Exon Junction Complex Mediates the Cap-Independent Translation of Circular RNA.

Evidence that circular RNAs (circRNA) serve as protein template is accumulating. However, how the cap-independent translation is controlled remains largely uncharacterized. Here, we show that the presence of intron and thus splicing promote cap-independent translation. By acquiring the exon junction complex (EJC) after splicing, the interaction between circRNA and ribosomes was promoted, thereby facilitating translation. Prevention of splicing by treatment with spliceosome inhibitor or mutating splicing signal hindered cap-independent translation of circRNA. Moreover, EJC-tethering using Cas13 technology reconstituted EJC-dependent circRNA translation. Finally, the level of a coding circRNA from succinate dehydrogenase assembly factor 2 (circSDHAF2) was found to be elevated in the tumorous tissues from patients with colorectal cancer, and shown to be critical in tumorigenesis of colorectal cancer in both cell and murine models. These findings reveal that EJC-dependent control of circSDHAF2 translation is involved in the regulation of oncogenic pathways. IMPLICATIONS: EJC-mediated cap-independent translation of circRNA is implicated in the tumorigenesis of colorectal cancer.

TRIPBASE: a database for identifying the human genomic DNA and lncRNA triplexes.

Long-non-coding RNAs (lncRNAs) are defined as RNA sequences which are >200 nt with no coding capacity. These lncRNAs participate in various biological mechanisms, and are widely abundant in a diversity of species. There is well-documented evidence that lncRNAs can interact with genomic DNAs by forming triple helices (triplexes). Previously, several computational methods have been designed based on the Hoogsteen base-pair rule to find theoretical RNA-DNA:DNA triplexes. While powerful, these methods suffer from a high false-positive rate between the predicted triplexes and the biological experiments. To address this issue, we first collected the experimental data of genomic RNA-DNA triplexes from antisense oligonucleotide (ASO)-mediated capture assays and used Triplexator, the most widely used tool for lncRNA-DNA interaction, to reveal the intrinsic information on true triplex binding potential. Based on the analysis, we proposed six computational attributes as filters to improve the in-silico triplex prediction by removing most false positives. Further, we have built a new database, TRIPBASE, as the first comprehensive collection of genome-wide triplex predictions of human lncRNAs. In TRIPBASE, the user interface allows scientists to apply customized filtering criteria to access the potential triplexes of human lncRNAs in the cis-regulatory regions of the human genome. TRIPBASE can be accessed at https://tripbase.iis.sinica.edu.tw/.

Short human eccDNAs are predictable from sequences.

BACKGROUND: Ubiquitous presence of short extrachromosomal circular DNAs (eccDNAs) in eukaryotic cells has perplexed generations of biologists. Their widespread origins in the genome lacking apparent specificity led some studies to conclude their formation as random or near-random. Despite this, the search for specific formation of short eccDNA continues with a recent surge of interest in biomarker development. RESULTS: To shed new light on the conflicting views on short eccDNAs' randomness, here we present DeepCircle, a bioinformatics framework incorporating convolution- and attention-based neural networks to assess their predictability. Short human eccDNAs from different datasets indeed have low similarity in genomic locations, but DeepCircle successfully learned shared DNA sequence features to make accurate cross-datasets predictions (accuracy: convolution-based models: 79.65 ± 4.7%, attention-based models: 83.31 ± 4.18%). CONCLUSIONS: The excellent performance of our models shows that the intrinsic predictability of eccDNAs is encoded in the sequences across tissue origins. Our work demonstrates how the perceived lack of specificity in genomics data can be re-assessed by deep learning models to uncover unexpected similarity.

Graphene Coated Dielectric Hierarchical Nanostructures for Highly Sensitive Broadband Infrared Sensing.

Broadband infrared (IR) absorption is sought after for wide range of applications. Graphene can support IR plasmonic waves tightly bound to its surface, leading to an intensified near-field. However, the excitation of graphene plasmonic waves usually relies on resonances. Thus, it is still difficult to directly obtain both high near-field intensity and high absorption rate in ultra-broad IR band. Herein, a novel method is proposed to directly realize high near-field intensity in broadband IR band by graphene coated manganous oxide microwires featured hierarchical nanostructures (HNSs-MnO@Gr MWs) both experimentally and theoretically. Both near-field intensity and IR absorption of HNSs-MnO@Gr MWs are enhanced by at least one order of magnitude compared to microwires with smooth surfaces. The results demonstrate that the HNSs-MnO@Gr MWs support vibrational sensing of small organic molecules, covering the whole fingerprint region and function group region. Compared with the graphene-flake-based enhancers, the signal enhancement factors reach a record high of 103 . Furthermore, just a single HNSs-MnO@Gr MW can be constructed to realize sensitively photoresponse with high responsivity (over 3000 V W-1 ) from near-IR to mid-IR. The graphene coated dielectric hierarchical micro/nanoplatform with enhanced near-field intensity is scalable and can harness for potential applications including spectroscopy, optoelectronics, and sensing.

CircVIS: a platform for circRNA visual presentation.

BACKGROUND: The collection of circRNAs mostly focused on their sequence composition such as protein/miRNA binding motif, and/or regulatory elements such as internal ribosome entry site. However, less attention was paid to subcellular localization. CircVIS aimed to provide a collection of circRNAs with information of subcellular compartments and also integrated the circRNA entries from previous circRNA databases. RESULTS: A collection of circRNAs from public circRNA databases and de novo identification were annotated according to subcellular localizations including nucleoplasm, chromatin-associated parts, cytoplasm and polyribosome. All circRNAs were aligned to a selected major transcript, and if presence, the circRNA-derived open reading frame with annotation of functional domain were compared to its parental protein. The results showed that distinct circRNAs may exert their molecular and cellular functions in different subcellular compartments. The web service is made freely available at http://lab-x-omics.nchu.edu.tw/circVIS . CONCLUSIONS: CircVIS allows users to visualize the alignment between a given circRNA and its most relevant reference transcript along with information of subcellular localization.

Enhancing diabetes care with community pharmacist-involved collaborative care model: A multi-centre randomised controlled trial.

AIM: To evaluate the clinical and humanistic outcomes of a community pharmacist-involved collaborative care model in diabetes management. METHODS: This was a parallel arm, open-label, multi-centre randomized controlled trial conducted over 6 months. Subjects with type 2 diabetes, HbA1c ≥ 7.0% (53 mmol/mol) and taking ≥ 5 medications were included. Participants were randomized into intervention (collaborative care) and control groups (physician-centric care). The intervention included medication therapy management and telephonic follow-up with visits to family physicians, nurses, and dietitians. Clinical outcomes included changes in HbA1c, systolic blood pressure (SBP), lipids, and hypoglycaemic incidences. Humanistic outcomes included self-care capabilities and quality of life. Linear mixed models were constructed. Intention-to-treat analyses, with sensitivity analyses, were conducted. RESULTS: A total of 264 participants were randomized (intervention: 131, control: 133). Significantly greater reduction in HbA1c was observed in the intervention group (intervention: -0.32% (-3.52 mmol/mol) vs. control: -0.06% (-0.66 mmol/mol), p = 0.038). Changes in SBP, lipids, and incidences of hypoglycaemia were not significant over 6 months between both groups. Significantly greater improvements in self-management (p < 0.001) and quality of life (p = 0.003) were observed within the intervention group. CONCLUSION: Partnering community pharmacists in a collaborative care team improved glycaemic control, quality of life and self-care capabilities of patients with diabetes and polypharmacy.

Analysis of common targets for circular RNAs.

BACKGROUND: The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typically overwhelming due to the synergistic complexity caused by two factors ─ the binding of multiple miRNAs to a circRNA and the existence of multiple targets for each miRNA. Analysis of common targets (ACT) was designed to facilitate the identification of potential circRNA targets. RESULTS: We demonstrated the feasibility of the proposed feature/measurement to assess which genes are more likely to be regulated by circRNAs with given sequences by calculating the level of co-regulation by multiple miRNAs. The web service is made freely available at http://lab-x-omics.nchu.edu.tw/ACT_Server . CONCLUSIONS: ACT allows users to identify potential circRNA-regulated genes and their associated pathways for further investigation.