Related Experiment Video
Updated: Aug 28, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
Published on: July 9, 2021
CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural
Tatsuya Ohhata1, Maya Suzuki2, Satoshi Sakai2
1Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, 431-3192, Japan. ohhata@hama-med.ac.jp.
Abstract:
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. Here, we 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, we 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.
Related Concept Videos
Cis-regulatory Sequences
siRNA - Small Interfering RNAs
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the...
lncRNA - Long Non-coding RNAs
RNA Interference
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Experimental RNAi

