Motif Analysis of CLAMP Binding Sites
I worked on this data analysis project during my time in the Larschan Lab at Brown University.
It involved employing computational techniques and data analysis to uncover the interactions between a novel protein discovered by the lab, CLAMP, and RNA to better understand its role in splicing.
I used strictly computational techniques, like RCAS to uncover motifs from BED file data or LocARNA to predict the three-dimensional structures of RNA, to analyze experimental data based on the output from targeted software tools to produce figures and summaries.
Ultimately, my efforts have lead to my authorship in a paper in eLife journal titled Sex-specific transcript diversity is regulated by a maternal transcription factor in early Drosophila embryos.
Multiple RNA binding proteins involved in splicing have target motifs in CLAMP bound RNA.
Bar plots showing the percentage of iCLIP CLAMP RNA targets in the S2 cell chromatin fraction (N=645), S2 cell nucleoplasmic fraction (N=53), Kc cell chromatin fraction (N=203) and Kc cell nucleoplasmic fraction (N=119) which have RNA binding sequence motifs for other RNA binding proteins involved in alternative splicing (noted along the x-axis).