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Year:: 2024
Contributor:: Carlson, Megan (creator); Erica Larschan (advisor); Mukulika Ray (advisor); Brown University. Karen T. Romer Undergraduate Teaching and Research Awards (research program)
Genre:: posters
Subject:: Genetics; Computational biology; RNA splicing; Genetic regulation
Extent:: 1 poster

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Abstract:: The 3D nuclear organization plays a crucial role in cellular functions via gene regulation. While many techniques like HiC, microC, and HiChIP have revealed the importance of 3D contacts in transcription, our understanding of how nuclear organization shapes transcript processing, including RNA splicing, is still limited. RNA splicing is vital for cell and sex-specific transcriptomes and is often disrupted in many human diseases. Therefore, research focusing on understanding how spatial organization regulates mRNA splicing in various contexts is integral to our understanding of the genetic basis of health. In this project, I have used a new technique called Split-Pool Recognition of Interactions by Tag Extension, or SPRITE, and its variant RD-SPRITE, developed by Guttman Lab in Caltech to identify three-dimensional contacts between DNA and RNA to determine clusters associated with sex-specific RNA splicing. Sex-specific splicing is conserved across different species, and many human neurological disorders are associated with splicing defects. Interestingly, many of these neurological disorders show gender biases. Thus, understanding how sex-specific splicing is regulated can improve management and therapeutics for these diseases. Therefore, I first customized the SPRITE/RD-SPRITE computational pipeline to explore sex-based splicing in Drosophila, a widely studied genetic model with extensive research in the field of sex-specific splicing. So far, this pipeline has only been used for mammalian datasets, so I compiled a container using the Guttman lab pipeline for Drosophila SPRITE data analysis to identify male and female-specific 3D clusters associated with splicing and determine unique genomic features that characterize the sex-specific clusters. Furthermore, I utilized published datasets, applying the SPRITE pipeline to identify cell-type specific 3D genomic clusters using mouse mammalian embryonic stem cells and myocyte data. I identified over one million clusters for each mammalian sample, each representing groups of DNAs and RNAs that share the same molecular barcode due to spatial proximity. Using heat maps as a visual tool, I compared clusters of different mouse cell types. I also ran human embryonic stem cell datasets and identified human 3D genomic clusters to determine the functional conservation of 3D nuclear organization between mice and humans. In the future, I plan to integrate computational analysis of SPRITE/RD-SPRITE Drosophila datasets with bulk and nascent transcriptomic datasets in male vs. female cells to elucidate the regulatory network that determines the targeting of sex-specific splicing events. This will help identify candidates that can shape particular splicing events, giving us scope to regulate splicing events to our advantage.

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Carlson, Megan, "Computational Analysis of Nuclear Organization Using SPRITE to Identify Three-dimensional DNA/RNA Contacts" (2024). Summer Research Symposium. Brown Digital Repository. Brown University Library. https://repository.library.brown.edu/studio/item/bdr:v68tufph/

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Summer Research Symposium

Each year, Brown University showcases the research of its undergraduates at the Summer Research Symposium. More than half of the student-researchers are UTRA recipients, while others receive funding from a variety of Brown-administered and national programs and fellowships and go …
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Computational Analysis of Nuclear Organization Using SPRITE to Identify Three-dimensional DNA/RNA Contacts