Talk abstracts
Talk on Friday 03:45-04:00pm submitted by Jingyi Liu
Unraveling Cell-Type-Specific Alternative Cleavage and Polyadenylation Regulatory Mechanisms Governed by CLP1
Jingyi Liu (Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine), Ashleigh E. Schaffer (Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine)
Abstract:
Alternative polyadenylation (APA) plays a pivotal role in generating diverse mRNA isoforms, fine-tuning gene expression, often in a cell-type-specific manner. Recent high-throughput data revealed cell-type-dependent preferences in APA usage, uncovering novel, unannotated isoforms in various contexts such as cancer, neurogenesis, and under different stress conditions. Neurons, in particular, are highly polarized cells that exhibit the greatest mRNA isoform diversity and typically express mRNAs with the longest 3’UTRs. However, the regulatory mechanisms explaining the cell-type- or context-specificity are not well understood. This study delves into the cell-type-specific regulatory role of Cleavage Factor Polyribonucleotide Kinase Subunit 1 (CLP1), one of the two components in CFIIm, which has not been fully characterized compared to other cleavage and polyadenylation (CPA) core complexes. We investigated transient transcriptomic changes upon CLP1 depletion in both human embryonic stem cells (hESCs) and hESC-derived motor neurons (MNs) using a chemically inducible degradation tag (dTag) system. We examined the affinity of core CPA factors by RNAPII pull-down in stem cells and compared results with iPSC-derived motor neurons. Interestingly, we observed that the core CPA complex remained intact upon CLP1 depletion, without affecting cell viability. Remarkably, this result is in contrast with what we observed in MNs, where CLP1 depletion resulted in preferential proximal APA usages, loss of the integrity of CPA complex, and impaired differentiation. These findings suggest that CLP1 regulates APA in a cell-type-specific manner, potentially contributing to distinct cellular phenotypes associated with pontocerebellar hypoplasia type 10. Moreover, we propose the existence of a "CPA code," comprising specific core CPA factors and associated proteins, collectively modulating gene-specific APA regulation. To explore this idea further, we employed transient transcriptomic sequencing (TT-seq) and nascent 3' end sequencing (4PAC) to interrogate CLP1-dependent cell and gene-specific regulation in an unbiased manner. Our results are expected to unveil a comprehensive cell-type- and gene-specific regulation of alternative polyadenylation by CLP1.
Keywords: alternative polyadenylation , CLP1, Cell-Type-Specific