Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans.

Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes (nervous system, muscle, and intestine) and two neuronal subtypes (dopaminergic and serotonergic neurons). We have identified hundreds of splice junctions that exhibit distinct splicing patterns between tissue types or within the nervous system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, are more highly conserved across Caenorhabditis species, and are enriched in specific cis regulatory motifs, when compared with other types of exons. By using this information, we have identified a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5' splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C. elegans that parallels the evolutionary forces and constraints observed across metazoa.

Traumatic Brain Injury Temporal Proteome Guides KCC2-Targeted Therapy.

Advancing therapeutics for traumatic brain injury (TBI) remains a challenge, necessitating testable targets with interventions appropriately timed to intercede on evolving secondary insults. Neuroproteomics provides a global molecular approach to deduce the complex post-translational processes that underlie secondary events after TBI. Yet method advancement has outpaced approaches to interrogate neuroproteomic complexity, in particular when addressing the well-recognized temporal evolution of TBI pathobiology. Presented is a detailed account of the temporal neuroproteomic response to mild-moderate rat controlled cortical impact within perilesioned somatosensory neocortex across the first two weeks after injury. Further, this investigation assessed use of artificial neural network and functional enrichment analyses to discretize the temporal response across some 2047 significantly impacted proteins. Results were efficiently narrowed onto ion transporters with phenotypic relevance to abnormal GABAergic transmission and a delayed decline amenable to intervention under managed care conditions. The prototypical target potassium/chloride co-transporter 2 (KCC2 or SLC12A5) was investigated further with the KCC2-selective modulator CLP290. Guided by post-translational processing revealed one-day after insult to precede KCC2 protein loss a day after, CLP290 was highly effective at restoring up to 70% of lost KCC2 localization, which was significantly correlated with recovery of sham-level function in assessed somatosensory behavioral tasks. The timing of administration was important, with no significant improvement observed if given earlier, one-hour after insult, or later when KCC2 protein decline begins. Results portend importance for a detailed post-translational characterization when devising TBI treatments, and support the therapeutic promise of KCC2-targeted CLP290 intervention for positive functional recovery after brain injury.

Frontal Cortex Proteome Perturbation after Juvenile Rat Secondhand Smoke Exposure.

Secondhand smoke remains a global concern for children's health. Epidemiological studies implicate exposure to secondhand smoke as a major risk factor for behavioral disorders, yet biological causation remains unclear. Model studies have mainly focused on secondhand smoke impacts to prenatal neurodevelopment, yet juvenile exposure represents a separate risk. Using ion mobility-enhanced data-independent mass spectrometry, the effect of juvenile secondhand smoke exposure on the prefrontal cortex, a principal part of the brain involved in behavioral control, is characterized. The produced dataset includes 800 significantly responsive proteins within the juvenile orbital frontal cortex, with 716 showing an increase in abundance. The neuroproteomic response reflects a prominent perturbation within the glutamatergic synaptic system, suggesting aberrant, disorganized excitation as observed underlying psychiatric disorders. Also disclosed are impacts to GABAergic and dopaminergic systems. Overall, the dataset provides a wealth of detail, facilitating further targeted research into the causal mechanisms underlying behavioral disorders associated with juvenile exposure to secondhand smoke and other environmental pollutants. All MS data have been deposited to the ProteomeXchange consortium with identifier PXD011744.