RNA stem–loops: To be or not to be cleaved by RNAse III
| العنوان: | RNA stem–loops: To be or not to be cleaved by RNAse III |
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| المؤلفون: | Daniel Gautheret, Matthieu Legendre, William Ritchie |
| المساهمون: | Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS) |
| المصدر: | RNA RNA, Cold Spring Harbor Laboratory Press, 2007, 13 (4), pp.457-62. ⟨10.1261/rna.366507⟩ |
| بيانات النشر: | Cold Spring Harbor Laboratory, 2007. |
| سنة النشر: | 2007 |
| مصطلحات موضوعية: | Ribonuclease III, MESH: RNA Interference, 0206 medical engineering, MESH: RNA Precursors, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 02 engineering and technology, MESH: Base Sequence, 03 medical and health sciences, MESH: Ribonuclease III, MESH: RNA, RNA interference, microRNA, RNA Precursors, Animals, Humans, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Models, Genetic, Molecular Biology, Protein secondary structure, 030304 developmental biology, Comparative genomics, Genetics, 0303 health sciences, MESH: Humans, Base Sequence, Models, Genetic, biology, MESH: Models, Chemical, RNA, Hypothesis, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Models, Structural, MicroRNAs, genomic DNA, MESH: Nucleic Acid Conformation, Models, Chemical, Duplex (building), biology.protein, Nucleic Acid Conformation, RNA Interference, MESH: Models, Structural, MESH: MicroRNAs, 020602 bioinformatics |
| الوصف: | Most of the vertebrate genome is transcribed into RNA. Transcribed regions contain hundreds of thousands of potential duplex structures that could serve as substrates for RNAse III enzymes of microRNA (miRNA) maturation pathways. Yet, only a minority of these potential precursors make their way to the cytoplasm to form mature miRNAs. We question here what specific structural features make an RNA stem–loop structure an adequate primary or precursor miRNA. We address this question by comparing known pre-miRNAs to other predicted noncoding transcripts obtained from comparative genomics scans, using the structure comparison program RNAforester. By analyzing a classification tree of 1200 such RNA structures, we observe that pre-miRNAs cluster distinctly from other duplex structures of apparently similar size and free energy. The most distinctive features of nonprecursor duplexes are increased lengths and numbers of bulges and internal loops when compared to real miRNA precursors. Thanks to these characteristics, secondary structure comparison can predict the miRNA precursor status of a candidate stem–loop with a surprising accuracy. Furthermore, predicted noncoding transcripts tend to depart from miRNA precursor characteristics more strongly than randomly occurring duplex structures in genomic DNA. This result suggests that many noncoding RNAs may be under selection to dodge the RNAi pathway. |
| تدمد: | 1469-9001 1355-8382 |
| DOI: | 10.1261/rna.366507 |
| DOI: | 10.1261/rna.366507⟩ |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d06758d943be3d2411e93fd9d7d8219e https://doi.org/10.1261/rna.366507 |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....d06758d943be3d2411e93fd9d7d8219e |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14699001 13558382 |
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| DOI: | 10.1261/rna.366507 |