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Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules

Nature Structural & Molecular Biology volume 19, pages 1044–1052 (2012)Cite this article

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Abstract

Most human genes produce multiple splicing isoforms with distinct functions. To systematically understand splicing regulation, we conducted an unbiased screen and identified >100 intronic splicing enhancers (ISEs), clustered by sequence similarity. All ISEs functioned in multiple cell types and in heterologous introns, and patterns of distribution and conservation across pre-mRNA regions were similar to those of exonic splicing silencers. Consistently, all ISEs inhibited use of splice sites from exons. Putative trans-factors of each ISE group were identified and validated. Five distinct groups were recognized by hnRNP H and hnRNP F, whose C-terminal domains were sufficient to render context-dependent activities of ISEs. The sixth group was controlled by factors that either activate or suppress splicing. We provide a comprehensive picture of general ISE activities and suggest new models of how single elements can function oppositely, depending on locations and binding factors.

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Figure 1: Identification and validation of ISEs.
Figure 2: Identification and validation of the core motifs of FAS-ISEs.
Figure 3: Similarity between FAS-ISE and FAS-ESSs.
Figure 4: FAS-ISEs function as splicing silencers in exonic contexts.
Figure 5: HnRNP H and hnRNP F recognize distinct ISE groups to control splicing mediated by their C-terminal domains.
Figure 6: Multiple factors with antagonistic activities bind ISE group F motifs to control splicing.

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Acknowledgements

We thank J. Hui from the Shanghai Institute of Biological Science, Shanghai, China and W.-Y. Tarn from the Institute of Biomedical Sciences, Academia Sinica, Taipei, China for providing the expression constructs and B. Marzluff and C. Burge for critical reading of manuscripts. We thank. Z. Dominski for helping in RNA affinity purifications. This work is supported by an American Heart Association grant (0865329E) and US National Institutes of Health grant (R01CA158283) to Z.W.

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Authors and Affiliations

  1. Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

    Yang Wang, Meng Ma & Zefeng Wang

  2. Department of Computer Science and Technology, Anhui University, Hefei, China

    Meng Ma

  3. Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA

    Xinshu Xiao

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Y.W. and Z.W. designed the research and performed the experiments. M.M. and X.X. developed computational methods to analyze the data. Y.W. and Z.W. wrote the paper.

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Correspondence to Zefeng Wang.

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Wang, Y., Ma, M., Xiao, X. et al. Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat Struct Mol Biol 19, 1044–1052 (2012). https://doi.org/10.1038/nsmb.2377

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