Abstract
Although alternative pre-mRNA splicing (AS) significantly diversifies the neuronal proteome, the extent of AS is still unknown due in part to the large number of diverse cell types in the brain. To address this complexity issue, we used an annotation-free computational method to analyze and compare the AS profiles between small specific groups of Drosophila circadian neurons. The method, the Junction Usage Model (JUM), allows the comprehensive profiling of both known and novel AS events from specific RNA-seq libraries. The results show that many diverse and novel pre-mRNA isoforms are preferentially expressed in one class of clock neuron and also absent from the more standard Drosophila head RNA preparation. These AS events are enriched in potassium channels important for neuronal firing, and there are also cycling isoforms with no detectable underlying transcriptional oscillations. The results suggest massive AS regulation in the brain that is also likely important for circadian regulation.
Highlights
Organisms ranging from cyanobacteria to mammals contain circadian clocks that synchronize physiology and behavior to time-of-day environmental cues, such as light and temperature
To investigate how alternative pre-mRNA splicing (AS) regulation differs with circadian neuron identity and function, we compared the pre-mRNA splicing profiles from three small groups of circadian neurons, the DN1s, LNds and LNvs, as well as from a non-circadian outgroup, the dopaminergic or tyrosine hydroxylase-expressing (TH) neurons
Since neurons often exhibit exceptionally diverse AS patterns that are not documented in current transcriptome annotations (Li et al, 2007; Wang et al, 2008; Irimia et al, 2014; Li et al, 2015), Junction Usage Model (JUM) allows for the discovery of novel and unannotated splicing events and patterns
Summary
Organisms ranging from cyanobacteria to mammals contain circadian clocks that synchronize physiology and behavior to time-of-day environmental cues, such as light and temperature. The photoreceptor, Cryptochrome (CRY) and the kinase, Doubletime (Dbt) contribute to the degradation of Tim/Per (Kim et al, 2007; Kloss et al, 1998; Emery et al, 1998; Stanewsky et al, 1998; Ceriani et al, 1999; HunterEnsor et al, 1996; Syed et al, 2011). Without these repressors, CLK/CYC-mediated transcription begins again restarting the daily cycle of transcription
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