SRTdb: an omnibus for human tissue and cancer-specific RNA transcripts

The production of functional mature RNA transcripts from genes undergoes various pre-transcriptional regulation and post-transcriptional modifications. Accumulating studies demonstrated that gene transcription carries out in tissue and cancer type-dependent ways. However, RNA transcript-level specificity analysis in large-scale transcriptomics data across different normal tissue and cancer types is lacking. We applied reference-based de novo transcript assembly and quantification of 27,741 samples across 33 cancer types, 29 tissue types, and 25 cancer cell line types. We totally identified 231,836 specific RNA transcripts (SRTs) across various tissue and cancer types, most of which are found independent of specific genes. Almost half of tumor SRTs are also tissue-specific but in different tissues. Furthermore, we found that 10 ~ 20% of tumor SRTs in most tumor types were testis-specific. The SRT database (SRTdb) was constructed based on these resources. Taking liver cancer as an example, we showed how SRTdb resource is utilized to optimize the identification of RNA transcripts for more precision diagnosis of particular cancers. Our results provide a useful resource for exploring transcript specificity across various cancer and tissue types, and boost the precision medicine for tumor patients.

Long-read transcriptomic analysis of orb-weaving spider Araneus ventricosus indicates transcriptional diversity of spidroins

Spider silk, which is composed of diverse silk proteins (spidroin), is a kind of natural high-mass biomaterial with great potential. However, due to the complexity of both the structure and the composition of the spidroins in natural spider silk, application of this valuable biomass is still limited to date. There are diverse kinds of spider silk in the orb-weaving spider with different mechanical and structural characteristics. In order to systematically illustrate the landscape of all the different spidrons, here we chose Araneus ventricosus, an orb-weaving spider with superior silk mechanical features and genome information, to generate a long-read whole body transcriptome. We deciphered the repeat arrangements of each kind of spidroin, based on which we found that there are substantially transcriptional diversity of each spidroin gene. Some repeat motifs are not documented before. Specifically, we discovered novel full-lengh MaSp transcript as well as a relatively small full-length AcSp isoforms, which are potential promising materials for bioengineering of recombinant spidroin. Our study provided a batch of new spidron resources with detail sequential information. The finding of transcriptional diversity may provide cues in understanding of within-species variation of the mechanical properties of the natural spider silk and further molecular designing of recombinant spidroin.