RNA Innovation Seminar: Chase Weidmann, Washington University School of Medicine in St. Louis
2020-10-05 16:00 - 17:00 (America/Detroit)
“Defining functional hubs in RNA-protein interaction networks”

Chase Weidmann, Ph.D.
Postdoctoral Research Scholar in the laboratory of Ben Major
Department of Cell Biology & Physiology, Washington University School of Medicine in St. Louis

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Keywords: mRNA regulation, noncoding RNA, RNA Structure, RNP granules
Abstract:
Chase Weidmann, Ph.D. has contributed broadly to the field of RNA Biology during his career, studying mechanisms of codon bias during translation, post-transcriptional regulation of mRNAs by RNA-binding proteins, the folding of long non-coding RNAs, and how RNA-protein interaction networks contribute to the function and assembly of functional RNP particles. Chase developed a chemical probing strategy and next-gen sequencing technology, called RNP-MaP, that maps the location of and cooperation between multi-protein networks on RNAs in live cells. Going forward, Chase is interested in understanding how alterations in RNA-binding protein profiles, a cell’s “RBPome”, confer deleterious activities onto noncoding RNAs in human disease, especially in cancer. To further empower this work and his future research program, Chase is now generating and integrating protein mass spectrometry data into his RBPome projects.

RNA Collaborative Seminar Series - The RNA Institute, University at Albany hosting
2020-10-07 16:00 - 17:00
Hosted by: The RNA Institute, University at Albany
Joseph Wade, Ph.D. “Pervasive translation in Mycobacterium tuberculosis”
Scott Tenenbaum, Ph.D., “sxRNA: The Engineering of trans-Acting 3-Way Junctions for Function”
Moderator: Thomas Begely, Ph.D.

Link: https://albany.zoom.us/j/92165416119?pwd=[REDACTED]
Recording of the session
For more information, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Innovation Seminar: Gene Yeo, University of California, San Diego
2020-10-19 16:00 - 17:00
Systematic discovery of molecular and cellular functions of RNA binding proteins
Gene Yeo, PhD
Professor, Dept of Cellular and Molecular Medicine, UCSD
Co-Director, UCSD Bioinformatics and Systems Biology Graduate Program
University of California, San Diego
Institute for Genomic Medicine
UCSD Stem Cell Program
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Abstract: The life-cycle of RNA from transcription to translational regulation is mediated by a diverse (>2000) set of proteins called RNA binding proteins. My lab studies the many roles that RNA binding proteins have in affecting RNA expression, splicing, transport and translation. Through our studies on RNA processing, we have introduced therapeutic strategies to treat neurodegenerative and muscular diseases, built cellular models of neurodevelopmental and neurodegenerative diseases and developed experimental and computational tools that enable the community to probe RNA binding protein-RNA interactions at scale. I will discuss (1) our established and new technologies to identify RNA targets of human RBPs at scale, (2) systematic assays to assign molecular roles to RBPs and (2) functional screens to identify RBPs implicated in cancer / RNA granule formation.

RNA Collaborative Seminar Series - University of Pennsylvania RNA Group hosting
2020-10-21 16:00 - 17:00
Hosted by: University of Pennsylvania RNA Group
Kathy Fange Liu, Ph.D.
“RNA species dance to the beat of modifications”
Yoseph Barash, Ph.D.
“Splicing quantification from RNASeq – How to get the signal out of the noise?”

Moderator: Jeremy E Wilusz, Ph.D.
Recording of the session
For more information, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Innovation Seminar: Aleksandra Filipovska, University of Western Australia
2020-10-26 09:00 - 10:00
Regulation of the mitochondrial transcriptome in health and disease
Aleksandra Filipovska, Ph.D.
Professor
The University of Western Australia Centre for Medical Research

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Abstract:
Mitochondria produce more than 90% of the energy required by our bodies and thereby have a fundamental role in cell and energy metabolism. Mitochondria are composed of proteins encoded by both the nuclear and mitochondrial genomes and the coordinated expression of both genomes is essential for energy production. Impaired energy production leads to mitochondrial dysfunction that causes or contributes significantly to a variety of diseases including metabolic disorders and cardiovascular diseases. Mitochondrial dysfunction is caused by mutations in nuclear or mitochondrial genes that encode proteins or regulatory RNAs essential for mitochondrial biogenesis. How uncoordinated gene expression causes mitochondrial dysfunction and compromised energy production in heart and metabolic diseases is poorly understood, making it difficult to develop effective treatments. To unravel how mitochondrial function fails and to identify therapeutic targets it is necessary (i) to understand how gene expression is regulated between mitochondria and the nucleus and (ii) how this regulation is disrupted in disease. We have created new and unique models of metabolic and cardiovascular diseases caused by mutations or loss of nuclear encoded RNA-binding proteins (RBPs) that regulate mitochondrial RNA metabolism and protein synthesis. These new models have identified that energy dysfunction can differentially affect specific organs such as the heart or liver, or multiple organs leading to heart failure or metabolic diseases that can be devastating, such as mitochondrial diseases, or may be as common as insulin resistance and obesity. I will discuss the mechanisms behind these diverse pathologies caused by impaired gene expression and energy dysfunction in heart and metabolic disease.
Keywords: mitochondria, RNA, ribosomes, translation

RNA Collaborative Seminar Series - University of Rochester Center for RNA Biology hosting
2020-11-04 16:00 - 17:00
For the seminar details, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Innovation Seminar: Michelle Hastings, Rosalind Franklin University
2020-11-16 16:00 - 17:00
“Splice-switching Antisense Oligonucleotides for the Treatment of Disease”

Michelle Hastings, Ph.D.
Professor, Cell Biology and Anatomy; Director, Center for Genetic Diseases
Rosalind Franklin University of Medicine and Science

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ABSTRACT: Antisense oligonucleotides (ASOs) have proven to be an effective therapeutic platform for the treatment of disease. These short, single-stranded, modified nucleotides function by base-pairing with the complementary sequence of an RNA and modulating gene expression in a manner that is dependent on the ASO design and targeting site. We have used ASOs to normalize aberrant gene expression associated with a number of diseases of the nervous system including Alzheimer’s and Parkinson’s disease and Usher syndrome. One of our approaches is under development for the treatment of CLN3 Batten disease, a fatal, pediatric lysosomal storage disease caused by mutations in a gene encoding the lysosomal membrane protein CLN3. The most common mutation associated with CLN3 Batten is a deletion of exons 7 and 8 (CLN3Δex78), which disrupts the mRNA open reading frame by creating a premature termination codon that results in the production of a truncated protein. We devised a therapeutic strategy for treating CLN3 Batten Disease using an ASO that basepairs to CLN3 pre-mRNA and alters splicing to correct the open reading frame of the mutated transcript. Treatment of CLN3Δex78 neonatal mice by intracerebroventricular injection of the ASO resulted in the desired splicing effect throughout the central nervous system, improved motor deficits associated with the disease in mice, reduced histopathological features of the disease in the brain and extended life in a severe mouse model of the disease. Our results demonstrate that ASO-mediated reading frame correction is a promising therapeutic approach for CLN3 Batten disease.
KEYWORDS: pre-mRNA splicing, Antisense oligonucleotides, Usher syndrome, Batten Disease, lysosomal storage diseases

RNA Collaborative Seminar Series - Harvard Medical School Initiative for RNA Medicine hosting
2020-11-18 16:00 - 17:00

RNA Collaborative Seminar Series - University of California, Santa Cruz hosting
2020-12-02 16:00 - 17:00

U-M Life Sciences Institute Seminar Series:Astrid D. Haase, M.D., Ph.D., NIH
2020-12-03 12:00 - 13:00
“A small RNA perspective on genomic conflict”
Astrid D. Haase, M.D., Ph.D., Stadtman Tenure-Track Investigator, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Hosted by: Vivian Cheung, M.D.
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RNA Innovation Seminar: John Mattick, University of New South Wales, Sydney, Australia
2020-12-07 17:00 - 18:00
RNA at the epicenter of cell and developmental biology

John Mattick, Ph.D.
Professor of RNA Biology
School of Biotechnology and Biomolecular Sciences
University of New South Wales, Sydney, Australia

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ABSTRACT: The genomic programming of the development of complex organisms appears to have been misunderstood. The human genome contains just ~20,000 protein-coding genes, similar in number and with largely orthologous functions as those in other animals, including simple nematodes with only 1,000 somatic cells. By contrast, the extent of non-protein-coding DNA increases with increasing developmental complexity, reaching 98.8% in humans. Moreover, it is now clear that the majority of the genome is not junk but is differentially and dynamically transcribed to produce not only mRNAs but also tens if not hundreds of thousands of short and long non-protein-coding RNAs that show specific expression patterns and subcellular locations. Many of these noncoding RNAs have evolved rapidly under positive selection for adaptive radiation, and many have been shown to have important roles in development, brain function, cancer and other diseases. They function at many different levels of gene expression and cell biology, including translational control, formation of subcellular (phase-separated) domains, and guidance of the epigenetic processes and chromatin dynamics that underpin development, brain function and physiological adaptation, with plasticity enabled by RNA editing, RNA modification and retrotransposon mobilization. These discoveries mean that the assumption that combinatorial control by transcription factors and other regulatory proteins is sufficient to account for human ontogeny is incorrect, as are the circular assumptions about the neutral evolution of the genome. The challenge now is to determine the structure-function relationships of these RNAs and their mechanisms of action, as well as their place in the decisional hierarchies that control human development, physiology, learning and susceptibility to disorders

RNA Innovation Seminar: Narry Kim, Seoul National University
2020-12-14 16:00 - 17:00
“RNA-based regulation of viruses”
Narry Kim, PhD
Professor, School of Biological Sciences
Seoul National University
Founding Director, RNA Research Center
Institute for Basic Science

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Abstract: Viruses rely heavily on RNA binding proteins for their success as pathogens. In this presentation, I will first talk about RNA tail modification which impacts viral and cellular gene expression. We found that TENT4 enzymes extend poly(A) tail of mRNAs with ‘mixed tails’ to delay deadenylation and stabilize the RNAs. Hepatitis B virus and human cytomegalovirus hijack this mechanism to efficiently stabilize their own RNAs. In the later part of my presentation, I will discuss our recent work on SARS-CoV-2. To delineate the viral transcriptomic architecture and provide a high-resolution map of SARS-CoV-2, we performed deep sequencing of infected cells. Our data define the canonical transcripts and noncanonical transcripts encoding unknown ORFs. More recently, we have also performed proteomic analyses of the SARS-CoV-2 ribonucleoprotein complex. We identify many proteins that directly interact with viral RNAs and modulate viral growth. Functional investigation of the viral transcripts and host proteins discovered in this study will open new directions to the research efforts to elucidate the life cycle and pathogenicity of SARS-CoV-2.

Bio: Narry Kim is a Professor in the School of Biological Sciences at Seoul National University and a founding director of RNA Research Center at Institute for Basic Science. She received her Ph.D. in 1998 from the University of Oxford where she studied lentiviruses and gene delivery. With keen interest in RNA biology, she joined the Gideon Dreyfuss lab at the University of Pennsylvania and researched the role of the exon junction complex in mRNA surveillance. Her current research group investigates how genes are regulated at the RNA level, with particular interests in microRNA, mRNA, and viral RNA. She is a recipient of the L’Oreal-UNESCO Women in Science Award, Hoam Prize, and Asan Prize, and a member of KAS, NAS and EMBO.

RNA Collaborative Seminar Series - European Molecular Biology Laboratory (EMBL) hosting
2020-12-16 09:00 - 10:00

RNA Collaborative Seminar Series - NCI RNA Biology Initiative hosting
2021-01-13 16:00 - 17:00

RNA Innovation Seminar: Elena Conti, Max Planck Institute of Biochemistry
2021-01-25 09:00 - 10:00
Talk title: The RNA exosome complex: the Dr Jekyll and Mr Hyde of RNA degradation
Elena Conti, PhD
Director, Max Planck Institute of Biochemistry

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Keywords: molecular mechanisms, RNA, ribosome, biochemistry, cryo-EM, X-ray crystallography
Abstract: All RNAs in eukaryotic cells are eventually degraded. The RNA exosome is a conserved macromolecular machine that degrades a vast number and variety of RNAs. Exosome-mediated RNA degradation leads to the complete elimination of nuclear and cytoplasmic transcripts in turnover and quality control pathways, and to the partial trimming of RNA precursors in nuclear processing pathways. How the exosome combines specificity and versatility to either eliminate or process RNAs has been a long-standing question.
Over the years, our group has used biochemical and structural approaches to understand how the exosome core complex channels RNA substrates for degradation and how it associates with its nuclear and cytoplasmic cofactors. Visualizing how the exosome cofactors interact with pre-ribosomes in the nucleus and with mature ribosomes in the cytoplasm has provided insights into the mechanisms with which different exosome-ribosome assemblies underpin opposite outcomes of RNA degradation: a constructive function of the nuclear exosome in the maturation of the large ribosomal subunit and a destructive function of the cytoplasmic exosome in the destruction of ribosome-bound mRNAs. Ongoing work is uncovering the unanticipated levels of regulation intrinsic to this multi-purpose degradation machinery.
Our group has a long-standing interest in RNA metabolism, with a particular focus on the molecular mechanisms of eukaryotic RNA transport and degradation. >more

RNA Innovation Seminar: Jeff Twiss, University of South Carolina
2021-02-01 16:00 - 17:00 | Virtual
“Regulating the axonal proteome through mRNA transport and translation”

Jeffrey L. Twiss, M.D., Ph.D.
SmartState Chair in Childhood Neurotherapeutics
Professor of Biological Sciences
University of South Carolina

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Abstract: Neurons are extremely polarized cells with axonal and dendritic processes extending 100 to 1000 fold longer or more than the cell body diameter. Our lab has been interested in how axons grow to such great distances and how they respond to injury. mRNAs are transported into axons, with their localized translation providing the axon with autonomy to respond to different stimuli by modifying their local proteome. Transport, translation, and stability of axonal mRNAs is driven by interactions with RNA binding proteins and different signaling cascades. I will focus on recent work that gives insight into how specificity of these mechanisms is driven for different cohorts of axonal mRNAs.
Keywords: Neuron, Axon, RNA transport, Translational regulation

LSI Seminar: Blanton S. Tolbert, Ph.D., Case Western Reserve University
2021-02-04 12:00 - 13:00
Structural biophysics of RNA interactions that contribute to viral replication
Blanton S. Tolbert, Ph.D.
Professor of Chemistry
Case Western Reserve University

LSI Seminar Series
Interests: Biochemistry, Biophysical Chemistry, Structural Biology
Blanton S. Tolbert is a professor of chemistry at Case Western Reserve University, where he oversees a diverse research group that endeavors to understand biochemical mechanisms by which human pathogenic RNA viruses replicate within cells, and to leverage this knowledge to identify novel drug targets for therapeutic intervention. Tolbert is the PI of multiple NIH grants, and he has published in top journals including Nature Communications, the Proceedings of the National Academy of Sciences and the Journal of the American Chemical Society. Tolbert also serves on the NIH Office of AIDS Research Advisory Council (OARAC), and he will become the next chair of OARAC in 2021. He is a member of the Burroughs Wellcome Fund Postdoctoral Enrichment Program Advisory Board and an editor for the Journal of Biological Chemistry and Microbiology and Molecular Biology Reviews. Tolbert is the proud father of two boys, and in his spare time he enjoys exploring the outdoors in the Cleveland Metroparks.

RNA Innovation Seminar: Karla Neugebauer, Yale University
2021-02-15 16:00 - 17:00
“Dynamics of co-transcriptional pre-mRNA processing and assembly of related biomolecular condensates”
Prof. Karla Neugebauer, Ph.D.
Professor of Molecular Biophysics and Biochemistry and of Cell Biology
Director of Graduate Studies, Molecular Biophysics and Biochemistry
Director, Yale Center for RNA Science and Medicine
Yale School of Medicine
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Abstract: My lab is interested in the coordination between transcription, RNA processing and nuclear organization that governs gene expression. We have established experimental systems in budding yeast, zebrafish embryos, and mammalian tissue culture cells to explore transcription and splicing regulation in a variety of biological contexts and with a diversity of tools, from imaging to genome-wide approaches. Our observations have provided novel insights into transcription and splicing mechanisms as well as principles of cellular organization that facilitate efficient gene expression. In this talk, I will be discussing rapid co-transcriptional splicing during erythropoiesis and how Cajal bodies assemble to ensure a steady supply of spliceosomal components.

BiolChem Seminar: Katrin Karbstein, Scripps Institute Florida
2021-02-23 12:00 - 13:00
“Choreographing Ribosome Assembly”

Katrin Karbstein, Ph.D.
Scripps Institute Florida

Department of Biological Chemistry, Greenberg Lecture
Zoom link: https://umich.zoom.us/j/96151442305

RNA Collaborative Seminar Series // Host: Helmholtz Institute for RNA-based Infection Research
2021-02-24 09:00 - 10:00
Presenters:
Neva Caliskan, Ph.D.
Mathias Munschauer, Ph.D.
For the seminar details, visit: https://www.rnasociety.org/rna-collaborative-seminar-series

RNA Innovation Seminar: Melissa J. Moore - Chief Scientific Officer, Moderna Therapeutics
2021-03-03 16:00 - 17:00
This event was rescheduled from February 10, 4:00 pm.
To attend on March 3rd, please register again. Apologies for the inconvenience.
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“A timely confluence: The backstory of Moderna’s COVID-19 vaccine”

Melissa Moore, Ph.D.,
Chief Scientific Officer, Moderna Therapeutics
Dr. Moore will address scientists and non-scientists, and will take live questions.
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In her role as Chief Scientific Officer, Platform Research, Dr. Melissa Moore is responsible for leading mRNA biology, delivery and computation science research at Moderna. She joined Moderna in 2016 from the University of Massachusetts Medical School, where she served as Professor of Biochemistry & Molecular Pharmacology, Eleanor Eustis Farrington Chair in Cancer Research and a long-time Investigator at the Howard Hughes Medical Institute (HHMI). Dr. Moore was also a founding Co-Director of the RNA Therapeutics Institute (RTI) at UMassMed, and was instrumental in creating the Massachusetts Therapeutic and Entrepreneurship Realization initiative (MassTERi), a faculty-led program intended to facilitate the translation of UMMS discoveries into drugs, products, technologies and companies. Dr. Moore is an elected member of the National Academy of Sciences (2017) and a Fellow of the American Academy of Arts and Sciences (2019).
Dr. Moore holds a B.S. in Chemistry and Biology from the College of William and Mary, and a Ph.D. in Biological Chemistry from MIT, where she specialized in enzymology under Prof. Christopher T. Walsh. She began working on RNA metabolism during her postdoctoral training with Phillip A. Sharp at MIT. During her 23 years as a faculty member, first at Brandeis and then at UMassMed, her research encompassed a broad array of topics related to the roles of RNA and RNA-protein (RNP) complexes in gene expression, and touched on many human diseases including cancer, neurodegeneration, and preeclampsia.

BiolChem Seminar: Lori Passmore, MRC Laboratory of Molecular Biology
2021-03-09 12:00 - 13:00
“Mechanistic Insights into the mRNA Poly(A) Tail Machinery”

Lori Passmore, Ph.D.
MRC Laboratory of Molecular Biology

Department of Biological Chemistry, Greenberg Lecture

RNA Collaborative Seminar Series // Host: Alberta RNA Research and Training Institute (ARRTI)
2021-03-10 16:00 - 17:00

RNA Innovation Seminar: James Nuñez, HHMI Hanna Gray Fellow, UCSF
2021-03-15 16:00 - 17:00
“Programmable transcriptional memory by CRISPR-based epigenome editing”
James Nuñez, Ph.D.
HHMI Hanna Gray Fellow
University of California, San Francisco
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ABSTRACT: General approaches for heritably altering gene expression would enable many discovery and therapeutic efforts. I will present CRISPRoff— a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications to turn off transcription. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks enabled us to explore the rules for heritable silencing. We identify sgRNAs capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. Our finding that targeted DNA methylation outside of CGIs leads to memorized gene silencing expands the canonical model of methylation-based silencing and broadly enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.
KEYWORDS: CRISPR, transcription, epigenetics

RNA Collaborative Seminar Series // Host: UMass Medical School, RNA Therapeutics Institute
2021-03-24 16:00 - 17:00

5th Annual RNA Symposium: "Processing RNA" - Day 1
2021-03-25 11:00 - 14:30
Day 1
11:00–11:05 / Welcome
11:05–12:00 / Keynote 1: Tracy Johnson, Ph.D., University of California – Los Angeles (RNA splicing)
12:00–12:10 / Short break
12:10–1:05 / Keynote 2: Kevin Weeks, Ph.D., University of North Carolina (RNA structure in vivo)
1:05–1:35 / Data Blitz (three finalists from the poster submissions)
1:35–2:30 / Keynote 3: Feng Zhang, Ph.D., MIT (CRISPR applications)
2:30–2:30 / Brief closing
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5th Annual RNA Symposium: "Processing RNA" - Day 2
2021-03-26 11:00 - 14:30
Day 2
11:00–11:05 / Welcome
11:05–12:00 / Keynote 4: Brenda Bass, Ph.D., University of Utah (RNA editing & silencing)
12:00–12:10 / Short break
12:10–1:05 / Keynote 5: Christopher Lima, Ph.D., Memorial Sloan-Kettering (RNA degradation)
1:05–1:35 / Data Blitz (three finalists from the poster submissions)
1:35–2:25 / Panel discussion with keynote speakers
2:25–2:30 / Closing
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RNA Innovation Seminar: Natoya Peart, University of Pennsylvania
2021-04-05 16:00 - 17:00
“Direct binding of ESRP1 to regulated transcripts is required for position-dependent splicing regulation”
Natoya Peart, Ph.D.
Postdoctoral Researcher – Carstens Lab/Lynch Lab
Department of Medicine/Department of Biochemistry and Molecular Biophysics
University of Pennsylvania
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KEYWORDS: Alternative splicing, RNAMap, Esrp1
ABSTRACT: Coordinated regulation of alternative splicing is essential to the establishment of cell identity. The Epithelial Splicing Regulatory Proteins (Esrps), ESRP1 and ESRP2, are highly conserved paralogous proteins required for organogenesis of multiple organ systems and compromised function of Esrps contributes to human diseases and pathologies. Esrps are robustly expressed in the epithelial cells of the epidermis, large and small intestines, salivary glands, stomach, and a variety of other tissues, where they are vital in promoting an epithelial splicing network. Although ESRP1 and ESRP2 share partial functional redundancy, ESRP1 appears to play a larger role in regulating gene expression.
Using a combination of enhanced immunoprecipitation coupled with high throughput sequencing (eCLIP) in the epithelial cells of mouse epidermis and RNA sequencing analysis of alterations in splicing and total gene expression that result from epidermal ablation of Esrp1 and Esrp2 we generate a map of Esrp1 binding to RNA. We show that ESRP1 regulates splicing primarily through direct binding in a position-dependent manner to either promote exon inclusion or skipping. In particular, we show that Esrp1 binding upstream of or withing alternatively spliced exons suppresses exon inclusion, whilst binding downstream of the non-constitutive exon promotes exon inclusion. In addition, we identified widespread binding of ESRP1 in 3’ and 5’ untranslated regions (UTRs) of genes enriched for epithelial cell function suggesting that it directly regulates post-transcriptional gene expression steps in addition to splicing.

Seminar: Eva Nogales, Ludwig Lecture
2021-04-06 12:00 - 13:00
“Exploring the Modularity of Large Complexes Involved in Transcription Initiation and Chromatin Modifications”

Eva Nogales, PhD
Howard Hughes Medical Institute investigator, Professor of Biochemistry and Molecular Biology
University of California, Berkeley
Senior Faculty Scientist
Lawrence Berkeley National Laboratory

Department of Biological Chemistry, Ludwig Lecture

RNA Collaborative Seminar Series // Host: Bay Area RNA Club (BARC)
2021-04-07 16:00 - 17:00
