TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence

Abstract

TransCirc (https://www.biosino.org/transcirc/) is a specialized database that provide comprehensive evidences supporting the translation potential of circular RNAs (circRNAs). This database was generated by integrating various direct and indirect evidences to predict coding potential of each human circRNA and the putative translation products. Seven types of evidences for circRNA translation were included: (i) ribosome/polysome binding evidences supporting the occupancy of ribosomes onto circRNAs; (ii) experimentally mapped translation initiation sites on circRNAs; (iii) internal ribosome entry site on circRNAs; (iv) published N-6-methyladenosine modification data in circRNA that promote translation initiation; (v) lengths of the circRNA specific open reading frames; (vi) sequence composition scores from a machine learning prediction of all potential open reading frames; (vii) mass spectrometry data that directly support the circRNA encoded peptides across back-splice junctions. TransCirc provides a user-friendly searching/browsing interface and independent lines of evidences to predicte how likely a circRNA can be translated. In addition, several flexible tools have been developed to aid retrieval and analysis of the data. TransCirc can serve as an important resource for investigating the translation capacity of circRNAs and the potential circRNA-encoded peptides, and can be expanded to include new evidences or additional species in the future.

A novel protein encoded by circular SMO RNA is essential for Hedgehog signaling activation and glioblastoma tumorigenicity

“…S2B). However, in a recently published database based on sequencing data [35], we cannot find any m 6 A modification on circ-SMO (Additional file 1: Fig. S2C).…”

circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

“…For high-quality circRNA isoforms (read counts ≥ 5), the exonic type accounted for 73.2% of the identified circRNA species, while only 0.1% were from read throughs (Figure 2c). Most exnoic types (99.8%) could be verified in at least one database [17][18][19][20][21][22] (Figure 2c), which could be attributed to their higher expression levels (Figure 2-figure supplement 5). The median length of each type varied from 402 nt of the intergenic type to 618 nt of read-throughs (Figure 2d), indicating that a notable proportion of circRNAs > 500 nt cannot be reconstructed by RNA-seq.…”

Circular RNAs’ cap-independent translation protein and its roles in carcinomas

“…The RiboCIRC analyzes 3168 publicly available Ribo-seq and 1970 matched RNA-seq data sets. These data cover 314 studies of 21 different species, and established a comprehensive translatable CircRNA database that is predicted by calculations and verified by experiments [ 108 ]. The TransCirc is also recently established a comprehensive database [ 109 ].…”