Genome-Wide Analysis of RiboSNitches in Human Long Non-Coding RNAs (lncRNAs)

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Restricted (Penn State Only)
Author:
Hohenwarter, Gabriela
Area of Honors:
Chemistry
Degree:
Bachelor of Science
Document Type:
Thesis
Thesis Supervisors:
Philip C Bevilacqua, Thesis Supervisor
David D Boehr, Thesis Honors Advisor
Edward Patrick O'Brien, Jr., Faculty Reader
Keywords:
RNA
riboSNitches
long non-coding RNAs
computational
Abstract:
Some long non-coding RNAs (lncRNAs) are known to contain structures that are important for function. Single nucleotide polymorphisms (SNPs) have the potential to alter these structures, thereby impacting their overall function. A genome-wide analysis was conducted to identify regions with SNPs depleted in riboSNitches and significantly stable structure. By focusing on these parameters, this thesis aimed to uncover putative functionally relevant regions within human lncRNAs that may be under selective pressure. Structurally altering SNPs, referred to as riboSNitches, were predicted in annotated human lncRNAs from Ensembl. The stability of these regions was assessed using ScanFold 2.0, which calculates minimum free energies (MFEs) and thermodynamic Z-scores. This thesis helps fill a gap in understanding the potential structure-function relationship in lncRNAs and may inform future studies.