IN SILICO DEVELOPMENT OF EPITRANSCRIPTOMIC ASSAYS FOR RAT BRAIN
Session Number
Project ID: BIO 36
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Advisor(s)
Dr. Monsheel Sodhi; Loyola University, Department of Molecular Pharmacology and Neuroscience
Discipline
Biology
Start Date
22-4-2020 11:00 AM
End Date
22-4-2020 11:25 AM
Abstract
An epitranscriptomic process known as RNA editing produces adenosine (A) to inosine (I) substitutions in RNA that are catalyzed by ADAR enzymes. Even though online databases have extensively annotated sequence information for the human and several strains of mouse, there is a dearth of sequencing data for the rat. In this project, we have mined information from RNA editing databases, such as RADAR and REDIPortal in addition to screening the scientific literature, to build a more comprehensive list of potential RNA editing events that are non-synonymous, in the rat brain. We now provide updated information from the latest genomic assembly of rat cDNA sequence. We identified 30 previously reported sites and discovered 33 novel RNA editing sites in the rat brain. This updated list covers over 35 genes across 18 different chromosomes. After composing this list, we designed PCR assays for these RNA editing sites in the rat, using Primer3 software. Subsequently, the RNA sequencing data generated will be analyzed in reference to the rat transcriptome by utilizing the STAR and Burrows-Wheeler Aligner package. The overall goal for this project is to test if RNA editing is differentially altered in the adult rat brain after exposure to psychological stress.
Creative Commons License
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IN SILICO DEVELOPMENT OF EPITRANSCRIPTOMIC ASSAYS FOR RAT BRAIN
An epitranscriptomic process known as RNA editing produces adenosine (A) to inosine (I) substitutions in RNA that are catalyzed by ADAR enzymes. Even though online databases have extensively annotated sequence information for the human and several strains of mouse, there is a dearth of sequencing data for the rat. In this project, we have mined information from RNA editing databases, such as RADAR and REDIPortal in addition to screening the scientific literature, to build a more comprehensive list of potential RNA editing events that are non-synonymous, in the rat brain. We now provide updated information from the latest genomic assembly of rat cDNA sequence. We identified 30 previously reported sites and discovered 33 novel RNA editing sites in the rat brain. This updated list covers over 35 genes across 18 different chromosomes. After composing this list, we designed PCR assays for these RNA editing sites in the rat, using Primer3 software. Subsequently, the RNA sequencing data generated will be analyzed in reference to the rat transcriptome by utilizing the STAR and Burrows-Wheeler Aligner package. The overall goal for this project is to test if RNA editing is differentially altered in the adult rat brain after exposure to psychological stress.