Event Title

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

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

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Apr 22nd, 11:00 AM Apr 22nd, 11:25 AM

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.