Noncanonical registers and base pairs in human 5' splice-site selection.

Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Citation

Jiazi Tan, Jia Xin Jessie Ho, Zhensheng Zhong, Shufang Luo, Gang Chen, Xavier Roca. Noncanonical registers and base pairs in human 5' splice-site selection. Nucleic acids research. 2016 May 05;44(8):3908-21

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PMID: 26969736

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