The RNA Transcript, March 20th 2023 | |
Keynote Speaker Highlights - Joseph Wedekind Ph.D | | |
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Joseph Wedekind, Ph.D
Redefining Riboswitches: Ribosome-Binding Site Sequestration is Dispensable for Gene Regulation by the Largest Group of preQ, Riboswitches
Abstract: Translational riboswitches are bipartite structured elements found in bacterial messenger RNAs. Metabolite sensing by a high-specificity riboswitch aptamer causes its downstream expression platform to adopt a mutually exclusive conformation that buries the Shine-Dalgarno sequence (SDS), blocking translation initiation. In the past decade, my lab determined co-crystal
structures of all five members of the prequeuosine 1 (preQ 1 )-sensing riboswitch family. Their diverse pseudoknot folds show three chemically distinct ways to recognize preQ 1 . Importantly, each fold communicates preQ 1 binding to the expression platform via four different strategies including: SDS burial via complementary base pairing; metabolite-induced dynamics; stacking-
spine formation; and direct preQ 1 sensing by the SDS. We contrast these strategies to a novel regulatory mode uncovered in our recent analysis of the C. antarcticum preQ 1 -I I (class I type I) riboswitch, which binds two preQ 1 metabolites in one binding pocket. Although the preQ 1 -I I
covariation model and crystallographic data suggest that this riboswitch buries its first two SDS bases, molecular dynamics, in-cell chemical probing, ribosome assembly and in-cell reporter assays indicate that the metabolite-induced pseudoknot fold — not SDS burial — is required for translation regulation. Based on this novel paradigm, we hypothesize the existence of
undiscovered translational riboswitches that do not sequester the SDS within a stable fold.
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Innovation Partnerships - Great Lakes Discovery | | |
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Congratulations to Dr. David Markovitz, whose project has been the first Great Lakes Discovery project that has been selected for Deerfield Management funding.
The announcement link from Innovation Partnerships is here.
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RNA Collaborative Seminar | | |
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Alberta RNA Research & Training Institue (ARRTI)
On the mathematical modeling of eIF5B-mediated non-canonical translation initiation as a chemotherapeutic target
Speaker: Elizabeth Trofimenkoff
Nucleolin Interacts with ZIKV RNA Terminal Regions and Modulates Virion Assembly
Speaker: Darren Gemmill
Moderator: Laura Keffer-Wilkes
Wednesday, March 15, 2023.
4:00 PM
Zoom.
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8th Annual RNA Symposium - Thursday, April 20th, 2023 | | |
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8th Annual Non-coding RNA Symposium sponsored by the HMS Initiative for RNA Medicine and the Cancer Center at Beth Israel Deaconess Medical Center.
April 20, 2023
8:00 AM - 5:00 PM
Joseph B Martin Conference Center at HMS
77 Avenue Louis Pasteur
Boston MA 02115
Speakers & Registration here
Questions: Email Grace Lee at glee8@bidmc.havarad.edu
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Lighting Talks Workshop & Competition | | |
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Are you passionate about your RNA research? Do you want to share your love of science with the world but need help with presentation skills? The RNA Society's RNA Collaborative will once again be offering the Lightning Talks Workshop and Competition. Prizes include a one-year membership to the RNA Society and features on our YouTube and social media channels.
Important dates:
March 21, 2023 - Applications due (apply here: https://forms.office.com/r/2ZmHmm9eSY)
April 1, 2023 - Participants notified
April 24, 2023 - Workshop
For more information contact Dr. Laura Keffer-Wilkes at kefferwilkesl@uleth.ca
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28th Annual Meeting of the RNA Society - May 30th thru June 4th | |
University of Michigan - Postdoctoral Position | | |
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Post-doctoral position in the lab of John Prensner, MD Ph.D
Chad Carr - Pediatric Brain Tumor Center, Michigan Medicine
Translating the cancer genome for children with brain tumors
One post-doctoral position is available in the Prensner lab in the Chad Carr - Pediatric Brain Tumor Center at the University of Michigan to study the therapeutic implications of non-canonical RNA translation in pediatric brain cancers. This is a fully funded position. We are supportive of post-doctoral research fellows obtaining independent funding and/or career development awards to advance their independent academic careers.
The successful candidate will be able to advance cancer-related work around our active projects in:
- RNA translational regulation
- Therapeutic targeting of RNA translation
- Non-canonical open reading frames
- Non-coding genome translation.
We use a variety of high-throughput techniques, functional genomics, biochemical and computational methods to investigate the cancer-relevant consequences of aberrant RNA translation. Recent publications: Prensner JR et al., Nature Biotechnology, 2021; Mudge JM*, Ruiz-Orera J*, Prensner JR*, et al., Nature Biotechnology, 2022.
Applicants should hold a PhD or equivalent degree (MD, MD/PhD) and have experience with molecular or developmental biology, cancer biology, or murine model systems of cancer.
Interested individuals should send a curriculum vitae and cover letter to prensner@umich.edu or
Submit an application via: https://careers.umich.edu/job_detail/230384/research-fellow
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University of Rochester - Postdoctoral Position | | |
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Post-doctoral Position Lab of Lynne Maquat, Ph.D
Director, Center for RNA Biology
Professor, Departments of Biochemistry & Biophysics, Oncology, and Pediatrics
School of Medicine and Dentistry
A Post-Doctoral Position is open in the Maquat Lab at the University of Rochester Medical Center in Rochester, NY. Applicants should hold a PhD or MD/PhD degree(s) and have expertise in molecular, cellular, or structural biology to study one of a number of very exciting and ongoing projects, including but not limited to FMRP function in Fragile X Syndrome (FXS), newly defined effectors of nonsense-mediated mRNA decay, or the mechanistic coupling of transcription and RNA processing on chromatin and beyond. A background in neurobiology and/or stem-cell biology would facilitate the work on FXS (see, e.g., https://www.nature.com/articles/s41556-020-00618-1), and a background in computational biology would facilitate all projects, but neither is required.
Interested individuals should submit:
a complete curriculum vitae,
the names and email addresses of three references (applicants should state their relationship to each), and
a description of RNA research experience, including experimental approaches and technologies with which the applicant has experience.
The successful applicant will join a very productive, interactive lab and a lively, supportive RNA community that consists of more than 25 labs spanning the University of Rochester Medical Center and the adjacent Colleges of Arts, Sciences & Engineering. The Maquat lab offers an outstanding research environment, excellent opportunities to collaborate with basic scientists and clinicians, and a strong record of training post-docs for academic positions.
Please submit applications to: Liz at elizabeth_leverenz@urmc.rochester.edu
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2023 Bay Area RNA Meeting - March 20th | | |
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In preparation of the upcoming meeting, we're collecting RSVPs to count how many attendees will show up in-person. This will help us ensure that we have the space, coffee, etc for the meeting.
Please reserve your seat by entering your RSVP on your profile page. Click the top 'Edit' tab to confirm your conference seat and indicate which workshops you will attend in-person.
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2023 RiboClub Annual Meeting - September 24 - 28 | | |
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The RiboClub Annual Meeting aims at encouraging the exchange of ideas and stimulates collaborations between RNA biologists around the world. The meeting covers different topics related to the chemistry, structure and biology of RNA with emphasis on upcoming and debatable biological questions. In addition, every year the RiboClub puts the focus on a local or regional RNA group to highlight their efforts and introduce them to the international community.
The meeting format provides principal investigators the opportunity to present their point of views on the current state of knowledge and ignite the curiosity of young scientists. The meeting size and its format give ample opportunity for discussions and interactions, so bring your thinking hat to uncover the next big idea.
Registration fees are subsidized to encourage the participation of students and upcoming researchers. All laboratory members are invited to attend, listen to the presentations of leading scientists and participate in poster competition.
Annual Meeting September 24-28, 2023
Chéribourg Hotel, Orford, Quebec, Canada
Register by: June 30th, 2023
More Inforamtion :www.riboclub.org
Questions: riboclub@riboclub.org
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Our members' publications are available through Altmetrics. Queries are currently available: CRISPR, microRNA, molecule, RNA, RNA therapeutics, transcriptome, and translation.
Below are recent highlights.
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Mandal, S., Khanna, K., Johnson-Buck, A., & Walter, N. G. (2022). A guide to accelerated direct digital counting of single nucleic acid molecules by FRET-based intramolecular kinetic fingerprinting. Methods (San Diego, Calif.), 197, 63–73. Highlighted in NCI's Epidemiology & Genomics Research Program (EGRP) https://doi.org/10.1016/j.ymeth.2021.06.014
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Wang, E. T., Freudenreich, C. H., Gromak, N., Jain, A., Todd, P. K., & Nagai, Y. (2023). What repeat expansion disorders can teach us about the Central Dogma. Molecular cell, 83(3), 324–329. https://doi.org/10.1016/j.molcel.2022.12.017 | |
Stephen V. Carney, Kaushik Banerjee, Anzar Mujeeb, Brandon Zhu, Santiago Haase, Maria Luisa Varela, Padma Kadiyala, Claire E. Tronrud, Ziwen Zhu, Devarshi Mukherji, Preethi Gorla, Yilun Sun, Rebecca Tagett, Felipe J. Núñez, Maowu Luo, Weibo Luo, Mats Ljungman, Yayuan Liu, Ziyun Xia, Anna Schwendeman, Tingting Qin, Maureen A. Sartor, Joseph F. Costello, Daniel P. Cahill, Pedro R. Lowenstein, Maria G. Castro; Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance. Clin Cancer Res 2023; https://doi.org/10.1158/1078-0432.CCR-22-1896 | | | | |
