The RNA Transcript, March 13th 2023 | |
Keynote Speaker Highlights - Amy Gladfelter Ph.D | | |
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Amy Gladfelter, Ph.D
RNA Structure Controls Composition & Network Dynamics of Condensates
Abstract: Many studies have characterized protein condensates, sometimes including model RNAs that are often nonspecific and/or homopolymeric. However, most biomolecular condensates in cells likely comprise mixtures of proteins and specific RNAs, including mRNAs that form dynamic structures. RNA sequence and structure control co-phase behavior with proteins in ways that are not well understood. We studied the influence of mRNA structure in phase separation using the Whi3 RNA binding protein protein and an mRNA binding partner, CLN3, which encodes a cyclin. Whi3-CLN3 condensates locally regulate the cell cycle in fungi. We first created an evolutionary algorithm that designs shuffled CLN3 RNA sequences which maximize or minimize predicted free energies of folding while preserving mass, known Whi3 binding sites, encoded amino acid sequence, and nucleotide composition. RNAs with minimized free energies of folding contain many stable duplexes, while RNAs with maximized energies have unstable structures and long single-stranded regions. Using mass photometry, we show that RNAs with stable structures are mostly monomeric, while RNAs with unstable structures can multimerize. When mixed with protein, these differential RNA-RNA interactions affect dense phase compositions. Specifically, unstable RNAs form condensates with high RNA and low protein concentrations, while the converse is true for RNAs with stable structures. Using microbead rheology, we observe that unstable RNAs form condensates with long viscoelastic relaxation times that increase with condensate age, indicating elastic properties at many timescales. By contrast, stable RNAs form less elastic condensates with shorter relaxation times that increase to a lesser degree with time. We hypothesize that such aging is controlled by the exchange of intra- for inter-molecular base pairing among RNAs whose folding free energies determine the timescale of such exchanges. Thus, RNA structure can have multi-scale consequences for biomolecular condensates, with impacts on condensate composition and material properties. Finally, the implications of RNA structure on temperature adaptation in fungi will be discussed.
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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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Ribosome Collisions as a Signaling Hub to Impact Cell Fate
Speaker: Rachel Green, Ph.D
Bloomberg Distinguished Professor
Johns Hopkins University
Monday, March 13, 2023.
3:00 PM
Rackham Amphitheatre
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RNA Collaborative Seminar | | |
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The hidden life of mRNAs: a non-coding role as sensors of cell environment
Speaker: Stefania Nicoli, Ph.D
Associate Professor
Director of the Zebrafish Phenotyping Core for Presicion Medicine
Internal Medicine & Genetics
Co-Director, Yale Cardiovascular Research Center (YCVRC)
Functions of mRNA 5′ terminal sequences
Speaker: Carson Thoreen, Ph.D
Associate Professor Term of Cellular & Molecular Physiology
Moderator: Karla Neugebauer, Ph.D
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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Baylor College of Medicine - Postdoctoral Position | | |
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Postdoctoral Positions to Investigate RNA Subcellular Localization at Baylor College of
Medicine
Two postdoctoral positions are available in Furqan Fazal’s lab in the Department of
Biochemistry and Molecular Biology at Baylor College of Medicine (BCM) to study the
organization of RNAs within cells. The Fazal lab focuses on systematically interrogating the
subcellular transcriptomes of mammalian cells and characterizing the scope, regulation, and
function of subcellular localization, particularly at the systems and organismal level.
Fazal’s lab interests span from computational to wet-lab work, though the ideal candidate
should have experience in molecular biology, RNA biology, cell biology, and/or informatics. We
use a variety of biochemical, biophysical, imaging, genomic and computational approaches to investigate the sequence-function relationship dictating RNA localization.
Email: furqan.fazal@bcm.edu for more information about the position.
Apply through Baylor College of Medicine website: https://jobs.bcm.edu. Requisitions ID's 8018 or 8019.
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Helmholtz Institute for RNA-based Infection Research (HIRI) - Assistant Professor Position | | |
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HIRI is looking to identify candidates for an open group leader position in RNA biology to be filled at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, Germany. These are attractive positions that come with good start-up packages and stable core funding. They offer a long-term perspective and strong ties with the Medical Faculty of the University of Würzburg, one of Germany’s leading universities in the life sciences. The call closes on March 19.
They are looking for group leaders on the assistant professor level, who want to work at the interface of RNA research and infection biology, covering bacterial and viral pathogens, the immune response to infections, and RNA delivery to infected tissue. Moreover, they have been developing a single-cell RNA-seq programme to achieve a better resolution of infection processes. For more details, please see: www.helmholtz-hiri.de/en/ They currently have nine PIs and are expected to grow to about 10-12 laboratories in the next few years.
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OSU Nakanishi Lab - Postdoctoral Position | | |
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Postdoctoral Position to Explore “Tiny RNAs” in Humans
An NIH-funded postdoctoral position is available in the laboratory of Dr. Kotaro Nakanishi at The Ohio State University. The Nakanishi group studies the roles of tiny RNAs, 10 - 18 nt non coding RNAs. We recently discovered that specific 3′→5′ exonucleases trim microRNAs to
tiny RNAs. While more than 200,000 papers about microRNAs have been reported, only about 10 articles have described tiny RNAs. The physiological functions of tiny RNAs remain to be studied. My group uses molecular biology, biochemistry, RNA-seq, cell biology (confocal microscope), and structural biology (cryo-EM and crystallography) to investigate tiny RNAs. We are looking for a postdoc who explores this new world together.
Qualifications
Strong candidates are highly motivated individuals with an excellent academic track record, including first-author publication(s). Candidates should have or be in the process of completing a Ph.D. in biochemistry, molecular biology, cell biology, or structural biology. Experience in large-scale protein purification and structure determination in cryo-EM and/or X ray crystallography will be advantageous.
To apply
For more information, please visit HERE.
Questions
If you have any questions, please email nakanishi.9@osu.edu.
Recent publications:
1. Sim GY, Kehling AC, Park MS, Secor J, Divoky C, Zhang H, Malhotra N, Bhagdikar D, Abd El Wahab EW, Nakanishi K. (2022). Proc. Natl. Acad. Sci. USA.
2. Park MS, Sim GY, Kehling AC, Nakanishi K (2020). Proc. Natl. Acad. Sci. USA. 3. Park MS, Araya-Secchi R, Brackbill JA, Phan HD, Kehling AC, Abd El-Wahab EW, Dayeh DM, Sotomayor M., Nakanishi K. (2019). Molecular Cell.
4. Dayeh DM., Cantara WA., Kitzrow J., Musier-Forsyth K., Nakanishi K. (2018). Nucleic Acids
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Institut Curie Research Center (Osray, France) - 6th Junior Group Leader Position | | |
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The Research unit “Chemistry and Modelling for Biology of Cancer” (CNRS UMR9187 / Inserm U1196) at Institut Curie is recruiting a Junior Group Leader to develop chemical biology approaches related to the studies of fundamental mechanisms of cancer and/or applied to the development of novel diagnostic or therapeutic tools. The recruited group leader will benefit from the expertise of several teams present at the Orsay site of Institut Curie and working on RNA secondary structure targeting, post-transcriptional gene regulation and RNA-protein interactions.
The key criteria for the selection of candidates will be the documented quality of their scientific record, a cutting-edge innovative research project, as well as their capacity to interact with other teams at the Research Centre and Clinical Department of the Institute and beyond, and to drive developments in the field of biomedical research and treatment of cancer as the main mission of Institut Curie.
The Unit (https://institut-curie.org/unit/umr9187-u1196) is located at the Research Centre of Institut Curie in Orsay, south of Paris, and close to the Paris-Saclay research hub. The three current research groups of the Unit focus their activities on the development of small molecules to probe and control the biological activities of key nucleic acid and protein targets involved in cancer. The drug- and probe-discovery activity is sustained by molecular modelling approaches and imaging. The CMBC unit is hosting the proprietary Institut Curie–CNRS chemical library comprised of over 12,000 compounds.
The newly recruited group will benefit from the access to the local state-of-the-art research equipment and Institut Curie’s core facilities (https://institut-curie.org/network/curiecoretech). Appropriate laboratory space for 6–7 people and a start-up package will also be available.
The successful candidate should be committed to apply for third-party funding form national and international agencies, as well as for a permanent position at a French institution (CNRS, INSERM, or Paris Saclay University).
The Deadline for application is March 25, 2023.
For information & applications please contact: call.umr9187@curie.fr
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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 | | | | |
