Alternative splicing and protein diversity: plants versus animals

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS

Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

• Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co-transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remains poorly understood. • Here, we generated transcriptome (RNA-Seq) and nucleosome positioning (MNase-Seq) data for Arabidopsis thaliana to understand how nucleosome positioning modulates cold-induced AS. • Our results show that characteristic nucleosome occupancy levels are strongly associated with the type and abundance of various AS events under normal and cold temperature conditions in Arabidopsis. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions. Likewise, nucleosome patterns differ between exitrons and retained introns pointing to their distinct regulation. • Collectively, our data show that characteristic changes in nucleosome positioning modulate AS in plants in response to cold

Effects of varying case definition on carpal tunnel syndrome prevalence estimates in a pooled cohort

OBJECTIVE: To analyze differences in carpal tunnel syndrome (CTS) prevalence using a combination of electrodiagnostic studies (EDSs) and symptoms using EDS criteria varied across a range of cutpoints and compared with symptoms in both ≥1 and ≥2 median nerve–served digits. DESIGN: Pooled data from 5 prospective cohorts. SETTING: Hand-intensive industrial settings, including manufacturing, assembly, production, service, construction, and health care. PARTICIPANTS: Employed, working-age participants who are able to provide consent and undergo EDS testing (N=3130). INTERVENTIONS: None. MAIN OUTCOME MEASURES: CTS prevalence was estimated while varying the thresholds for median sensory latency, median motor latency, and transcarpal delta latency difference. EDS criteria examined included the following: median sensory latency of 3.3 to 4.1 milliseconds, median motor latency of 4.1 to 4.9 milliseconds, and median-ulnar sensory difference of 0.4 to 1.2 milliseconds. EDS criteria were combined with symptoms in ≥1 or ≥2 median nerve–served digits. EDS criteria from other published studies were applied to allow for comparison. RESULTS: CTS prevalence ranged from 6.3% to 11.7%. CTS prevalence estimates changed most per millisecond of sensory latency compared with motor latency or transcarpal delta. CTS prevalence decreased by 0.9% to 2.0% if the criteria required symptoms in 2 digits instead of 1. CONCLUSIONS: There are meaningful differences in CTS prevalence when different EDS criteria are applied. The digital sensory latency criteria result in the largest variance in prevalence