PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing

Abstract

Generated by 3′ end cleavage and polyadenylation at alternative polyadenylation (poly(A)) sites, alternative terminal exons account for much of the variation between human transcript isoforms. More than a dozen protocols have been developed so far for capturing and sequencing RNA 3′ ends from a variety of cell types and species. In previous studies, we have used these data to uncover novel regulatory signals and cell type-specific isoforms. Here we present an update of the PolyASite (https://polyasite.unibas.ch) resource of poly(A) sites, constructed from publicly available human, mouse and worm 3′ end sequencing datasets by enforcing uniform quality measures, including the flagging of putative internal priming sites. Through integrated processing of all data, we identified and clustered sites that are closely spaced and share polyadenylation signals, as these are likely the result of stochastic variations in processing. For each cluster, we identified the representative - most frequently processed - site and estimated the relative use in the transcriptome across all samples. We have established a modern web portal for efficient finding, exploration and export of data. Database generation is fully automated, greatly facilitating incorporation of new datasets and the updating of underlying genome resources.

A long read optimizedde novotranscriptome pipeline reveals novel ocular developmentally regulated gene isoforms and disease targets

“…Next, since we observed an enrichment in novel first and last exons within our data set, we decided to compare the TSS and TES within the DNTX annotation to two well-established annotation databases from FANTOM and the polyA Atlas (Noguchi et al, 2017), (Herrmann et al, 2020). We compared DNTX and Gencode TSS’s to CAGE-seq data from the FANTOM consortium; as CAGE-seq is optimized to detect the 5’ end of transcripts, we reasoned that it can serve as a valid ground truth set to evaluate TSS detection (Takahashi et al, 2012).…”

Beyond the RNA-dependent function of LncRNA genes

“…These elements are ubiquitously present in the genome. In humans, one can find 569,005 elements that meet the criterion of a pA signal (301,001 in mouse and 20,931 in C. elegans ) ( Herrmann et al, 2020 ). Moreover, this high number likely ensures successful termination of transcription ( Eaton and West, 2020 ).…”

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

“…• whose TSS were within 50bps of a published CAGE-peak 77 • whose mapped read-end fell within 50bps of a published polyA-site 78 • whose intron-chains were inconsistent with any annotated transcript or any truncated version of an annotated transcript 82,83 • whose internal exons (meaning both splice sites) were each supported by two or more single short reads (with >=2 splicing events) or paired-end Illumina read pairs from a bulk-sequencing experiment • whose introns were each supported by two or more spliced Illumina reads from a bulk sequencing experiment • who could not be interpreted as a truncated version of another such novel isoform This resulted in an enhanced annotation, in which all added isoforms had a unique, previously absent intron-chain.…”

“…This was done as described in our previous publication 26 with added filtering in place for incomplete reads using published CAGE peaks and polyA site data 77,78 .…”