ArticleScientific reports2022
CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 6 citations in OpenAlex.
- Early replication fragile sites are associated with cancer-related CNVs and SNVs in human embryonic stem cells.Stem cell reports · 2026Article
- Non-coding RNA notations, regulations and interactive resources.Functional & integrative genomics · 2024Review
- Natural antisense transcripts as versatile regulators of gene expression.Nature reviews. Genetics · 2024Review
- CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions.Scientific reports · 2023Article
- The emerging roles of long non-coding RNA in host immune response and intracellular bacterial infections.Frontiers in cellular and infection microbiology · 2023Review
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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