Center for RNA Biomedicine

RNA Collaborative Seminar Series // Host: Helmholtz Institute for RNA-based Infection Research
2021-10-20 09:00 - 10:00 (America/Detroit)
For the seminar details, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Innovation Seminar: Tim Stasevich, Ph.D.
2021-10-18 16:00 - 17:00
“Imaging single-mRNA translation dynamics in living color”
Tim Stasevich, Ph.D.
Associate Professor
Dean and Pingping Tsao Professor of Biochemistry
CSU Monfort Professor
Boettcher Investigator
Colorado State University
Registration: https://umich.zoom.us/webinar/register/WN_OzTuwf2zRN-6zCZk1pA_lQ

Flyer in PDF
Keywords:
translational regulation, gene expression, fluorescence microscopy, intrabodies, single-molecule imaging
Abstract:
My lab is creating technology to image mRNA translation in real time and with single-molecule precision in living cells. In this talk, I will introduce our technology and describe how it can be used to amplify fluorescence from newly synthesized proteins as they are being translated from single mRNAs. I will show how we quantify these signals to determine the size, shape, subcellular localization, and mobilities of mRNA translation sites, as well as their protein synthesis dynamics. I will then highlight a few recent applications of our technology, focusing mainly on a new biosensor we have developed to quantify how individual regulatory factors impact single mRNA translation dynamics. Using this biosensor, we provide evidence that human Argonaute2 (Ago2) shuts down translation by down regulating translation initiation on the minutes timescale and helping usher translationally silent mRNAs into P-bodies on the hours timescale. I will conclude by discussing new fluorescent intrabodies my lab is engineering to light up nascent and mature proteins in multiple colors. As these intrabodies can be encoded on plasmids, they can easily be adapted by other labs to image gene activity in diverse living systems.
Timothy J. Stasevich is an Associate Professor in the Department of Biochemistry and Molecular Biology at Colorado State University (CSU). His lab uses a combination of advanced fluorescence microscopy, genetic engineering, and computational modeling to study the dynamics of gene regulation in living mammalian cells. His lab helped pioneer the imaging of real-time single-mRNA translation dynamics in living cells1. Dr. Stasevich received his B.S. in Physics and Mathematics from the University of Michigan, Dearborn, and his Ph. D. in Physics from the University of Maryland, College Park. He transitioned into experimental biophysics as a post-doctoral research fellow in the laboratory of Dr. James G. McNally at the National Cancer Institute. During this time, he developed technology based on fluorescence microscopy to help establish gold-standard measurements of live-cell protein dynamics. Dr. Stasevich next moved to Osaka University, where he worked with Dr. Hiroshi Kimura as a Japan Society for the Promotion of Science Foreign Postdoctoral Research Fellow. While there, he helped create technology to image endogenous proteins and their post-translation modifications in vivo. This allowed him to image the live-cell dynamics of epigenetic histone modifications during gene activation for the first time2. Before joining the faculty at CSU, Dr. Stasevich spent a year as a Visiting Fellow at the HHMI Janelia Research Campus, where he applied superresolution fluorescence microscopy to improve the spatiotemporal resolution of endogenous protein imaging in live cells.
1. Morisaki, T. et al. Real-time quantification of single RNA translation dynamics in living cells. Science 352, 1425–1429 (2016).
2. Stasevich, T. J. et al. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516, 272–275 (2014).

BiolChem Seminar: Sam Sternberg, Columbia University
2021-10-12 12:00 - 13:00
“Functional Interplay Between CRISPR-Cas and Transposable Elements”
Sam Sternberg, Columbia University
Department of Biological Chemistry seminar
Location: 3330 MS I
Hosts: Yan Zhang and Nils Walter

RNA Collaborative Seminar Series // Host: NUS-CSI Singapore RNA Biology Center
2021-10-06 09:00 - 10:00

Human Genetics Seminar: Rajesh Rao, Ophthalmology & Visual Science, U-M Medical School
2021-10-05 15:00 - 16:00
“Genetics through the Lens of an Ophthalmologist and Vision Scientist”
Rajesh C. Rao, M.D.
Leonard G. Miller Professor
Associate Professor
Department of Ophthalmology & Visual Sciences
Department of Pathology

Department of Human Genetics seminar
ZOOM MEETING ID: 947 5800 7294
PASSCODE: 900076
https://umich.zoom.us/j/94758007294?pwd=Sk9VMGlnTXRZWWJwbnZCZUx4MlI0QT09
FLYER IN PDF

RNA Innovation Seminar: Byron Purse, Ph.D.
2021-10-04 16:00 - 17:00
“Fluorescent nucleoside analogues with new properties”
Byron Purse, Ph.D.
Associate Professor
Organic Chemistry
San Diego State University

HYBRID SEMINAR:
In-person: Forum Hall, Palmer Commons
Zoom: https://umich.zoom.us/webinar/register/WN__vvE2dtHQi-R3h05JUHBzQ
FLYER IN PDF
Abstract:
Fluorescent nucleoside analogues (FNAs) are powerful probes for studying the structure and dynamics of nucleic acids, which are vital to understanding RNA function, DNA damage repair, nucleic acid–protein interactions, regulatory mechanisms for gene expression, and other aspects of nucleic acid function. Existing FNAs are prone to quenching by base pairing and stacking, are clustered at the blue–green end of the visible spectrum, and have limited brightness as compared with conventional fluorophores. Studies of nucleic acid function would benefit greatly from overcoming these limitations. We have designed, synthesized, and studied a series of fluorescent pyrimidine analogues, aiming to address these limitations and develop a detailed understanding of the relationships between chemical structure and fluorescent responses to local environment in nucleic acids. Included in this series is a tricyclic cytidine analogue DEAtC that is nearly non-fluorescent as a nucleoside, but responds to matched base pairing and stacking with a fluorescence turn-on. A chlorinated tricyclic cytidine 8-Cl-tCO reports on local environment by changes in the vibrational fine structure of its emission spectra. To address the problem of limited brightness, we have design and synthesized a new NFA that we call ABN, which has a conjugated push–pull system similar to those found in bright fluorophores such as rhodamines. ABN is the brightest known FNA when present in duplex nucleic acids, and it is readily detected in single-molecule fluorescence measurements using both 1-photon and 2-photon excitation. Collectively, these FNAs offer new capabilities for biophysical studies on nucleic acids. Comparisons of their structure and properties help to reveal mechanisms for fluorescence changes in response to local environment in nucleic acids.

Jayakrishnan Nandakumar, MCDB
2021-09-24 10:00 - 11:00
“Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites”
Jayakrishnan Nandakumar, Ph.D.
U-M LSI Structure Series
Location: LSI Library

RNA Collaborative Seminar Series // Host: NCI RNA Biology Initiative
2021-09-22 16:00 - 17:00

BiolChem Seminar: Alexis Komor, UCSD
2021-09-21 12:00 - 13:00
“Base Editing-Performing Chemistry on the Genome”
Alexis Komor, UCSD
Department of Biological Chemistry seminar
Location: Zoom Webinar https://umich.zoom.us/j/91821866007
Hosts: Yan Zhang and Nils Walter

BiolChem Seminar: Jason McLellan, University of Texas at Austin
2021-09-14 12:00 - 13:00
“Structure-Function Studies of the SARS-CoV-2 Spike and Development of COVID-19 Interventions”
Jason McLellan, University of Texas at Austin
Department of Biological Chemistry seminar
Location: 3330 MS I
Host: Janet Smith

RNA Innovation Seminar, Rhiju Das, Ph.D.
2021-09-13 16:00 - 17:00
“Recent improvements in modeling and design of RNA-only structures”
Rhiju Das, Ph.D.
Associate Professor
Departments of Biochemistry and (by courtesy) Physics
Stanford University
Registration: https://umich.zoom.us/webinar/register/WN_i7vWSsxDQfSVbQP1C7HGSQ

Abstract:
The discovery and design of biologically important RNA molecules is outpacing three-structural characterization. I’ll describe results from my and Wah Chiu’s groups that demonstrate that cryo-electron microscopy can resolve maps of several kinds of RNA-only systems. These maps enable subnanometer-resolution 3D coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. If time allows, I’ll describe work from the Eterna project to stabilize mRNA molecules to help accelerate worldwide COVID immunization.

Bioinnitiatives in Brain Cancer (BIBC) | Castro & Lowenstien
2021-09-10 16:00 - 17:00
BIBC Hybrid Seminar Series: Dr. Pedro Lowenstein and Dr. Maria G. Castro
DATE: Friday, September 10, 2021
TIME: 4:00 pm—5:00 pm
LOCATION: NCRC, B10 Research Auditorium
Dr. Maria G. Castro and Dr. Pedro Lowenstein, Richard C. Schneider Collegiate Professors of Neurosurgery will be presenting their novel work studying glioma invasion, migration, growth, and the immune tumor microenvironment.
The BIBC seminars will showcase the multidisciplinary research of faculty studying brain cancer biology and novel technologies that can be used for brain cancer diagnosis and treatment. The seminars will be held on campus with a hybrid option. If you have not already received building access for NCRC, enter through the Building 10 front entrance.
Anyone attending the seminar in person must complete the ResponsiBLUE questionnaire and show the screening check when entering the research auditorium. At this time, masks are required for all individuals regardless of vaccination status. We will update this event if University policy changes with regards to in-person events.

RNA Collaborative Seminar Series // Host: Rochester
2021-09-08 16:00 - 17:00

Dipali Sashital, Iowa State University
2021-09-07 12:00 - 13:00
“Achieving and Balancing Specificity in the CRISPR-Cas Systems”
Dipali Sashital, Iowa State University
Department of Biological Chemistry seminar
Zoom link: https://umich.zoom.us/j/91821866007
Hosts: Yan Zhang and Nils Walter

RNA Collaborative Seminar Series // Host: Institute of Molecular Biology (IMB)
2021-08-25 09:00 - 10:00

RNA Collaborative Seminar Series // Host: RiboClub Sherbrooke
2021-08-11 16:00 - 17:00

RNA Collaborative Seminar Series // Host: MD Anderson Center for RNA Interference and Non-Coding RNAs
2021-07-28 09:00 - 10:00

RNA Collaborative Seminar Series // Host: iRNA @ Istituto Italiano di Tecnologia (IIT)
2021-07-14 09:00 - 10:00

RNA Collaborative Seminar Series // Host: University of Michigan
2021-06-30 16:00 - 17:00
REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_6OEQ6sDAQ0-21GHm6d7VEQ

“Dynamic multivalent interactions drive mammalian RNA regulation”

Sethu Pitchiaya, Ph.D.
Department of Urology

“Characterizing cellular RNA-protein interaction networks with chemical probes”
Chase Weidmann, Ph.D.
Department of Biological Chemistry

For the seminar details, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Collaborative Seminar Series // Host: Yale Center for RNA Science and Medicine
2021-06-16 16:00 - 17:00

RNA Innovation Seminar featuring Rising Scholars: Khan & McMillan
2021-06-14 16:00 - 17:00
Registration: https://umich.zoom.us/webinar/register/WN_uLz-ONHVQPuRINMYUNvBJQ
Flyer: Khan & McMillan Seminar flyer

“CCR5 as a model to examine reporter assays in evaluating translational phenomena”
Yousuf Khan
Knight-Hennessy Scholar
NSF fellow
Stanford University

Keywords: dual luciferase, frameshifting, recoding, CCR5
Abstract: During the decoding of a subset of mRNAs, a proportion of ribosomes productively shift to the −1 reading frame at specific slippage-prone sites in a phenomenon known as programmed −1 ribosomal frameshifting (−1 PRF) to generate a frameshifted, C-terminally unique protein. The first experimentally verified occurrence of functionally utilized non-retroelement derived −1 PRF in humans has been reported in the mRNA encoding the immune-functioning C-C chemokine receptor 5 (CCR5). Here, we show that frameshifting does not occur during CCR5 decoding. Apart from its importance in understanding expression of a gene relevant to cancer, an HIV-1 receptor (and the associated claimed rationale for generating the first humans derived from genetically modified embryos), the findings imply that caution is appropriate in assessing results from translational reporter assays.
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“Intersection between RNA methylation and TDP43-mediated toxicity in ALS”

Mike McMillan
Ph.D. candidate
Cellular and Molecular Biology
University of Michigan

Keywords: TDP43, m6A, ALS, RNA stability
Abstract: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease resulting in the death of upper and lower motor neurons. ALS has no known cure and limited therapeutic options, and the underlying pathological mechanisms remain unclear. Despite considerable variability in clinical presentation, over 95% of ALS cases exhibit cytoplasmic inclusions of the RNA binding protein TDP43. Emerging evidence suggests that TDP43 is crucial for RNA stability, and that dysregulation of RNA homeostasis may contribute to ALS pathogenesis.
Methylation of RNA at the 6th position nitrogen (N6-methyladenosine methylation, or m6A) by methyltransferases (writers) or removal of methyl groups by demethylases (erasers) has dramatic effects on RNA stability and translation mediated by a family of RNA biding proteins that recognize methylated RNA (readers). m6A writers and erasers specifically localize to nuclear speckles, membraneless nuclear organelles rich in RNA binding proteins and splicing factors, including TDP43. Together with our data showing that TDP43 regulates RNA stability, these observations suggest that TDP43 may destabilize m6A modified RNA. Here, we show that methylated RNA co-purified with TDP43 from cultured cells via RNA immunoprecipitation, and abrogation of methylation sites disrupted TDP43 binding, suggesting that TDP43 recognizes m6A modified RNA in cellulo. We also noted profound and widespread hypermethylation of coding and non-coding transcripts in ALS spinal cord, many overlapping with confirmed TDP43 target transcripts. Consistent with a central role for m6A modification in TDP43-mediated toxicity, we identified several factors operating within the m6A pathway that enhance or suppress the toxicity of TDP43 in rodent primary cortical neurons via a single-cell CRISPR/Cas9 candidate-based screen. Genetic knockout of the established m6A reader YTHDF2 rescued TDP43 toxicity in primary neurons, and YTHDF2 was also upregulated in ALS postmortem sections. Together, these data imply a fundamental link between m6A RNA modifications and ALS pathogenesis, potentially mediated by TDP43-dependent RNA destabilization.

RNA Collaborative Seminar Series // Host: European Molecular Biology Laboratory (EMBL)
2021-06-02 16:00 - 17:00

26th Annual RNA Society Virtual meeting
2021-05-25 - 2021-06-05
For more details, visit: https://www2.rnasociety.org/conferences/rna-2021/
2021 ORGANIZERS:
Gene Yeo – University of California San Diego, USA
Jörg Vogel – University of Würzburg, Germany
Katrin Karbstein – Scripps Research Institute, Florida, USA
Xavier Roca – Nanyang Technological University, Singapore
V. Narry Kim – Seoul National University, South Korea
Anna Marie Pyle – Yale University, USA

RNA Collaborative Seminar Series // Host: Groupe de Recherche RNA (GDR)
2021-05-19 09:00 - 10:00

Seminar: Nick Ingolia, UC Berkeley
2021-05-18 16:00 - 17:00
ZOOM LINK
“Dissecting gene regulatory networks with CiBER-Seq”
Nicholas Ingolia, PhD
Assistant Professor
Department of Molecular & Cell Biology
University of California, Berkeley
Faculty host:
Kristin Koutmou, Ph.D.
Seyhan N. Ege Assistant Professor of Chemistry
Department of Chemistry
Department of Chemistry Seminar
ABSTRACT: Cells integrate environmental signals and internal physiology to dynamically control gene expression. We have developed a technique to dissect this regulatory logic by linking targeted, genome-wide genetic perturbations with a deep-sequencing readout that quantitatively measures the expression phenotype induced by each perturbation. Our approach combines CRISPR interference (CRISPRi) with barcoded expression reporters (CiBER-seq) to profile transcriptional, translational, and posttranslational regulatory responses, connecting each guide in a genome-scale library with its individual phenotypic consequences. Applying CiBER-Seq to the well-studied integrated stress response (ISR) pathway recapitulated the known biology of this pathway and uncovered further triggers for ISR activation that were not previously appreciated. The quantitative phenotypic measurements from CiBER-Seq are well suited to epistasis analysis, and we measure dual-perturbation phenotypes and compare patterns of genetic interaction to gain further insight into regulatory pathways. CiBER-Seq is an incisive tool for dissecting genetic networks, and can be applied to study a wide range of biological processes, using gene expression regulation as a sensitive and specific readout of the state of the cell.

RNA Innovation Seminar: Thomas Martinez, Salk Institute for Biological Studies
2021-05-17 16:00 - 17:00
“Annotation and Characterization of Human Protein-coding Small Open Reading Frames”
Thomas Martinez, Ph.D.
Postdoctoral Fellow
Salk Institute for Biological Studies
ZOOM
REGISTRATION REQUIRED:
https://umich.zoom.us/webinar/register/WN_90RkcQTGQZa7ifQ8kbSdNQ
FLYER IN PDF
KEYWORDS: microprotein, smORF, ribosome profiling
ABSTRACT: Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. Several smORF-encoded microproteins have been characterized and implicated in a variety of critical processes, including regulation of mRNA decay, DNA repair, and muscle formation. Thus, rigorous and comprehensive annotation of protein-coding smORFs is critical to our understanding of basic biology and physiology, as well as disease. We recently developed an improved workflow that integrates de novo transcriptome assembly and ribosome profiling to overcome obstacles with previous methods to more confidently annotate thousands of novel smORFs across multiple human cell lines, including hundreds encoded on putative non-coding RNAs. Over 1,500 smORFs are found in two or more cell lines, and ~40% lack a canonical AUG start codon. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. We also find that smORF-derived peptides are detectable on human leukocyte antigen complexes, positioning smORFs as a source of novel antigens. The annotation of protein-coding smORFs radically alters the current view of the human genome’s coding capacity and will provide a rich pool of unexplored, functional human genes.
BIOGRAPHY: Thomas received his B.S. in Biological Engineering from MIT and trained in Prof. JoAnne Stubbe’s laboratory, where he studied the mechanism of ribonucleotide reductase. He then received his Ph.D. in Biochemistry & Molecular Biophysics from Caltech as an NIH NRSA predoctoral fellow under the mentorship of Prof. Peter Dervan. His thesis work focused primarily on characterizing the effects of DNA binding pyrrole-imidazole polyamides on DNA replication in prostate cancer cells. Thomas is currently an NIH NRSA postdoctoral fellow in Prof. Alan Saghatelian’s laboratory, where he has developed an integrative platform combining ribosome profiling and de novo transcriptome assembly to discover functional smORF encoded microproteins in the human genome.

RNA Collaborative Seminar Series // Host: Cambridge RNA Club
2021-05-05 09:00 - 10:00

Seminar: Tatjana Trcek, Johns Hopkins University
2021-05-04 15:00 - 16:00
Zoom link
“RNA Granules: A View from the RNA Perspective”
Tatjana Trcek, PhD
Assistant Professor
Department of Biology
Johns Hopkins University

Hosted by:
Stephanie Moon, Ph.D.
Assistant Professor of Human Genetics
Faculty Scholar of the Center for RNA Biomedicine
Affiliate Faculty, Biological Chemistry
FLYER IN PDF
Department of Human Genetics Seminar

RNA Innovation Seminar: Olivia Rissland, University of Colorado School of Medicine
2021-05-03 16:00 - 17:00
“Regulating the Regulators: Control of RNA Binding Proteins during Embryogenesis”
Olivia Rissland, Ph.D.
Assistant Professor
RNA Bioscience Initiative | Department of Biochemistry & Molecular Genetics
University of Colorado School of Medicine
ZOOM
REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_vA9zYS5nSEenf8Zmt1f-qA
FLYER IN PDF

ABSTRACT: The maternal-to-zygotic transition (MZT) is a conserved step in animal development, where control is passed from the maternal to the zygotic genome. Although the MZT is typically considered from its impact on the transcriptome, we previously found that three maternally deposited Drosophila RNA binding proteins (ME31B, Trailer Hitch [TRAL], and Cup) are also cleared during the MZT by unknown mechanisms. Here, we show that these proteins are degraded by the ubiquitin-proteasome system. Marie Kondo, an E2 conjugating enzyme, and the E3 CTLH ligase are required for the destruction of ME31B, TRAL, and Cup. Structure modeling of the Drosophila CTLH complex suggests that substrate recognition is different than orthologous complexes. Despite occurring hours earlier, egg activation mediates clearance of these proteins through the Pan Gu kinase, which stimulates translation of Kondo mRNA. Clearance of the maternal protein dowry thus appears to be a coordinated, but as-yet underappreciated, aspect of the MZT.

RNA Collaborative Seminar Series // Host: Shanghai RNA Club
2021-04-21 09:00 - 10:00
