Alternative polyadenylation in the nervous system: To what lengths will 3′ UTR extensions take us?

Abstract

Alternative cleavage and polyadenylation (APA) can diversify coding and non-coding regions, but has particular impact on increasing 3′ UTR diversity. Through the gain or loss of regulatory elements such as RNA binding protein and microRNA sites, APA can influence transcript stability, localization, and translational efficiency. Strikingly, the central nervous systems of invertebrate and vertebrate species express a broad range of transcript isoforms bearing extended 3′ UTRs. The molecular mechanism that permits proximal 3′ end bypass in neurons is mysterious, and only beginning to be elucidated. This landscape of neural 3′ UTR extensions, many reaching unprecedented lengths, may help service the unique post-transcriptional regulatory needs of neurons. A combination of approaches, including transcriptome-wide profiling, genetic screening to identify APA factors, biochemical dissection of alternative 3′ end formation, and manipulation of individual neural APA targets, will be necessary to gain fuller perspectives on the mechanism and biology of neural-specific 3′ UTR lengthening.

Gadd45α modulates aversive learning through post‐transcriptional regulation of memory‐related mRNA s

“…We discovered a remarkable feature in the transcriptome of Gadd45a ‐KO mice where the great majority of the down‐regulated mRNAs at 1 h after PA training contained long extensions of the 3′UTR, which are characteristic for neurons and are particularly abundant in hippocampus as compared to other brain regions and non‐neuronal tissues . Of note, the length of these extensions is not Gadd45α‐dependent.…”

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage

“…To validate results from PAPERCLIP, we first performed northern blotting and detected mRNAs at the expected size based on PAPERCLIP annotation (Figure 2B and 2C). Although it is known that RNA-seq lacks sufficient resolution to identify exact mRNA 3′ ends (Miura et al, 2014), we reasoned that it might provide additional support for 3′ UTR extensions identified by PAPERCLIP and broaden the scope of our validation in a high-throughput fashion. Indeed, through RNA-seq, we identified 17 genes that had 100% base coverage in the extended 3′ UTR regions annotated by PAPERCLIP and additional 61 genes with more than 90% coverage (Figure S2A and Table S2).…”

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

“…Furthermore, standard RNA-seq has limited abilities in precisely pinpointing poly(A) sites and therefore depends on existing poly(A) site annotations to identify potential APA shifts, while oligo(dT) primer-based APA mapping methods suffer from low specificity and commonly misidentify internal adenine-rich regions as the poly(A) sites (Miura et al, 2014; Shi, 2012). We recently developed a new mRNA 3′ end mapping method, PAPERCLIP (Hwang et al, 2016), based on the popular CLIP (Crosslinking Immunoprecipitation) technique.…”