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Systematic approaches to deciphering cis regulation of A-to-I RNA editing

破译 A-to-I RNA 编辑顺式调控的系统方法

基本信息

批准号：
9554985
负责人：
Jin Billy Li
金额：
$ 41.84万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-09-01 至 2021-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9554985
关键词：
Adenosine Affect Affinity Alternative Splicing Amino Acid Sequence Binding Biological Assay Biology Case Study Catalytic RNA Cell Nucleus Cell physiology Cells Clustered Regularly Interspaced Short Palindromic Repeats Code Complex Computational Technique DNA Methylation DNA Sequence Alteration Data Data Set Disease Double-Stranded RNA Drosophila genus Engineering Enzymes Event Family Gene Expression Gene Expression Regulation Genes Genetic Transcription Genome engineering Genomics Genotype Genotype-Tissue Expression Project Goals Guanosine Human Human Genome In Vitro Individual Initiator Codon Inosine Lead Libraries Link Location Lower Organism Maps Measurement Measures MicroRNAs Microfluidics Mutagenesis Mutation Nucleotides Oligonucleotides Pattern Play Population Quantitative Trait Loci RNA RNA Binding RNA Decay RNA Editing RNA Processing RNA Splicing Regulation Regulatory Element Role Sampling Site Specificity Structure Techniques Technology Terminator Codon Tissues Translations Triplet Multiple Birth Variant Work adenosine deaminase base computerized tools genetic variant genome sequencing genome-wide genome-wide analysis histone modification mRNA Precursor malignant neurologic neoplasms nervous system disorder protein expression repaired synthetic biology transcriptome transcriptome sequencing transcriptomics tumor initiation tumor progression

项目摘要

Given that there are much fewer genes in metazoans than previously predicted, there are several mechanisms in biology to generate diversity at the transcriptional and translational level. One such mechanism is RNA editing, in which a base in RNA is modified by an enzyme to form a different base. The most common type of RNA editing is Adenosine-to-Inosine (A- to-I), catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes. ADAR binds to double-stranded RNA and de-aminates Adenosine to form Inosine, which is then read as Guanosine by the cellular machinery. Thus, RNA editing can contribute to the diversity of the transcriptome by changing the amino acid sequences of proteins, altering the locations of start or stop codons, influencing alternative splicing patterns, and affecting the ability of miRNAs to bind to their target sites. Tight regulation by RNA editing plays import roles as exemplified by a number of cases linked to diseases. Our recent results suggest that cis regulation plays a major role in RNA editing regulation. However, how RNA editing is regulated by cis regulatory elements remains largely unexplored. There is a lack of systematic, genome-wide studies to elucidate the cis regulation of RNA editing. In this work, we aim to develop systematic approaches to deciphering the regulatory code of RNA editing cis regulation. First, we will map cis quantitative trait loci (QTLs) that are associated with RNA editing levels across human individuals. Second, we will examine editing QTLs also involved in other cellular processes that may be functionally related to RNA editing. Third, we will apply synthetic biology approaches to introduce mutations in the dsRNA substrates to measure editing specificity and efficiency for variants at each base in vitro and in human cells, and experimentally determine ADAR binding affinity and RNA secondary structure in vitro. Taken together, the goals of this proposed project will provide an unprecedented understanding of primary sequence and secondary structure features that govern the cis regulation of A-to-I RNA editing, and reveal the functional relationship between RNA editing and other cellular processes.

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