Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation

Abstract

Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. Here we report that, unlike previously characterized cell lineages, differentiation of syncytiotrophoblast (SCT), a cell type critical for hormone production and secretion during pregnancy, elicits widespread transcript shortening through APA in 3'UTRs and in introns. This global APA change is observed in multiple in vitro trophoblast differentiation models, and in single cells from placentas at different stages of pregnancy. Strikingly, the transcript shortening is unrelated to cell proliferation, a feature previously associated with APA control, but instead accompanies increased secretory functions. We show that 3'UTR shortening leads to transcripts with higher mRNA stability, which augments transcriptional activation, especially for genes involved in secretion. Moreover, this mechanism, named secretion-coupled APA (SCAP), is also executed in B cell differentiation to plasma cells. Together, our data indicate that SCAP tailors the transcriptome during formation of secretory cells, boosting their protein production and secretion capacity.

MAAPER: model-based analysis of alternative polyadenylation using 3’ end-linked reads

“…To this end, we downloaded 10X Genomics data of placental samples (Vento-Tormo et al, 2018), which included scRNA-seq data from five donors (D8-D12). We focused on the three trophoblast cell populations we recently found to have substantial APA differences (Cheng et al, 2020), namely, villous cytotrophoblasts (VCTs), extravillous trophoblasts (EVTs) and syncytiotrophoblasts (SCTs) (Figures 4A and S9). Because VCTs are the precursor cells of the other two subtypes (Chang et al, 2018), we compared APA profiles of EVTs of SCTs with those of VCTs.…”

Rbm24 Displays Dynamic Functions Required for Myogenic Differentiation During Muscle Regeneration

“…There is now accumulating evidence that Rbm24 performs post-transcriptional functions in the cytoplasmic compartment of different cell types entered into the differentiation program. Indeed, our recent studies showed that both mouse and zebrafish Rbm24 is localized in the cytoplasm of differentiating cells in the head sensory organs to regulate mRNA stability and cytoplasmic polyadenylation 30,47,48 . This raises an interesting possibility that Rbm24 may also regulate the poly(A) tail length and thus the translational efficiency of muscle-specific mRNAs during early stages of muscle development and regeneration.…”

The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers

“…S ignificance A nalysis of A lternative P olyadenylation using R NA- S eq ( SAAP-RS ) [ 111 ] uses RNA-seq samples from bulk, single cell and 3 focused (e.g., 3 READS+ [ 10 ]) approaches to identify APA events. The method calculates RNA-seq read counts upstream (UP) and downstream (DN) of every poly(A) site identified from PolyA_DB3 database and performs a statistical test to derive a p-value to compare the read distribution in UP and DN regions between two samples.…”

“…Most scRNA-seq methods use 3 tag-based approach to generate reads enriched at 3 ends of mRNA similar to the approaches described above ( Table 1 ). Several laboratories have already turned to scRNA-seq to study complex APA regulatory patterns in tissues and organs [ 10 , 81 , 82 , 83 ].…”

“…This occurs due to the presence of alternative adenylation sites in the genome and leads to significant transcriptome diversity. Nearly 70% of mammalian genes harbour multiple cleavage and polyadenylation sites i.e., poly(A) sites [ 7 , 8 , 9 , 10 ]. These sites can cause differential expression of mRNA transcripts by influencing their nuclear export, stability, subcellular localization, interaction with microRNAs, RNA binding proteins (RBPs), long non-coding RNAs (lncRNAs) and translation efficiency [ 11 , 12 , 13 , 14 , 15 ].…”