دورية أكاديمية
CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles
| العنوان: | CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles |
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| المؤلفون: | Tatsuya Ohhata, Maya Suzuki, Satoshi Sakai, Kosuke Ota, Hazuki Yokota, Chiharu Uchida, Hiroyuki Niida, Masatoshi Kitagawa |
| المصدر: | Scientific Reports, Vol 12, Iss 1, Pp 1-12 (2022) |
| بيانات النشر: | Nature Portfolio, 2022. |
| سنة النشر: | 2022 |
| المجموعة: | LCC:Medicine LCC:Science |
| مصطلحات موضوعية: | Medicine, Science |
| الوصف: | 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 2045-2322 |
| Relation: | https://doaj.org/toc/2045-2322 |
| DOI: | 10.1038/s41598-022-19782-5 |
| URL الوصول: | https://doaj.org/article/be2471143ee647f58a9585074de508c9 |
| رقم الأكسشن: | edsdoj.be2471143ee647f58a9585074de508c9 |
| قاعدة البيانات: | Directory of Open Access Journals |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 20452322 |
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| DOI: | 10.1038/s41598-022-19782-5 |