Center for RNA Biomedicine

RNA Faculty Candidate Seminar: Rachel Niederer, Yale School of Medicine
2022-01-10 16:00 - 17:00 (America/Detroit)
“Uncovering novel translational control elements within 5′ UTRs”
Rachel Niederer, Ph.D.
Postdoctoral Researcher
Yale School of Medicine

Co-Hosts: The Center for RNA Biomedicine, Department of Biological Chemistry, and the Department of Human Genetics
Hybrid Seminar:
In-person: Biomedical Science Research Buliding (BSRB), ABC Seminar rooms
Zoom: https://umich.zoom.us/webinar/register/WN_qg4fyCUbQZyVu0oGrBLmWQ
Abstract: Translational control of gene expression plays an essential role during development, response to stress and a wide range of cellular processes. However, the key mRNA features that distinguish efficiently translated from poorly translated mRNAs remain largely unknown. This talk will describe the development of direct analysis of ribosome targeting (DART) and its use both in discovering novel regulatory elements within 5′ untranslated regions (5′ UTRs) as well as revealing unexpected behaviors from features that were previously thought to be well understood.
In-person event COVID guidelines
Flyer in PDF

RNA Faculty Candidate Seminar: Dr. Alisha 'Jonesy' Jones, Institute of Structural Biology, Helmholtz Zentrum Munich
2021-12-20 16:00 - 17:00
“Modulation of the MALT1 pre-mRNA structure by hnRNP proteins regulates T cell activation”
Dr. Alisha ‘Jonesy’ Jones
Postdoctoral Researcher
Institute of Structural Biology
Helmholtz Zentrum Munich

Flyer in PDF
Co-Hosts: The Center for RNA Biomedicine, Department of Biological Chemistry, and the Program in Biophysics
Hybrid Seminar:
In-person: Biomedical Science Research Buliding (BSRB), ABC Seminar rooms
Zoom: https://umich.zoom.us/webinar/register/WN_3yrQ47UuTKKuzigbe38Sww
Keywords: pre-mRNA, hnRNP, NMR, SHAPE, structure
Abstract: Alternative splicing is controlled by differential binding of trans-acting RNA binding proteins (RBPs) to cis-regulatory pre-mRNA elements. How pre-mRNA secondary structure affects recognition by RBPs and determines alternative exon usage is poorly understood. The MALT1 paracaspase is a key component of signaling pathways that mediate innate and adaptive immune responses. Alternative splicing of MALT1 exon7 is critical for controlling optimal T cell activation. Here, we demonstrate that MALT1 pre-mRNA splicing depends on RNA structural elements that shield the splice sites of the alternatively spliced exon7. The RBPs hnRNP U and hnRNP L bind comparably and competitively to identical stem-loop RNA structures flanking the 5’ and 3’ splice sites of MALT1 exon7. While hnRNP U stabilizes RNA stem-loop conformations that maintain exon7 skipping, hnRNP L destabilizes these RNA elements to facilitate recruitment of the essential splicing factor U2AF2 to promote exon7 inclusion. This work represents a paradigm for the control of splice site selection by differential RBP binding and modulation of pre-mRNA structure.
In-person event COVID guidelines

RNA Collaborative Seminar Series // Host: Harvard Medical School Initiative for RNA Medicine
2021-12-15 16:00 - 17:00
For the seminar details, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Faculty Candidate Seminar: Paul Donlin-Asp, Max Planck Institute for Brain Research
2021-12-13 16:00 - 17:00
“Resolving the localisation and dynamics of mRNA and protein synthesis within neurons”
Paul Donlin-Asp, Ph.D.
Postdoctoral Researcher
Department of Synaptic Plasticity
Max Planck Institute for Brain Research

Flyer in PDF
Co-Host: The Department of Molecular, Cellular, and Developmental Biology
Hybrid Seminar:
In-person: Biomedical Science Research Building (BSRB), ABC Seminar rooms
Zoom: https://umich.zoom.us/webinar/register/WN_tZjYxppSQwaDVTYIuC0jkw
Keywords: mRNA dynamics, local protein synthesis, neurons, neuronal cell biology, synaptic plasticity, in vivo imaging
In-person event COVID guidelines

Chase Beisel, Helmholtz Center for infection Research
2021-12-07 12:00 - 13:00
“Multiplexable RNA Detection by Cas9 Paves the Way for Novel COVID Testing Method”
Chase Beisel, Helmholtz Center for infection Research
Department of Biological Chemistry seminar
Location: 3330 MS I
Hosts: Yan Zhang and Nils Walter

RNA Collaborative Seminar Series // Host: Penn RNA Group - University of Pennsylvania
2021-12-01 16:00 - 17:00

RNA Collaborative Seminar Series // Host: The RNA Institute, University At Albany
2021-11-17 16:00 - 17:00

BiolChem Seminar: Ailong Ke, Cornell University
2021-11-09 12:00 - 13:00
“Structural Basis of Bacterial CRISPR Immunity”
Ailong Ke, Cornell University
Department of Biological Chemistry seminar
Location: 3330 MS I
Hosts: Yan Zhang and Nils Walter

RNA Innovation Seminar: Zhonggang Hou & Jun Hee Lee
2021-11-08 16:00 - 17:00
“Harnessing diverse compact CRISPR-Cas3 for long-range genome engineering”
Zhonggang Hou, Ph.D.
Research Investigator
Biological Chemistry
ABSTRACT: Leading CRISPR-Cas technologies employ Cas9 and Cas12 enzymes that generate RNA-guided dsDNA breaks. Yet, the most abundant microbial adaptive immune systems, Type I CRISPR, is under-exploited for eukaryotic application. I will discuss our effort on adopting the first minimal CRISPR-Cas3 from Neisseria Type I-C system, to create targeted large chromosomal deletions in human cells. RNP delivery of the processive Cas3 nuclease and target recognition complex Cascade, gave up to 90% editing efficiency. Unexpectedly, Type I-C Cascade assembly in bacteria requires a previous unknown internal translation product Cas11 from within the cas8 gene. Our data show that expression of a separately encoded Cas11 is the key to enable plasmid- and mRNA- based editing in human cells. We demonstrate that “supplying cas11” is a universal strategy to harness divergent and streamlined Type I-C, I-D and I-B editors with distinct PAM preferences and guide orthogonality. Our findings expand the CRISPR toolbox for long-range genome engineering.
KEYWORDS: CRISPR; genome editing; Cascade; Cas3; Cas11; DNA targeting; crRNA; large deletion; Neisseria; genome engineering

“Microscopic Examination of Spatial Transcriptome through Seq-Scope”
Jun Hee Lee, Ph.D.
Associate Professor
Molecular & Integrative Physiology
KEYWORDS: Spatial Transcriptomics, Seq-Scope

Registration: https://umich.zoom.us/webinar/register/WN_qBK6mw7vQa6jOkZuS81_VQ
FLYER IN PDF

RNA Collaborative Seminar Series // Host: UCSC Center for Molecular Biology of RNA
2021-11-03 16:00 - 17:00

BiolChem Seminar: Michael Terns, University of Georgia
2021-10-26 12:00 - 13:00
“Know Thy Enemy: Making CRISPR Memories”
Michael Terns, University of Georgia
Department of Biological Chemistry seminar
Location: 3330 MS I
Hosts: Yan Zhang and Nils Walter

RNA Collaborative Seminar Series // Host: Helmholtz Institute for RNA-based Infection Research
2021-10-20 09:00 - 10:00

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: [REDACTED]
https://umich.zoom.us/j/94758007294?pwd=[REDACTED]
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
