期刊
RNA BIOLOGY
卷 16, 期 8, 页码 1044-1054出版社
TAYLOR & FRANCIS INC
DOI: 10.1080/15476286.2019.1612692
关键词
Mrna structure in vivo; deep neural networks; the degree of mRNA structure unwinding; DMS probing; ribosome profiling
资金
- National Natural Science Foundation of China [(31771474)]
The structure of mRNA in vivo is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA in vitro. In this study, we have proposed a novel application of deep neural networks, named DeepDRU, to predict the degree of mRNA structure unwinding in vivo by fitting five quantifiable features that may affect mRNA folding: ribosome density (RD), minimum folding free energy (MFE), GC content, translation initiation ribosome density (INI) and mRNA structure position (POS). mRNA structures with adjustment of the simulated structural features were designed and then fed into the trained DeepDRU model. We found unique effect regions of these five features on mRNA structure in vivo. Strikingly, INI is the most critical factor affecting the structure of mRNA in vivo, and structural sequence features, including MFE and GC content, have relatively smaller effects. DeepDRU provides a new paradigm for predicting the unwinding capability of mRNA structure in vivo. This improved knowledge about the mechanisms of factors influencing the structural capability of mRNA to unwind will facilitate the design and functional analysis of mRNA structure in vivo.
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