Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis

Abstract

Alternative polyadenylation (APA) is an important post-transcriptional modification implicated in many diseases, including cancer. Although extensively characterized, the functional consequence of APA modulation on tumorigenesis remains elusive. Here, we developed a deep sequencing-based approach that specifically profiles 3' termini of polyadenylated RNAs (herein termed 3T-seq) and analyzed APA events in two gastric cancer cell lines and one non-transformed counterpart. Overall, we identified >28 000 poly(A) sites, 70% of which are potentially novel. Further, we observed widespread APA-mediated 3' UTR shortening of 513 genes (false discovery rate < 0.05) across gastric cancer genome. We characterized one of these genes, NET1, in detail and found that the shortening of NET1 3' UTR significantly enhances transcriptional activity. Moreover, the NET1 isoform with short 3' UTR promotes cellular migration and invasion in vitro. Collectively, our work provides an effective approach for genome-wide APA site profiling and reveals a link between APA modulation and gastric cancer metastasis.

Characterization and Potential Antitumor Activity of Polysaccharide from Gracilariopsis lemaneiformis

“…Invasion and migration assays were performed as described previously [28]. Briefly, 8 μm pore transwell filters (BD Biosciences, San Jose, CA, USA) were used for the invasion assay, and transwell membranes were coated with Matrigel™ Basement Membrane (356,234, BD Biosciences, San Jose, CA, USA).…”

Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq

“…Precise mapping of transcription start sites (TSS) and 3΄ UTRs is therefore critical to understand gene regulation and transcript diversity, as the use of alternative promoters and cleavage and polyadenylation sites (PAS) can have profound impact on the molecular and cellular physiology of cells (2–6). To date, several strategies have been specifically designed for accurately mapping and quantifying 5΄- or 3΄-ends of transcripts (7–22). Although these methods have been used to accurately map TSS and 3΄ UTRs in cell lines, their applicability to in vivo or primary cell cultures has lagged because of the challenges of current methods.…”

“…On the contrary, some 3΄ library construction methods are the bases for building low input RNA-seq quantification libraries and even for single cell RNA sequencing (26,27). However, these methods are not optimal for annotation purposes, mainly because of their reliance on oligo(dT) primed cDNA (9,11,13–15,18,19,22). Oligo(dT) tends to also prime internal A-rich sequences that need to be computationally identified a posteriori (13,14,28–30).…”

Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data

“…Alternative polyadenylation might depend on the environment38 and is implicated in many diseases11. PAS number and usage provide the possibility for alternative polyadenylation.…”

“…The poly(A) tail in eukaryotic mRNA plays a key role in its stability, translation and transport789. A short or absent poly(A) tail might lead to the degradation of the transcript and changes in the abundance of gene expression1011. However, more than one PAS can exist in protein coding genes and long non-coding RNAs in eukaryotes and produce various transcript isoforms with different lengths12 in a process, called alternative polyadenylation (APA), which depends on the PAS number and poly(A) signals1314.…”