Center for RNA Biomedicine

RNA Innovation Seminar: Jailson (Jay) Brito Querido, MRC Laboratory of Molecular Biology
2021-04-19 16:00 - 17:00 (America/Detroit)
“Structural insights into mRNA translation initiation in humans”
Jailson (Jay) Brito Querido, Ph.D.
Postdoctoral Scientist
MRC Laboratory of Molecular Biology
Cambridge, UK
ZOOM
FLYER IN PDF
REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_78YYOhIhTbOBy2_JSdM7Wg
ABSTRACT: A key step in translational initiation is the recruitment of the 43S pre-initiation complex (43S PIC) by the cap-binding complex (eIF4F) at the 5´ end of mRNA. Eukaryotic initiation factors eIF1, eIF1A, eIF3, eIF5, and the ternary complex (TC) of eIF2–GTP–tRNAiMet bind to the 40S ribosomal subunit to form the 43S PIC. Once assembled, the 43S PIC is recruited to the cap-binding complex eIF4F at the 5´end of mRNA to form a 48S initiation complex (48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we determined the structure of a reconstituted human 48S using cryo-electron microscopy. The structure reveals insights into early events of translation initiation complex assembly. It reveals how eIF4F interacts with subunits of the eIF3 structural core near the mRNA exit channel in the 43S. The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests a “blind-region” that would preclude recognition of start sites upstream of the location of the P site at the point of recruitment.
KEYWORDS: mRNA, ribosome, eIF4F, eIF4A, translation

RNA Collaborative Seminar Series // Host: Shanghai RNA Club
2021-04-21 09:00 - 10:00
For the seminar details, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

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.

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

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: Groupe de Recherche RNA (GDR)
2021-05-19 09:00 - 10:00

RNA Collaborative Seminar Series // Host: European Molecular Biology Laboratory (EMBL)
2021-06-02 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: Yale Center for RNA Science and Medicine
2021-06-16 16:00 - 17:00

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: iRNA @ Istituto Italiano di Tecnologia (IIT)
2021-07-14 09:00 - 10:00

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: RiboClub Sherbrooke
2021-08-11 16:00 - 17:00

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

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.

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: 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).

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 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

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 Faculty Candidate Seminar: Rachel Niederer, Yale School of Medicine
2022-01-10 16:00 - 17:00
“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: Jailson (Jay) Brito Querido, MRC Laboratory of Molecular Biology
2022-01-31 16:00 - 17:00
“The scanning mechanism of mRNA translation initiation in humans”
Jailson (Jay) Brito Querido, Ph.D.
Postdoctoral Scientist
MRC Laboratory of Molecular Biology
Cambridge, UK

Co-Hosts: The Center for RNA Biomedicine, Department of Biological Chemistry, and the Program in Biophysics
Hybrid Seminar:
In-person: Biomedical Science Research Building (BSRB), ABC Seminar rooms
Zoom: https://umich.zoom.us/webinar/register/WN_pcS-fWIdSS-hDnKzoRhXeg
Keywords: mRNA, translation, ribosome, helicase
Abstract: Decoding the genetic information into protein is fundamental for all kingdoms of life. It requires precise mechanisms to transcribe the DNA into mRNA, which then can be translated by the ribosome to produce proteins. Translation initiation of eukaryotic mRNAs is a dynamic process regulated by over a dozen protein eukaryotic initiation factors (eIFs). This process starts with the binding of eukaryotic initiation factors eIF1, eIF1A, eIF3, eIF5, and a ternary complex of eIF2–GTP–tRNAiMet (TC) to the 40S small ribosomal subunit, forming the 43S preinitiation complex (43S PIC). Once assembled, the 43S PIC is recruited to the 5′ untranslated region (UTR) of mRNA by the multifactor cap-binding complex eIF4F, forming the 48S initiation complex (48S). The 48S then scans along the 5′ UTR mRNA to locate a start codon. The eIF4F binding site in the 48S and how mRNA is inserted into the mRNA channel in the 40S small ribosomal subunit remained unknown. To gain insights into the molecular mechanism underlining the assembly of the 48S, we used cryo-electron microscopy to determine the structure of a reconstituted human 48S. The structure sheds light on the early events of translation initiation complex assembly, including how eIF4F interacts with the 43S during the scanning process.
In-person COVID Events Policy

RNA Faculty Candidate Seminar: Margaret (Maggie) Rodgers, Johns Hopkins University
2022-02-14 16:00 - 17:00
“Mechanisms of co-transcriptional ribonucleoprotein assembly”
Margaret (Maggie) Rodgers, Ph.D.
Postdoctoral Researcher
Johns Hopkins University

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_Icqg8jRbQNGCBEFkj_u5Gw
Keywords: RNA, RNP, ribosome assembly, transcription, single-molecule fluorescence
Seminar flyer in PDF
In-person event COVID guidelines

Seminar: John Prensner, MD, PhD
2022-02-28 16:00 - 17:00
“Translating the cancer genome: dark matter proteins”
John Prensner, M.D., Ph.D.
Physician, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center
Instructor of Pediatrics, Harvard Medical School

Co-Hosts: The Center for RNA Biomedicine, Department of Computational Medicine & Bioinformatics, and Department of Pediatric Oncology
Hybrid Seminar:
In-person: Biomedical Science Research Building (BSRB), ABC Seminar rooms
Zoom: https://umich.zoom.us/webinar/register/WN_bC6oy6VZTLy3ke4iMS2sKQ
Keywords: cancer, ribosome profiling, functional genomics, gene discovery
Abstract: Although genomic analyses predict many non-canonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins in diseases such as cancer. Here, we have developed functional genomics platforms to systematically interrogate non-canonical ORFs identified in ribosome profiling data. Using CRISPR loss-of-function screens in numerous human cancer models, we define the frequency with which ORFs contribute to cell essentiality phenotypes. We further constructed large-scale ORF plasmid libraries to assess their capacity to encode a protein and induce cancer cell transcriptional changes. We pursued focused investigation of several uncharacterized protein-coding loci, defining roles for the lncRNA-ORF GREP1 in breast cancer and the ASNSD1 upstream ORF (uORF) in medulloblastoma. Lastly, we have assembled a pathway to bring such ORF candidates into the mainstream of biological research via an international consortium of gene database stakeholders. Together, this work establishes non-canonical ORFs as critical mediators of cancer cell biology, suggests their potential promise as therapeutic targets in cancer, and outlines a path forward for dissemination of these ORFs amongst the global research community.
In-person COVID Events Policy

RNA Therapeutics Seminar, Michelle Hastings, Rosalind Franklin University
2022-03-21 15:00 - 16:00
Inaugural RNA Therapeutics Seminar
Michelle Hastings, Ph.D.
Professor, Cell Biology and Anatomy; Director, Center for Genetic Diseases
Rosalind Franklin University of Medicine and Science

This is an internal U-M event:
In-person: Palmer Commons, Forum Hall
Zoom: https://umich.zoom.us/webinar/register/WN_mUj40sudTwmI6hXANnlJEg
Keywords: pre-mRNA splicing, Antisense oligonucleotides, Usher syndrome, Batten Disease, lysosomal storage diseases
Seminar flyer in PDF
In-person COVID Events Policy

RNA Innovation Seminar: Sika Zheng, UC Riverside, School of Medicine
2022-05-09 16:00 - 17:00
“Unexpected determinants of neuronal identity and properties: the curious cases of PTBP1, PTBP2, and neuronal splicing”
Sika Zheng, Ph.D.
Associate Professor, Director of Center for RNA Biology and Medicine
UC Riverside, School of Medicine

Flyer in PDF

Virtual Seminar
Zoom: https://umich.zoom.us/webinar/register/WN_dltbxWdHQ5KrC3rTl4hqLQ
Abstract:
Alternative splicing is the major contributor to transcriptome diversity, but splicing is noisy and to what extend alternative splicing regulation is indispensable for biolgical processes has been controversial. Our studies have revealed the regulation and function of neural-specific splicing in shaping neuronal identity and estalishing neurons’ two unique attributes: 1. Axonogenesis (Only neurons but no other cell types have one and single axon); 2. Neuronal longevity (Neurons are the most long-lived cell types). We show that obtaining these neuronal features is coordinated by RNA binding proteins PTBP1 and PTBP2, while PTBP1 was suggested by others to be a reprogramming factor of neuronal fate. I will discuss the regulatory mechanism of neural specific splicing underlying neurogensis and maturation.
References:
Zhang M, Ergin V, Lin L, Stork C, Chen L, Zheng S. Neuron. 2019 Feb 20;101(4):690-706.e10.
Ergin V, Zheng S. J Mol Biol. 2020 Jun 26;432(14):4154-4166.
Zheng S. Wiley Interdiscip Rev RNA. 2020 Jul;11(4):e1585.
Lin L, Zhang M, Stoilov P, Chen L, Zheng S. Neuron. 2020 Sep 23;107(6):1180-1196.e8.
Vuong J, Ergin V, Zheng S. Nature Communications (accepted)

RNA Innovation Seminar: Daniel O’Reilly
2022-05-16 16:00 - 17:00
“An Academic Approach to Oligonucleotide Therapeutics”
Daniel O’Reilly Ph.D., MRSC
Post-Doctoral Associate
Khvorova Lab
RNA Therapeutics Institute
University of Massachusetts Medical School
Flyer in PDF

HYBRID SEMINAR:
In-person: BSRC, ABC seminar rooms
Zoom: https://umich.zoom.us/webinar/register/WN_dM1a1aKVTM2KfwiieutOWg
Keywords: Oligonucleotides, Chemical Modifications, RNA, Huntington’s Disease
Abstract: Nucleic acids (NA) are becoming the third major pillar of therapeutic modalities on par with small molecules and biologics. The diversity of NA molecular mechanisms, ranging from vaccines, antisense, short interfering RNA (siRNAs), and guide RNA for CRISPR gene editing systems, enable impact on most aspects of cellular biology and thus human medicine. The foundation behind the recent oligonucleotides’ clinical success is fundamental chemical innovations in RNA stability, delivery, and synthesis.
Oligonucleotides are informational drugs; thus, if chemical architectures supporting safe and efficient delivery to the tissue of interest are achieved, they can be easily reprogrammed to modulate any gene expression on demand, creating an opportunity for academic institutions to drive therapeutic innovation. However, the process is limited by access to oligonucleotide chemistry and synthetic expertise.
In the first half of the talk, I will share the experience of building and running Nucleic Acid Chemistry Center in a context of a large academic institution. The NACC provides access to therapeutic quality screening leads and large manufacturing of preclinical compounds for the academic community. The impact of the NACC and chemical innovation will be discussed in the context of two significant projects. First, I will discuss the systematic structure-activity relationship study of chemical modifications to modulate RISC loading and cleavage. Screening 1200 siRNA variants allow for defining the chemical and thermodynamic rules for RISC assembly.

RNA Innovation Seminar: Zhipeng Lu, USC
2022-09-12 16:00 - 17:00
“RNA Structures, Interactions and Modifications”
Zhipeng Lu (鲁志鹏), Ph.D.
Assistant Professor
Pharmacology and Pharmaceutical Sciences
University of Southern California

Flyer in PDF
In-person: BSRB, ABC seminar rooms / hybrid link
Abstract: RNA in living cells are in constant motion, form dynamic structures, and interact with many molecules, including other RNAs. Direct determination of RNA structures and interactions in vivo is essential to understanding their functions, but has been challenging in the past. We developed a number of novel chemical and computational tools to capture the 2D and 3D RNA structurome and interactome in cells, providing a comprehensive view of RNA conformations that underlie their roles in gene regulation and human diseases. Applications of these methods revealed new mechanisms in lncRNA functions, RNA modifications and splicing regulation.

RNA Innovation Seminar: David Shechner, University of Washington
2022-09-26 16:00 - 17:00
“Meet the neighbors: A universal technology for probing RNA-interactions and RNA-scaffolded subcellular compartments in situ”
David Shechner Ph.D.
Assistant Professor of Pharmacology
University of Washington

Flyer in PDF
In-person: BSRB, ABC seminar rooms / hybrid link
Keywords: RNA, proximity-biotinylation, subcellular architecture, nuclear architecture, spatial biology, biomolecular condensates, interactomics, nucleolus, Xist.

Abstract: In the context of the living cell, very little RNA is naked. RNA molecules form complex, dynamic networks of molecular interactions that underlie a host of biochemical functions, and which are central to organizing subcellular compartmentalization. In humans, for example, RNAs are key determinants of chromatin folding, and they nucleate and scaffold a host of biomolecular condensates that collectively control cellular metabolic, epigenetic, and stress-signaling pathways. But, characterizing these structures—identifying the biomolecules within an RNA’s subcellular microenvironment—remains technically cumbersome.
To address this challenge, I introduce oligonucleotide-mediated proximity-interactome mapping (O-MAP), a straightforward and flexible method for identifying the proteins, RNAs, and genomic loci near a target RNA, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA. These enzymes then pervasively label all nearby (~20 nm) molecules, enabling their enrichment by streptavidin pulldown. O-MAP induces exceptionally precise RNA-targeted biotinylation, and its modular design enables straightforward validation of probe pools and real-space optimization of the biotinylation radius, thus overcoming key technical challenges for the field. Moreover, O-MAP can be readily ported across different target RNAs and specimen types, including patient-derived organoids and tissue samples. And, O-MAP achieves this without complex cell-line engineering, using only off-the-shelf parts and standard manipulations.
Using a small cohort of model RNAs, we have developed a robust O-MAP toolkit for proteomic (O-MAP-MS), transcriptomic (O-MAP-Seq) and genome interaction (O-MAP-ChIP) discovery. O-MAP of the 47S-pre-rRNA—the long noncoding RNA that scaffolds the nucleolus—enabled a comprehensive “multi-omic” analysis of this subnuclear structure, and revealed hundreds of novel nucleolar protein-, RNA-, and chromatin interactions. O-MAP of XIST—the master regulator of X-chromosome inactivation—revealed novel RNAs that may play a role in this process, and unanticipated interactions between XIST and other chromatin-regulatory RNAs. Finally, targeting O-MAP to introns within a key cardiac developmental gene enabled unprecedented molecular dissection of a subnuclear compartment that would be impossible to purify biochemically.
Given these results, we believe that O-MAP will be a powerful tool for elucidating the mechanisms by which RNA molecules drive subcellular compartmentalization in time and space, with particular impact on our understanding of nuclear architecture. Moreover, with O-MAP’s precision, flexibility, and ease, we anticipate its broad use in studying countless other RNA phenomena throughout biology, and as a clinical diagnostic- and discovery tool.
