CCIVR – comprehensive cis-NATs identifier via RNA-seq data

Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Researchers at the Hamamatsu University School of Medicine have developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, the researchers demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.

Overview of CCIVR and the processing steps of its pipeline

Figure 1

(A) Definition of four types of cis-NAT analyzed in this study, “embedded”, “fully-overlapped”, “head-to-head”, and “tail-to-tail”, which can be identified by CCIVR. TSS: transcription start site; TTS: transcription termination site. (B) Overview of CCIVR. The program generates a list of all cis-NAT types from a processed RNA-seq data. The processed RNA-seq data must contain five different gene annotation columns including “id”, “Chr”, “Strand”, “Start”, and “End”. Attaching information for expression profiling obtained from RNA-seq analysis is also available such as “TPM”, “FPKM”, “fold-change”, and “padj”. (C) An example of the process for a target gene, Xist, and identification of its cis-NAT, Tsix, during the process that identifies fully-overlapped cis-NATs from minus to plus strand.


Ohhata T, Suzuki M, Sakai S, Ota K, Yokota H, Uchida C, Niida H, Kitagawa M. (2022) CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 12(1):15525. [article]

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