This repository contains information for the quantification of Alternative Polyadenylation (APA) in RNA-seq datasets over neurodevelopment time This project uses the QAPA and DEXseq methods to identify 3'UTR lengthening or shortening by comparing two timepoints in neuron differentiation (day 30 with day 0).
Abstract: The role of post-transcriptional regulation in neurodevelopment is quite pervasive, activating gene programs that give rise to specialized cell features and functions. In this context, 3’ untranslated regions (3’UTRs) play a significant role in regulating mRNA translation, stability, and subcellular localization. This is mediated by factors such as miRNAs, lncRNAs and RNA-binding proteins (RBPs) that bind regions at the 3’UTR. Longer 3’UTRs present multiple such regions, leading to complex regulation patterns, while shorter ones are characterized by simpler patterns. The process through which one gene can have transcripts with longer or shorter 3’UTRs is known as alternative polyadenylation (APA). This study aims to characterize APA events in an RNA-seq dataset of iPSCs differentiating into cortical neurons.
Figure description: Certain RNA transcripts can contain only 1 site for cleavage and polyadenylation, which we call single. When there are multiple cleavage and polyadenylation sites, we name the one closest to the coding sequence (CDS) Proximal (P), while the sites downstream are called Distal (D).
Step 1: Data alignment to the reference transcriptome (hg38) using Salmon https://salmon.readthedocs.io/en/latest/salmon.html
Step 2: Quantification of APA using QAPA https://github.com/morrislab/qapa
Step 3: Data preprocessing
Step 4: Identifying lengthening and shortening events
Step 5: Visualizing reads using Gviz
Step 6: Quantification of APA using DEXseq
Step 7: Comparison of QAPA and DEXseq (Venn Diagram to identify common genes)
Step 8: Analysis of Proteomic data and comparison with APA events
-- Contact --
Author: Maria Eleni Fafouti
Email: marlen.fafouti@outlook.com
LinkedIn: linkedin.com/in/maria-eleni-fafouti-72950920b
Feel free to reach out if you have any questions or need further assistance!