Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana.

The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian-regulated genes and splicing events. Using a stringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 3' splice site usage, 48 alternative 5' splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Depletion of the circadian-regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset of clock-controlled splicing events. Altogether, our global circadian RNA-seq coupled with an in silico, event-centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian-regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this co/post-transcriptional regulatory layer.

Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.

The AAA-ATPase NVL2 associates with an RNA helicase MTR4 and the nuclear RNA exosome in the course of ribosome biogenesis. In our proteomic screen, we had identified a ribosome biogenesis factor WDR74 as a MTR4-interacting partner, whose dissociation is stimulated by the ATP hydrolysis of NVL2. In this study, we report the identification of splicing factor 30 (SPF30), another MTR4-interacting protein with a similar regulatory mechanism. SPF30 is a pre-mRNA splicing factor harboring a Tudor domain in its central region, which regulates various cellular events by binding to dimethylarginine-modified proteins. The interaction between SPF30 and the exosome core is mediated by MTR4 and RRP6, a catalytic component of the nuclear exosome. The N- and C-terminal regions, but not the Tudor domain, of SPF30 are involved in the association with MTR4 and the exosome. The knockdown of SPF30 caused subtle delay in the 12S pre-rRNA processing to mature 5.8S rRNA, even though no obvious effect was observed on the ribosome subunit profile in the cells. Shotgun proteomic analysis to search for SPF30-interacting proteins indicated its role in ribosome biogenesis, pre-mRNA splicing, and box C/D snoRNA biogenesis. These results suggest that SPF30 collaborates with the MTR4-exosome machinery to play a functional role in multiple RNA metabolic pathways, some of which may be regulated by the ATP hydrolysis of NVL2.

Combination of benzoyl peroxide 5% gel with liquid cleanser and moisturizer SPF 30 in acne treatment results in high levels of subject satisfaction, good adherence and favorable tolerability.

BACKGROUND: Skin care products (cleansers and moisturizers) to complement benzoyl peroxide (BPO) in the treatment of acne may improve treatment tolerability and adherence. OBJECTIVE: Evaluate subject satisfaction after use of BPO 5% gel in combination with liquid cleanser and moisturizer SPF 30. METHODS: Open-label study including subjects aged ≥12 years with mild-to-moderate facial acne; ClinicalTrials.gov Identifier: NCT02589405. Once daily BPO 5% gel, twice daily liquid cleanser and once daily moisturizer SPF 30 were applied for 12 weeks. Assessments included a subject satisfaction questionnaire, investigator global assessment of improvement, lesion counts, the presence of Propionibacterium acnes, and safety. RESULTS: Fifty subjects were enrolled. Most subjects were overall satisfied with the three-part regimen (87%) and felt better about themselves (94%). Subjects indicated the skin care products helped prepare the skin for treatment (85%), relieve itchy skin (81%) and reduce irritation (87%). Most subjects considered that the liquid cleanser (80%) and moisturizer SPF 30 (84%) were a necessary part of acne treatment. BPO reduced P. acnes load by 89% at week 1. The treatment was well tolerated. CONCLUSIONS: The combination of BPO 5% gel with liquid cleanser and moisturizer SPF 30 resulted in high levels of subject satisfaction, good tolerability and treatment adherence.

Molecular evolution of the moonlighting protein SMN in metazoans.

The spinal muscular atrophy (SMA) associated protein survival of motor neuron (SMN) is known to be a moonlighting protein: having one primary, ancestral function (presumed to be involvement in U snRNP assembly) along with one or more secondary functions. One hypothesis for the evolution of moonlighting proteins is that regions of a structure under relatively weak negative selection could gain new functions without interfering with the primary function. To test this hypothesis, we investigated sequence conservation and dN/dS, which reflects the selection acting on a coding sequence, in SMN and a related protein, splicing factor 30 (SPF30), which is not currently known to be multifunctional. We found very different patterns of evolution in the two genes, with SPF30 characterized by strong sequence conservation and negative selection in most animal taxa investigated, and SMN with much lower sequence conservation, and much weaker negative selection at many sites. Evidence was found of positive selection acting on some sites in primate genes for SMN. SMN was also found to have been duplicated in a number of species, and with patterns that indicate reduced negative selection following some of these duplications. There were also several animal species lacking an SMN gene.