upon tRNAPro. Together, these results demonstrate that the D arm of tRNALys3 is a major determinant of strong inhibition of MA membrane binding and that this inhibitory effect requires not only the D loop, which was recently reported to contact the MA highly basic region, but the loop sequence in the context of the D arm structure.

Keywords: acidic phospholipid; highly basic region; lipid-protein interaction; tRNA–protein interaction; virus assembly.
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