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Principal Investigator: Wyatt ALLEN MILLER
Organization: IOWA STATE UNIVERSITY
Fiscal Year: 2021
Award: $174,750
Funding agency: National Institute of Allergy and Infectious Diseases
Flaviviruses include many serious pathogens such as Zika, dengue, West Nile, and yellow fever viruses. In infected cells these viruses produce abundant, noncoding, short flavivirus RNAs (sfRNAs) that comprise most of the ~500 nucleotide 3’ untranslated region of the viral genome. These novel viral RNAs have been shown recently to interact with numerous host proteins and inhibit translation (protein synthesis) of certain genes of the innate immune system. Thus, virus strains that produce high levels of sfRNA are more pathogenic, and mutants that produce no sfRNA are so mild as to be promising vaccine candidates. However, a picture of how sfRNA globally affects translation of cellular mRNAs is lacking. The Zika virus (ZIKV) epidemic of 2014-16 resulted in frighteningly frequent cases of microcephaly and other developmental and neurological disorders caused by exposure to ZIKV in utero. In addition to inhibiting the immune response, ZIKV sfRNA inhibits Fragile X Mental Retardation Protein (FMRP), a key translational regulator of neurological development. Thus, this knowledge of the global effects of ZIKV sfRNA on host translation could contribute to future research on understanding how this virus manipulates the host and causes disease. Method: We will employ the transformative method of ribosome profiling (RiboSeq) to sample the level of translation across the entire population of mRNAs in the cell in order to identify genes that are translationally up- or down-regulated in the presence of sfRNA, either alone, or in the context of replicating ZIKV. RiboSeq - a modification of high-throughput mRNA sequencing (RNAseq) - reveals only the fragments of mRNAs that are protected by translating ribosomes. The number of reads of ribosome-protected fragments from a given mRNA is proportional to how actively that mRNA is translated. This highly informative method has been applied only sparingly to flaviviruses and, to our knowledge, never to determine specifically the effects of sfRNA, a known translational regulator. We will also develop new statistical methods to improve on current imperfect approaches for calculating significance of changes in translational efficiency of mRNAs in response to a treatment. Finally, we will use a variety of bioinformatics tools to identify common structural features of mRNAs whose translation efficiencies are similarly affected by sfRNA. Expected Outcomes. Identification of genes whose translation is affected by sfRNAs will reveal potential genes and genetic pathways that facilitate - or defend against – ZIKV infection. These can be the focus of future studies by us and others to determine their role and regulation in virus infection, the immune response, or possibly neurodevelopmental disorders. Moreover, these results may reveal new ways of regulating translation. This research can benefit human health by informing rational design of vaccines or antivirals targeting ZIKV and other flaviviruses, and by providing better understanding of control of protein synthesis by RNA.
Terms: <3' Untranslated Regions><3'UTR><5' Untranslated Regions><5'UTR><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Address><Affect><Americas><Antiviral Agents><Antiviral Drugs><Antivirals><Basic Research><Basic Science><Binding><Breakbone Fever Virus><Cell Body><Cell Function><Cell Line><Cell Nucleus><Cell Process><Cell physiology><CellLine><Cells><Cellular Function><Cellular Physiology><Cellular Process><Clinical Trials><Data Analyses><Data Analysis><Dengue><Dengue Virus><Dengue fever virus><Detection><Development><Disease><Disorder><Egypt 101 virus><Epidemic><Exposure to><FMR-1 Protein><FMR1><FMR1 Gene><FMR1 Protein><FMRP protein><FRAXA><Female Genital System><Fetus><Flavivirus><Fragile X Mental Retardation 1 Gene><Fragile X Mental Retardation Protein><Functional RNA><Future><Gene Action Regulation><Gene Expression><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Genes><Genetic><Genome><Group B Arbovirus><HIV><Health><Host Defense><Host Factor><Host Factor Protein><Human><Human Immunodeficiency Viruses><IFN><Immune response><Immunological response><Immunomodulation><Infection><Innate Immune System><Innate Immunity><Integration Host Factors><Interferons><Invaded><Knowledge><LAV-HTLV-III><Lymphadenopathy-Associated Virus><Messenger RNA><Methods><Microcephaly><Modern Man><Modification><Molecular><Molecular Interaction><Mothers><Native Immunity><Natural Immunity><Nervous System Diseases><Neurodevelopmental Disorder><Neurologic><Neurologic Disorders><Neurological><Neurological Development Disorder><Neurological Disorders><Non-Coding><Non-Coding RNA><Non-Polyadenylated RNA><Non-Specific Immunity><Non-translated RNA><Noncoding RNA><Nonspecific Immunity><Nontranslated RNA><Nucleotides><Nucleus><Outcome><Parasites><Pathogenicity><Pathway interactions><Pattern><Polyribosomes><Polysomes><Population><Position><Positioning Attribute><Protein Biosynthesis><Proteins><Quantitative RTPCR><Quantitative Reverse Transcriptase PCR><RNA><RNA Gene Products><RNA Seq><RNA chemical synthesis><RNA replication><RNA sequencing><RNA synthesis><RNAseq><Regulation><Research><Ribo-seq><Ribonucleic Acid><Ribosomal Peptide Biosynthesis><Ribosomal Protein Biosynthesis><Ribosomal Protein Synthesis><Ribosomes><Role><Sampling><Severity of illness><Specific qualifier value><Specified><Statistical Methods><Strains Cell Lines><Structure><Subcellular Process><Testing><Therapeutic><Transcript><Transfection><Translating><Translational Regulation><Translations><Untranslated RNA><Vaccine Design><Vaccines><Viral Diseases><Viral Genome><Virus><Virus Diseases><Virus Replication><Virus-HIV><WNV><West Nile><West Nile virus><Yellow fever virus><ZIKA><ZIKV><ZIKV infection><ZIKV positive><Zika Virus><Zika virus infection><anti-viral agents><anti-viral drugs><anti-virals><bio-informatics tool><bioinformatics tool><cultured cell line><data interpretation><developmental><developmental disease><developmental disorder><disease severity><female reproductive body system><female reproductive organ system><female reproductive system><fragile X FMR1 protein><fragile X mental retardation 1><fragile X mental retardation-1 protein><genomic RNA><gynecologic body system><gynecologic organ system><host response><immune modulation><immune regulation><immune system response><immunologic reactivity control><immunomodulatory><immunoregulation><immunoregulatory><immunoresponse><improved><in utero><infected neonate><infected newborn><mRNA><mRNA Leader Sequences><mRNA seq><mRNA sequencing><mRNA-seq><mRNAseq><micrencephaly><microencephaly><mutant><neonatal infection><nervous system disorder><neurological disease><newborn infection><noncoding><novel><pathogen><pathway><protein synthesis><qRTPCR><response><ribosome footprint profiling><ribosome profiling><social role><tool><transcriptome sequencing><vaccine candidate><vector mosquito><viral RNA><viral genomics><viral infection><viral multiplication><viral replication><virology><virus RNA><virus genome><virus genomics><virus infection><virus multiplication><virus-induced disease><zika infection><zika viral infection><zikav>