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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
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CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators
Madeline H Kowalski1,2,3, Hans-Hermann Wessels1,2, Johannes Linder4,5
1New York Genome Center, New York, NY, USA.
Biorxiv : the Preprint Server for Biology
|February 17, 2023
Summary
This study introduces CPA-Perturb-seq to map how cleavage and polyadenylation (CPA) proteins control gene expression diversity. The findings reveal a regulatory code governing polyadenylation site choice and cellular heterogeneity.
Area of Science:
- Molecular Biology
- Genomics
- Computational Biology
Background:
- Mammalian genes exhibit transcript diversity through alternative polyadenylation (APA) regulated by cleavage and polyadenylation (CPA) machinery.
- Understanding CPA protein function is crucial for deciphering gene expression regulation.
Approach:
- Developed CPA-Perturb-seq, a multiplexed perturbation screen with 3' scRNA-seq, to analyze transcriptome-wide polyadenylation site usage.
- Created a statistical framework to identify changes in intronic and tandem polyadenylation.
- Trained a multi-task deep neural network (APARENT-Perturb) to predict APA site choice and regulatory interactions.
Key Points:
- Discovered modules of co-regulated polyadenylation sites with distinct functional properties.
- Delineated a cis-regulatory code predicting response to CPA perturbation.
- Identified novel regulators of alternatively polyadenylated transcripts and characterized 3' UTR length heterogeneity in antibody-producing cells.
Conclusions:
- Multiplexed single-cell perturbation screens offer powerful insights into post-transcriptional regulation.
- The developed framework and neural network advance the study of APA and gene regulation.
