Talk abstracts
Friday 03:30-03:45pm: Disruption of Minor Intron Splicing in Inherited Developmental Disorders
Elizabeth DeLaney (Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute), Rosemary C. Dietrich (Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute), James M. Hiznay (Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute), David E. Symer (Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center), Richard A. Padgett (Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute)
Abstract:
Mutation to components of the pre-mRNA splicing machinery is a significant cause of human disease, and in particular mutations to the minor spliceosome suggest it plays a crucial role in human development. Biallelic mutations in the gene encoding the minor spliceosomal small nuclear RNA (snRNA) U4atac (RNU4ATAC) have been identified in patients with three developmental disorders: microcephalic osteodysplastic primordial dwarfism type I (MOPDI), Roifman Syndrome (RS), and Lowry-Wood Syndrome (LWS). Common features include microcephaly, skeletal dysplasia, and growth retardation. Twenty-six unique disease-causing mutations have been identified in RNU4ATAC. Current data suggests that RNU4ATAC mutations disrupt U4atac snRNA function and impair minor splicing through several mechanisms. Using our in vivo orthogonal splicing assay, we have characterized the effects of RNU4ATAC mutations on minor splicing. Mutations to the 5’ stem-loop region of U4atac and the Sm protein binding site severely reduce splicing, while mutations in the Stem II base pairing region are much more moderate. The mechanism of the splicing defects seen with RNU4ATAC mutations varies depending on the mutation’s location. Mutations to the 5’ stem-loop impair binding of essential U4atac/U6atac di-snRNP protein components and reduce U4atac/U6atac.U5 tri-snRNP formation. Mutations to the Sm protein binding site and Stem II base pairing region result in reduced U4atac abundance, likely due to interference with the recruitment of protein factors such as the Sm proteins and Prpf3. There is a wide range in both the nature and severity of phenotypes observed in patients with RNU4ATAC mutations. We observe a rough correlation when comparing the degree of the splicing defect measured for individual mutations in our assay and the overall severity of the phenotype reported in patients. Collectively, our data suggests there are likely multiple mechanisms that impair minor splicing in MOPDI, RS, and LWS patients.
Keywords: Minor splicing, snRNA, MOPDI
Friday 03:45-04:00pm: Development and characterization of an inducible, hepatocyte-specific mouse model of myotonic dystrophy type 1
Andrew Gupta (Department of Biochemistry, University of Illinois at Urbana-Champaign, IL), Zac Dewald (Department of Biochemistry, University of Illinois at Urbana-Champaign, IL), Ullas Chembazhi (Department of Biochemistry, University of Illinois at Urbana-Champaign, IL), Auinash Kalsotra (Department of Biochemistry, Carl R. Woese Institute for Genomic Biology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, IL)
Abstract:
Myotonic Dystrophy Type 1 (DM1) is a multi-systemic human genetic disorder characterized by muscle wasting, myotonia, cardiac and gastrointestinal abnormalities, and cognitive impairment, among other symptoms. The disease originates from abnormal expansions of CTG repeats in the 3’ UTR of the DMPK gene which, upon transcription, generates DMPK RNA with extended CUG repeats. The repeat-containing RNA bind to and sequester muscleblind-like (MBNL) proteins, a family of alternative splicing regulators, into nuclear foci. Such sequestration induces missplicing of a wide variety of genes, leading to the disease phenotype. Although the disease phenotype has been well-characterized in muscle and heart, the effects of the disease in the liver remain poorly understood. To study the effects in the liver, we have developed a transgenic mouse model for DM1 that recapitulates the disease phenotype in an inducible, liver-specific manner. Namely, a DMPK gene containing 960 CTG repeats has been inserted into the mouse genome and placed under the control of a hepatocyte-specific Tetracycline-on system. We have characterized this mouse model by examining its molecular and physiological phenotypes. qPCR confirms that toxic mRNA is expressed at significant levels following induction with doxycycline. RNA-FISH and immunofluorescence performed on the mouse model shows the formation of toxic RNA foci and the sequestration of MBNL therein, consistent with known disease pathology. Furthermore, we have demonstrated that significant shifts in splicing patterns occur in the transgenic mice compared to wild-type mice. The physiological effects of the disease were then observed using histological stains, which revealed changes in liver morphology, inflammation, and lipid accumulation. Along with characterizing the mouse model, we have successfully used the model to investigate the therapeutic potential of a small-molecule compound.
References:
Chau, A. & Kalsotra, A. Developmental insights into the pathology of and therapeutic strategies for DM1: back to the basics. Developmental Dynamics, 244, 377-390 (2015).
Brook, J.D. et al. Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member. Cell, 68, 799-808 (1992).
Keywords: Myotonic Dystrophy Type 1, alternative splicing, mouse model
Friday 04:00-04:15pm: The kernel of truth: The role of ASAP complex in abscisic acid response regulation during seed germination and early seedling development in Arabidopsis thaliana
Anna Hu (Biochemistry Program, Department of Biology), Claire Schaef (Biochemistry Program, Department of Biology), Xiao-Ning Zhang (Biochemistry Program, Department of Biology)
Abstract:
In eukaryotes, a series of post-transcriptional events produce diverse gene products. These events are mediated by different RNA-binding proteins (RBP). One such conserved complex of RBPs is the apoptosis-and splicing-associated protein (ASAP) complex. In Arabidopsis thaliana, the ASAP complex is composed of three subunits, SERINE/ARGININE-rich 45 (SR45), apoptotic chromatin condensation inducer in the nucleus (Acinus), and Sin3A associated protein 18 (SAP18). Previously, we found that SR45 is required to maintain a normal level of SAP18 protein in the nucleus. Overexpressing SAP18-GFP in the sr45-1 null mutant caused an increase in the expression of FlOWER LOCUS C (FLC), a suppressor for flowering, and a delay in reproduction initiation (flowering) compared to the non-transgenic sr45-1 mutant, suggesting that the ASAP complex may be involved in the regulation of vegetative-to-reproductive transition. In addition, the sr45-1 mutant exhibits abnormal sensitivity to abscisic acid (ABA), a plant hormone that inhibits seed germination and is important for plant abiotic stress response. To investigate whether the ASAP complex is involved in the regulation of ABA response, the wild-type (Col-0), the sr45-1 mutant, Col-0 overexpressing SAP18-GFP and the sr45-1 mutant overexpressing SAP18-GFP were subjected to either mock or 1 uM ABA treatment. Their germination percentages and hypocotyl growth were assessed. All etiolated seedlings were found to have shorter hypocotyls with ABA treatment. The most dramatic difference was seen in the sr45-1 mutant lines overexpressing SAP18-GFP, where most of the seeds were arrested immediately after the exposure to ABA. This suggests that an abnormal distribution of ASAP component proteins may be a reason for the observed hypersensitivity to ABA. In order to understand how this hypersensitivity was achieved, the expression of genes involved in ABA metabolism, ABA signaling pathways, or ABA response was evaluated using qPCR among different genotypes described above. Future research includes an investigation of ABA sensitivity and the expression of these genes in SAP18 knockdown mutant lines as well.
References:
Chen, S. L., Rooney, T. J., Hu, A. R., Beard, H. S., Garrett, W. M., Mangalath, L. M., . . . Zhang, X.-N. (2019). Quantitative proteomics reveals a role for SERINE/ARGININE-RICH 45 in regulating RNA metabolism and modulating transcriptional suppression via the ASAP complex in Arabidopsis thaliana. Fronteirs in Plant Science.
Questa, J. I., Song, J., Geraldo, N., An, H., & Dean, C. (2016). Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science, 353(6298), 485-8. https://doi.org/10.1126/science.aaf7354
Xing, D., Wang, Y., Hamilton, M., Ben-Hur, A., & Reddy, A. S. (2015). Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININE-RICH45 uncovers the unexpected roles of this RNA binding protein in RNA processing. Plant Cell, 27(12), 3294-308. https://doi.org/10.1105/tpc.15.00641
Keywords: apoptosis-and splicing-associated protein (ASAP), Arabidopsis thaliana, abscisic acid
Friday 04:15-04:30pm: Pre-clinical models of PCH10 link CLP1 p.R140H mutation with mRNA misprocessing in motor neuron degeneration
Geneva R. LaForce (Department of Genetics and Genome Sciences, Case Western Reserve University), Jordan S. Farr, Cydni Akesson (Department of Genetics and Genome Sciences, Case Western Reserve University), Evren Gumus (Department of Medical Genetics, Faculty of Medicine, University of Harran), Eric J. Wagner (Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston), Polyxeni Philippidou (Department of Neurosciences, Case Western Reserve University), Ashleigh E. Schaffer (Department of Genetics and Genome Sciences, Case Western Reserve University)
Abstract:
Pontocerebellar Hypoplasia Type 10 (PCH10) is a pediatric neurodegenerative disorder caused by a homozygous p.R140H mutation in CLP1 that leads to hypoplasia of the cerebellum and brainstem with motor neuron degeneration1,2. Here, we present new clinical data from PCH10 patients showing severe frontotemporal cortical and motor neuron degeneration, with minor cerebellar atrophy. These findings suggest phenotypic variability in the penetrance of brain, but not motor neuron features. To date, the pathogenic mechanism of neurodegeneration in PCH10 is unknown. To study the disease pathogenesis of PCH10 in vivo, we developed a mouse model harboring the p.R140H mutation. Mutant mice present with spasticity and seizures. Analysis of the brain revealed no change in cerebellar morphology or cell density, but a decrease in cell density in the anterior isocortex in CLP1 mutant mice compared to controls. Further, we found smaller neuromuscular junctions without overt changes in phrenic motor neuron innervation in the diaphragms of mutant mice. These findings are consistent with the described clinical features of PCH10. To determine the molecular consequence of CLP1 p.R140H in motor neuron disease pathogenesis, we generated iPSC-derived motor neurons from PCH10 patients and an unaffected relative. Characterization of mature motor neurons revealed a phrenic-like identity. During differentiation, we found reduced cell density in PCH10 motor neurons compared to control motor neurons, possibly akin to motor neuron degeneration. CLP1 is a multifunctional RNA kinase important for tRNA and mRNA maturation3. To determine if tRNA or mRNA processing is altered in PCH10 motor neurons, Northern blot and RNA-sequencing analysis of iPSC-derived motor neurons found defects in mRNA processing resulting in differential gene expression, alternative splicing events, and alternative polyadenylation, without changes in tRNA biogenesis. Our data expand the clinical spectrum of PCH10, develop accurate pre-clinical models for the disease, and link p.R140H CLP1 mutation with dysregulation of mRNA processing leading to motor neuron degeneration.
References:
1. Schaffer, A.E. et al. CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Cell 157, 651-63 (2014).
2. Karaca, E. et al. Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Cell 157, 636-50 (2014).
3. Paushkin, S.V., Patel, M., Furia, B.S., Peltz, S.W. & Trotta, C.R. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation. Cell 117, 311-21 (2004).
Keywords: CLP1, Pontocerebellar Hypoplasia Type 10, Neurodegeneration
Friday 04:30-04:45pm: Post-transcriptional regulation of poly(A) binding proteins controls protein synthesis and cardiac growth during development and disease
Joe Seimetz (Department of Biochemistry, University of Illinois Urbana-Champaign), Bo Zhang (Department of Biochemistry, University of Illinois Urbana-Champaign), Sandip Chorghade (Department of Biochemistry, University of Illinois Urbana-Champaign), Stefan Bresson (Department of Microbiology, University of Texas Southwestern Medical Center), Nicholas Conrad (Department of Microbiology, University of Texas Southwestern Medical Center), Auinash Kalsotra (Department of Biochemistry, University of Illinois Urbana-Champaign)
Abstract not available online - please check the printed booklet.
Saturday 08:45-09:00am: Many commutes to work: species specific movement of intron-containing pre-tRNAs from nucleus to cytoplasm by multiple, parallel nuclear tRNA export pathways in yeast
Kunal Chatterjee (Molecular Genetics, The Ohio State University), Anita K.Hopper (Molecular Genetics,The Ohio State University)
Abstract:
In eukaryotic cells, tRNAs are exported out of the nucleus, their site of synthesis, to the cytoplasm, their site of function. We recently reported that the mRNA exporter Mex67-Mtr2 heterodimer co-functions with the canonical tRNA nuclear exporter Los1. Recent genetic and cytological data showed that Crm1, an exporter of proteins containing Leucine rich motif, also functions in tRNA nuclear export. We show that Crm1 is indeed a bonafide nuclear tRNA exporter as in vivo co-immunoprecipitation studies demonstrate that Crm1 co-purifies with tRNA. Moreover, like Mex67-Mtr2 and Los1, Crm1 exhibits substrate specificity for tRNA cargoes. Previous biochemical and structural studies documented that Los1 preferentially binds end-processed, appropriately structured tRNA. Therefore, Los1 also provides a tRNA quality control step, as it ensures tRNA end-processing prior to tRNA nuclear export. The tRNA structural features recognized by Mex67-Mtr2 and Crm1, and whether they participate in tRNA quality control, are unknown. Thus, we assessed the fidelity of the Los1-independent tRNA nuclear export pathways by three independent approaches and show these alternate pathways of tRNA nuclear export are error-prone. The question thus arises, why do cells employ multiple, parallel, but error-prone tRNA nuclear export pathways? We learned that environmental conditions can affect tRNA fidelity. For example, upon subjecting yeast to oxidative stress there is an increase in level of Mex67 and a concomitant elevated level of aberrant 5’-end extended tRNA. Thus, yeast seems to employ Los1-independent, error prone tRNA nuclear export pathways in varying environmental conditions, which may confer yet unknown selective advantages to cells.
Keywords: tRNA nuclear export, Yeast
Saturday 09:00-09:15am: Role of the bifunctional aminoacyl-tRNA synthetase EPRS in human disease
Nathan Kudlapur (Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University), Danni Jin (Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University), Ronald Wek (Department of Biochemistry and Molecular Biology, Indiana University School of Medicine), Karin Musier-Forsyth (Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University)
Abstract not available online - please check the printed booklet.
Saturday 09:15-09:30am: Title not available online - please see the printed booklet.
Jenna M. Lentini (Department of Biology, Center for RNA Biology, University of Rochester), Hessa S. Alsaif (Department of Genetics, King Faisal Specialist Hospital and Research Center), Eissa Faqeih (Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University), Fowzan S. Alkuraya (Department of Genetics, King Faisal Specialist Hospital and Research Center), Dragony Fu (Department of Biology, Center for RNA Biology, University of Rochester)
Abstract not available online - please check the printed booklet.
Saturday 09:30-09:45am: Elucidating the mechanism of BMAA misincorporation and its impact on translation
Nien-Ching Han (Department of Microbiology, The Ohio State University), Tammy J. Bullwinkle (Department of Microbiology, The Ohio State University), Kaeli F. Loeb (Department of Microbiology, The Ohio State University), Kym F. Faull (Pasarow Mass Spectrometry Laboratory, University of California at Los Angeles), Michael Ibba (Department of Microbiology, The Ohio State University)
Abstract:
beta-N-methylamino-L-alanine (BMAA) is a non-proteinogenic amino acid that has been associated with neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease (AD). BMAA has been found in human protein extracts, however, the mechanism by which it enters the proteome is still unclear. It has been suggested that BMAA is misincorporated at serine codons during protein synthesis, but no direct evidence has ever been shown. Here, using LC-MS purified BMAA, we sought to identify which aaRS will utilize BMAA as a substrate for aminoacylation. Despite BMAA’s previously predicted misincorporation at serine codons, following a screen for amino acid activation, we observed that BMAA is not a substrate for human SerRS. Instead, we showed that BMAA is a substrate for human AlaRS and is able to form BMAA-tRNAAla, while escaping from the intrinsic AlaRS proofreading activity. Furthermore, we found that BMAA acts as an inhibitor to both the cognate amino acid activation and the editing function of AlaRS. These results reveal that BMAA disrupts the integrity of protein synthesis through multiple different pathways, hence may be more problematic than previously suggested.
Keywords: BMAA, aminoacyl-tRNA synthetase, non-cognate amino acids
Saturday 09:45-10:00am: Title not available online - please see the printed booklet.
Kommireddy Vasu (Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, USA), Abul Arif, Fulvia Terenzi, Iyappan Ramachandiran, Aayushi Chechi, Debjit Khan, Arnab China, Paul L. Fox (Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, USA)
Abstract not available online - please check the printed booklet.
Saturday 10:00-10:15am: RNA Folding as a Trigger for the Release of Pre-Ribosomes from the Nucleolus
Amber J. LaPeruta (Carnegie Mellon University Department of Biological Sciences), Jelena Micic (Carnegie Mellon University Department of Biological Sciences), Melissa Tosiano (Carnegie Mellon University Department of Biological Sciences), David Kim (Carnegie Mellon University Department of Biological Sciences), John L. Woolford Jr. (Carnegie Mellon University Department of Biological Sciences)
Abstract:
Ribosome biogenesis is an extremely dynamic process requiring the assembly of ~80 ribosomal proteins and 4 rRNAs into the large and small ribosomal subunits in eukaryotes. This process is enabled by ~200 assembly factors, including RNA chaperones, RNA modifiers, scaffolds, molecular mimics, switches and timers, as well as structural and functional proofreaders. Ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is completed in the cytoplasm. We want to determine what triggers the exit of nascent large ribosomal precursors from the nucleolus to the nucleoplasm at a very specific point in subunit maturation. This transition coincides with a particularly complicated, energetically expensive, and dramatic alteration in preribosome protein composition and rRNA structure, which irreversibly alters the biophysical properties of the particles.
Knocking out the gene encoding the non-essential assembly factor Puf6, a known RNA folding chaperone in the PUF family of proteins, slows down this stage of ribosome assembly at cold temperatures. Thus, this puf6Δ mutant is a powerful tool to accumulate assembly intermediates within this stage, and to discern the role of rRNAs, assembly factors and ribosomal proteins in facilitating this uncharacterized transition. To identify interactions among factors participating at this stage, we carried out a multicopy suppressor screen and a selection for genomic suppressors of the puf6Δ cold sensitive phenotype. By coupling these results to biochemical and structural assays, we discerned distinct stages of assembly that occur during this essential transition and discovered additional functions for a number of ribosomal proteins and rRNA structures during this step. Because most molecules work in concert with other molecules in multimolecular complexes, this study will be important for defining principles of RNA and protein cooperation in molecular machines, and how multimolecular complexes are assembled.
Keywords: RNA chaperones, Ribosome Biogenesis, RNA folding
Saturday 10:15-10:30am: MicroRNA-574-FAM210A Axis Regulates Mitochondrial Translation and Influences Pathological Cardiac Remodeling
Kadiam C Venkata Subbaiah (Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14586), Jiangbin Wu (Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14586), Peng Yao (Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14586)
Abstract not available online - please check the printed booklet.
Saturday 11:00-11:15am: Competition between ligand and transcription factor NusA binding modulates riboswitch-mediated regulation of transcription
Adrien Chauvier (University of Michigan - Department of Chemistry), Pujan Ajmera (University of Michigan - Department of Chemistry), Nils Walter (University of Michigan - Department of Chemistry)
Abstract not available online - please check the printed booklet.
Saturday 11:15-11:30am: Structural insight into small Molecule Targeting IRES Domain and Inhibition of Enterovirus 71 Replication
Liang-Yuan Chiu (Case Western Reserve University, Chemistry department), Jesse Davila-Calderon (Case Western Reserve University, Chemistry department), Andrew Sugarman (Case Western Reserve University, Chemistry department), Gary Brewer (Rutgers University, Biochemistry department), Amanda E. Hargrove (Duke university, Chemistry department), Blanton S. Tolbert (Case Western Reserve University, Chemistry department)
Abstract not available online - please check the printed booklet.
Saturday 11:30-11:45am: RNA structure elucidation at single molecule resolution using an integrated framework of long read sequencing and SHAPE-Seq
Swapna Vidhur Daulatabad (Department of Biohealth Informatics, School of Informatics and Computing, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States), Molly E. Evans (Department of Chemical and Biological Engineering, Northwestern University, Evanston IL. Center for Synthetic Biology, Northwestern University, Evanston IL), Quoseena Mir (Department of Biohealth Informatics, School of Informatics and Computing, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States), Julius B. Lucks (Department of Chemical and Biological Engineering, Northwestern University, Evanston IL. Center for Synthetic Biology, Northwestern University, Evanston IL), Sarath Chandra Janga (Department of Biohealth Informatics, School of Informatics and Computing, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States)
Abstract not available online - please check the printed booklet.
Saturday 11:45-12:00pm: Behavior of G-quadruplexes in the presence of biological ions and small molecules
Allison M. Williams (Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA), Philip C. Bevilacqua (Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA)
Abstract not available online - please check the printed booklet.
Saturday 12:00-12:15pm: Investigating TRAP-mediated attenuation of the trp operon with cotranscriptional SHAPE-Seq
Kiel D. Kreuzer (Department of Biological Sciences, University at Buffalo), Molly E. Evans (Department of Chemical and Biological Engineering, Northwestern University), Julius B. Lucks (Department of Chemical and Biological Engineering, Northwestern University), Paul Gollnick (Department of Biological Sciences, University at Buffalo)
Abstract:
In Bacillus subtilis, the trp RNA-binding attenuation protein (TRAP) regulates the expression of the trp (trpEDCFBA) operon that is required for tryptophan biosynthesis1. In excess tryptophan, the 11-mer TRAP is activated to bind to the 11 (G/U)AG triplet repeats in the trp operon leader region and promotes transcription attenuation. The proposed model for this regulatory mechanism involves mutually exclusive RNA structures, where TRAP binding to the leader RNA causes formation of an intrinsic transcription terminator. In the absence of TRAP binding, the terminator is prevented from forming due to overlap with an upstream antiterminator structure that is more thermodynamically stable. Recently, additional studies of TRAP-dependent transcription regulation in vivo and in vitro suggest that the published model of mutually exclusive RNA structures may not fully explain the regulatory mechanism. To further investigate the role of TRAP in RNA structural rearrangement and attenuation during the timescale of transcription, we used cotranscriptional SHAPE-Seq2. This method determines the SHAPE reactivity of nascent RNAs at nucleotide resolution and can reveal folding pathways and kinetically trapped structural intermediates that form as the RNA is transcribed. These structures provide additional information of TRAP-dependent regulation and may be more biologically relevant compared to the structural studies of the RNA under equilibrium conditions. Here, we describe the cotranscriptionally folded trp leader RNA in the presence and absence of TRAP, identify a signature of SHAPE reactivity for TRAP binding, and challenge the existing regulatory model for the role of TRAP in transcription attenuation.
References:
1. Gollnick P. 1994. Regulation of the Bacillus subtilis trp operon by an RNA‐binding protein. Molecular Microbiology. 11: 991-997.
2. Strobel EJ, Watters KE, Nedialkov Y, Artsimovitch I, Lucks JB. 2017. Distributed biotin–streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. Nucleic Acids Res. 45:e109–e109.
Keywords: SHAPE, Termination, Gene regulation
Saturday 12:15-12:30pm: Trypanosoma brucei RAP1 has an RNA binding activity that is essential for VSG monoallelic expression
Amit Kumar Gaurav, Marjia Afrin (Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University), Xian Yang, Xuehua Pan (Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, Peoples Republic of China), Ranjodh Sandhu, Arpita Saha (Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University), Yanxiang Zhao (Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, Peoples Republic of China), Bibo Li (Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University)
Abstract not available online - please check the printed booklet.
Saturday 12:30-12:45pm: Multidomain Convergence of Argonaute During RISC Assembly Correlates with the Formation of Internal Water Clusters
Mi Seul Park (Department of Chemistry and Biochemistry, The Ohio State University), Raul Araya-Secchi, James A. Brackbill (Department of Chemistry and Biochemistry, The Ohio State University), Hong-Duc Phan (Ohio State Biochemistry Program, The Ohio State University), Audrey C. Kehling, Ekram W. Abd El-Wahab (Department of Chemistry and Biochemistry, The Ohio State University), Daniel M. Dayeh (Ohio State Biochemistry Program, The Ohio State University), Marcos Sotomayor, Kotaro Nakanishi (Department of Chemistry and Biochemistry, The Ohio State University)
Abstract not available online - please check the printed booklet.
Saturday 02:30-02:45pm: Catalytic flexibility of the lariat-debranching enzyme, Dbr1
Aiswarya Krishnamohan (Molecular Genetics and Cell Biology, University of Chicago), Daoming Qin (Molecular Genetics and Cell Biology, University of Chicago), Xiuqi Chen (School of Life Science, Tsinghua University), Jonathan Staley (Molecular Genetics and Cell Biology, University of Chicago)
Abstract not available online - please check the printed booklet.
Saturday 02:45-03:00pm: MDM2 alternative splicing is regulated by microRNA binding: A novel pathway of MDM2 regulation
Matias Montes (Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University), Dawn Chandler (Center for Childhood Cancer and Blood Diseases, Nationwide Childrens Hospital)
Abstract not available online - please check the printed booklet.
Saturday 03:00-03:15pm: Human nonsense-mediated mRNA decay is largely independent of UPF3B
Zhongxia Yi (Department of Molecular Genetics, Center for RNA Biology, The Ohio State University), Guramrit Singh (Department of Molecular Genetics, Center for RNA Biology, The Ohio State University)
Abstract not available online - please check the printed booklet.
Saturday 03:15-03:30pm: Inhibition of cytoplasmic cap methylation identifies 5’ TOP mRNAs as recapping targets and reveals recapping sites downstream of native 5’ ends
Daniel del Valle-Morales (Center for RNA Biology, Department of Biological Chemistry and Pharmacology, Molecular, Cellular and Developmental Biology Program, The Ohio State University), Jackson B. Trotman (Center for RNA Biology, Department of Biological Chemistry and Pharmacology,The Ohio State University), Ralf Bundschuh (Center for RNA Biology, Department of Physics,Division of Hematology, The Ohio State University), Daniel R. Schoenberg (Center for RNA Biology, Department of Biological Chemistry and Pharmacology, The Ohio State University)
Abstract:
Cap homeostasis is the cyclical process of decapping and recapping that maintains the translation and stability of a subset of the transcriptome. Previous work showed levels of some recapping targets decline following transient expression of an inactive form of RNMT (ΔN-RNMT), likely due to degradation of mRNAs with improperly methylated caps. The current study examined transcriptome-wide changes following inhibition of cytoplasmic cap methylation. This identified mRNAs with 5’-terminal oligopyrimidine (TOP) sequences as the largest single class of recapping targets. Cap end mapping of several TOP mRNAs identified recapping events at native 5’ ends and downstream of the TOP sequence of EIF3K and EIF3D. This provides the first direct evidence for downstream recapping. Inhibition of cytoplasmic cap methylation was also associated with mRNA abundance increases for a number of transcription, splicing, and 3’ processing factors. Previous work suggested a role for alternative polyadenylation in target selection, but this proved not to be the case. However, inhibition of cytoplasmic cap methylation resulted in a shift of upstream polyadenylation sites to annotated 3’ ends. Together, these results solidify cap homeostasis as a fundamental process of gene expression control and show cytoplasmic recapping can impact regulatory elements present at the ends of mRNA molecules.
References:
1) Trotman JB, Giltmier AJ, Mukherjee C, Schoenberg DR. RNA guanine-7 methyltransferase catalyzes the methylation of cytoplasmically recapped RNAs. Nucleic Acids Res. 2017;45:10726-10739.
2) Mukherjee C, Patil DP, Kennedy BA, Bakthavachalu B, Bundschuh R, Schoenberg DR. Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Rep. 2012;2:674-684.
3)Gentilella, Morón-Duran F, Fuentes P,eZweig-Rocha G, Riaño-Canalias F,Pelletier J, Ruiz M,Turón G, Castaño J, Tauler A, Bueno C, Menéndez P,Kozma SC, Thomas G. Autogenous Control of 5′TOP mRNA Stability by 40S Ribosomes. Molecular Cell 2017;67:55-70
Keywords: RNA, Cytoplasmic capping
Saturday 03:30-03:50pm: High-resolution integrative analyses define precise cytoplasmic RNA recapping sites in mammalian cells
Trinh T. Tat (Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX), Dongyu Zhao (Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX), Kaifu Chen (Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX), Daniel L. Kiss (Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX)
Abstract not available online - please check the printed booklet.
Saturday 03:50-04:10pm: Non-canonical Function of the piRNA Pathway in C. elegans
Wen Tang (The Department of Biological Chemistry and Pharmacology, The Ohio State University), Craig Mello (RNA Therapeutics Institute, University of Massachusetts Medical School)
Abstract:
piRNAs are expressed in the germline and are required for fertility. The best-established function of piRNAs is to defend genome against transposons. It remains unclear whether these piRNAs have additional functions beyond genome defense, and whether they impact animal development outside of the germline.
we identified a single piRNA derived from the X-chromosome (21ux-1). It plays an important role in dosage compensation and sex determination in the nematode C. elegans. 21ux-1 targets the transcript of xol-1, a pivotal regulator of sexual development and dosage compensation. Mutations of 21ux-1 sensitize hermaphrodite embryos to dosage compensation and sexual transformation defects. We show 21ux-1 functions in preserving the gender naiveté of embryos by preventing maternal transmission of xol-1 mRNA and protein from the mother to embryos. X-chromosome derived non-coding RNAs such as Xist are associated with dosage compensation. Here we describe the first example of a nematode X-derived non-coding RNA that regulate such process through a novel maternal repressive mechanism. Our findings suggest that Piwi pathways have conserved functions linked to these and potentially many other critical gene regulatory events.
Keywords: small RNAs, Gene regulation