Global Analysis of RNA Secondary Structure in Two Metazoans

作者：Li Fan; Zheng Qi; Ryvkin Paul; Dragomir Isabelle; Desai Yaanik; Aiyer Subhadra; Valladares Otto; Yang Jamie; Bambina Shelly; Sabin Leah R; Murray John I; Lamitina Todd; Raj Arjun; Cherry Sara; Wang Li San^*; Gregory Brian D

来源：Cell Reports, 2012, 1(1): 69-82.

DOI：10.1016/j.celrep.2011.10.002

The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

• 出版日期2012-1
• 单位上海生物信息技术研究中心