The polyadenylation landscape after in vivo LTP in the rat brain
The regulation of synaptic translation via cytoplasmic polyadenylation, long proposed as a mechanism for controlling local protein synthesis in neurons, remains poorly understood despite extensive research. We implemented Nanopore sequencing to study post-transcriptional gene expression regulatory mechanisms during synaptic plasticity. We used in vivo long-term potentiation (LTP) in the rat hippocampus as our primary experimental model, supplemented by in vitro chemical stimulation of synaptoneurosomes. We generated a rich resource of long-read transcriptomic data enabling investigation into mRNA 3' ends, poly(A) tail lengths, and their composition. Dynamic shifts in polyadenylation site preference post-LTP induction were detected, highlighting their potential regulatory role in synaptic plasticity. However, significant poly(A) tail lengthening was limited to transcriptionally induced mRNAs. Moreover, no substantial poly(A) tail extension was observed in synaptoneurosomes following chemical stimulation. Exploring mRNA tail composition, particularly the presence of non-adenosine residues, showed a predominance of cytosine and uridine over guanosine after LTP, with increased decorated tail reads only in transcriptionally activated genes. However, we also discovered a group of transcripts with tails abundant in non-A residues. These, however, originate from extremely A-rich 3' UTRs and are thus semi-templated. Overall, our work provided a rich resource focusing on the 3' end dynamics during LTP, revealing an interesting group of neuronal mRNA with semi-templated poly(A) tails rich in non-A residues.