Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs; however, the principles of biogenesis are currently not fully understood. Here, we identify two factors, splicing factor proline/glutamine rich (SFPQ) and non-POU domain-containing octamer-binding protein (NONO), to be enriched around circRNA loci. We observe a subclass of circRNAs, coined DALI circRNAs, with distal inverted Alu elements and long flanking introns to be highly deregulated upon SFPQ knockdown. Moreover, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing, premature transcription termination, and polyadenylation, particularly prevalent for long introns. Aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we identify missplicing in the immediate upstream region to be a conserved driver of circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.

SMAUG1 is a human RNA-binding protein that is known to be dysregulated in a wide range of diseases. It is evolutionarily conserved and has been shown to form condensates containing translationally repressed RNAs. This indicates that condensation is central to proper SMAUG1 function; however, the factors governing condensation are largely unknown. In this work, we show that SMAUG1 drives the formation of liquid-like condensates in cells through its non-conventional C-terminal prion-like disordered region. We use biochemical assays to show that this liquid-liquid phase separation is independent of RNA binding and does not depend on other large, disordered regions that potentially harbor several binding sites for partner proteins. Using a combination of computational predictions, structural modeling, in vitro and in cell measurements, we also show that SMAUG1-driven condensation is negatively regulated by direct interactions with the members of the 14-3-3 protein family. These interactions are mediated by four distinct phospho-regulated short linear motifs embedded in the disordered regions of SMAUG1, working synergistically. Interactions between SMAUG1 and 14-3-3 proteins drive the dissolution of condensates, alter the dynamics of the condensed state, and are likely to be intertwined with currently unknown regulatory mechanisms. Our results provide information on how SMAUG1 phase separation is regulated and the first known instance of 14-3-3 proteins being able to completely dissolve condensates by directly interacting with a phase separation driver, which might be a general mechanism in cells to regulate biological condensation.

Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. Using transient knockdown of both proteins in two human cell lines followed by total RNAseq, we found a subclass of circRNAs with distal inverted Alu elements and long introns to be highly deregulated upon SFPQ knockdown. In addition, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing prevalent for long introns causing in some cases premature transcription termination and polyadenylation. While SFPQ depletion has an overall negative effect on circRNA production, premature termination is not the main causative explanation. Instead, data suggests that aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we observe a conserved impact of missplicing in the immediate upstream region to drive circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.

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Background With an aging population worldwide and in Ireland, comes more age-related health problems, including problems with hearing and vision. Ageing is also associated with a gradual decline in some cognitive functions. Sensory impairments (both hearing and vision) have been shown to have an association with cognitive impairment, with a greater cognitive decline seen in those with a combined hearing and vision loss. There is a well-established association between sensory and cognitive impairment, however, no study to date has looked at similar data collected in Ireland. The objective of this study is to analyse data from an Irish sample. Methods This study used data collected from Wave 4 of the Irish Longitudinal Study on Ageing (TILDA). Participants with missing data or information were excluded, leaving a complete dataset of 4,612, for analysis. Multiple linear regression analyses were carried out to compare Mini-Mental State Examination (MMSE) scores to self-reported sensory impairment (hearing impairment alone, vision impairment alone and Dual Sensory Impairment (DSI)) while adjusting for several covariates (age, gender, level of education, alcohol consumption, smoking history, depressive symptoms, mobility, loneliness, and physical activity). Results Self-reported fair/poor hearing and self-reported fair/poor vision had statistically significant lower MMSE scores than participants with self-reported excellent/very good/good hearing and self-reported excellent/very good/good vision respectively (hearing estimated standard error: –0.055, p value: 3.67e-11; vision estimated standard error: –0.080, p value: 5.14e-15). Self-reported DSI was associated with lower MMSE scores compared to participants without DSI (DSI estimated standard error: –0.13, p value: 5.55e-13). Conclusion This cross-sectional study and secondary data analysis demonstrated that in older Irish adults there is an association between hearing impairment, vision impairment and dual sensory impairment and lower cognitive function. These findings contribute to the growing body of research done internationally using other large scale health surveys.