CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions

Abstract

Pairs of sense and antisense transcriptions that are adjacent at their 5′ and 3′ regions are called divergent and convergent transcription, respectively. However, the structural properties of divergent/convergent transcription in different species or RNA biotypes are poorly characterized. Here, we developed CCIVR2, a program that facilitates identification of both overlapping and non-overlapping antisense transcripts produced from divergent/convergent transcription whose transcription start sites (TSS) or transcript end sites (TES) are located within a specified region. We used CCIVR2 to analyze antisense transcripts starting around the sense TSS (from divergent transcription) or ending around the sense TES (from convergent transcription) in 11 different species and found species- and RNA biotype-specific features of divergent/convergent transcription. Furthermore, we confirmed that CCIVR2 enables the identification of multiple sense/antisense transcript pairs from divergent transcription, including those with known functions in processes such as embryonic stem cell differentiation and TGFβ stimulation. CCIVR2 is therefore a valuable bioinformatics tool that facilitates the characterization of divergent/convergent transcription in different species and aids the identification of functional sense/antisense transcript pairs from divergent transcription in specified biological processes.

XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells

“…We found that the corresponding annotations for these overlapping transcript pairs are oriented preferentially in a configuration with their 5′ ends exposed for degradation by XRN1 rather than the configuration where the 5′ ends are protected from XRN1 degradation ( Figure S5F and Table S5 ), as determined by the comprehensive cis -natural anti-sense transcripts identifier via RNA-sequencing data (CCIVR2) computational tool. 35 The exposed 5′ ends of these annotated overlapping transcripts also contain at least four “overhanging” base pairs in 98.0% of 150 transcripts ( Figure S5G and Table S5 ), consistent with findings from RNA:DNA hybrid substrates that are susceptible to XRN1 degradation. 25 These data suggest that XRN1 deletion in HCC366 cells causes accumulation of complementary sense/anti-sense transcripts that are normally degraded by XRN1.…”

“…In addition, although it is tempting to consider whether inhibition of XRN1 may be an effective therapeutic strategy in human cancer, Xrn1 deletion in mice results in embryonic lethality, 35 suggesting that XRN1 inhibition may cause substantial toxicity. Thus, XRN1 would need to be targeted specifically or at least preferentially in cancer cells.…”

“…Annotated complementary sense/anti-sense transcript pairs that were increased after XRN1 KO and/or XRN1/PKR double KO were analyzed using the CCIVR2 35 tool to determine the configuration of these overlapping transcripts, either with their 5′ or 3′ ends exposed. To determine the length of the 5′ overhang of annotated overlapping transcript pairs with exposed 5′ ends, as determined by the CCIVR2 tool, we generated individual BAM files for transcripts derived from both (+) and (−) DNA strands using SAMtools v1.6.…”

Economy of Effort or Sophisticated Programming? The Prevalence of Bidirectional Promoter Complexes in the Human Genome

“…The relative strength of competing sense and antisense promoters could therefore program the frequency at which specific differentiation events occur. A recent comprehensive evaluation of antisense transcription across multiple species revealed a similar pattern of convergent and divergent antisense TSS near the start site of genes in xenopus, chicken, mouse, and human, with a clustering of divergent antisense within 200 bp and convergent antisense within 2 kb [24].…”