Alternative 3′ UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments

Abstract

Neurons localize mRNAs near synapses where their translation can be regulated by synaptic demand and activity. Differences in the 3' UTRs of mRNAs can change their localization, stability, and translational regulation. Using 3' end RNA sequencing of microdissected rat brain slices, we discovered a huge diversity in mRNA 3' UTRs, with many transcripts showing enrichment for a particular 3' UTR isoform in either somata or the neuropil. The 3' UTR isoforms of localized transcripts are significantly longer than the 3' UTRs of non-localized transcripts and often code for proteins associated with axons, dendrites, and synapses. Surprisingly, long 3' UTRs add not only new, but also duplicate regulatory elements. The neuropil-enriched 3' UTR isoforms have significantly longer half-lives than somata-enriched isoforms. Finally, the 3' UTR isoforms can be significantly altered by enhanced activity. Most of the 3' UTR plasticity is transcription dependent, but intriguing examples of changes that are consistent with altered stability, trafficking between compartments, or local "remodeling" remain.

FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences

“…We then asked what other transcript features were associated with FMRP localization targets. We observed that FMRP localization targets had much longer open reading frames and 3′ UTRs than expected (Fig 2F), consistent with previous reports that 3′ UTR extensions and alternative 3′ UTRs can regulate RNA localization in neurons (Taliaferro et al, 2016a;Tushev et al, 2018). We observed no relationship between the overall abundance of a transcript and whether or not it was an FMRP localization target.…”

Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity

“…This phenomenon has been under positive evolutionary pressure, as the median length and diversity of 3′UTRs increases in higher organisms (Derti et al, 2012). Importantly, 3′UTR complexity is especially relevant in neurons, as they are the cell type expressing the longest and most varied 3′ ends (Hilgers et al, 2011; Ji et al, 2009; Miura et al, 2013; Andreassi et al, 2017; Tushev et al, 2018). These observations support the notion that 3′UTR frequently harbors regulatory elements necessary for most, if not all, aspects of mRNA metabolism, from stability and subcellular localization to translation and degradation (Andreassi and Riccio, 2009; Miura et al, 2014).…”

“…Alternative polyadenylation plays an essential role in dendritic and axonal localization of many transcripts (Shigeoka et al, 2016; Taliaferro et al, 2016; Andreassi et al, 2017; Tushev et al, 2018), including BDNF (An et al, 2008; Will et al, 2013; Vicario et al, 2015), Impa1 (Andreassi et al, 2010, 2017), importin β1 (Perry et al, 2012), mTOR (Terenzio et al, 2018), and Shank (Bockers et al, 2004; Epstein et al, 2014). Localization signals present in isoforms within the 3′UTR usually mediate the transport and activate local translation in response to extrinsic stimuli, such as neurotrophins, synaptic activation and during regeneration after injury.…”

“…Importantly, 3′UTR cleavage may not be limited to axons and may be relevant in other physiological contexts. In the rat hippocampus, 3′ end sequencing of RNA isolated from either the soma or the neuropil (that contains only dendrites) revealed extensive differential expression of 3′UTR isoforms following neuronal activation (Tushev et al, 2018). Although in most cases, differential expression of short isoforms was due to transcription rate and/or selective peripheral transport, at least for some transcripts, isoforms with short 3′UTRs were generated by local remodeling of longer 3′UTRs.…”

A 5’ UTR G-quadruplex controls localisation and translation of a potassium leak channel mRNA

“…Recently, nearly 2000 actively translating mRNAs were identified within the axon through an axonspecific translating ribosome affinity purification (TRAP) approach (24,25). Similarly, identification of translating polyribosomes and over 2500 distinct mRNA transcripts through deep-sequencing within the hippocampal neuropil (26,27) further suggests that neurons have a dependency on the local translation of mRNAs in distal neurite compartments (23,28).…”