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Stabilised DNA secondary structures with increasing transcription localise hypermutable bases for somatic hypermutation in IGHV3-23

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Abstract

Somatic hypermutation (SHM) mediated by activation-induced cytidine deaminase (AID) is a transcription-coupled mechanism most responsible for generating high affinity antibodies. An issue remaining enigmatic in SHM is how AID is preferentially targeted during transcription to hypermutable bases in its substrates (WRC motifs) on both DNA strands. AID targets only single stranded DNA. By modelling the dynamical behaviour of IGHV3-23 DNA, a commonly used human variable gene segment, we observed that hypermutable bases on the non-transcribed strand are paired whereas those on transcribed strand are mostly unpaired. Hypermutable bases (both paired and unpaired) are made accessible to AID in stabilised secondary structures formed with increasing transcription levels. This observation provides a rationale for the hypermutable bases on both the strands of DNA being targeted to a similar extent despite having differences in unpairedness. We propose that increasing transcription and RNAP II stalling resulting in the formation and stabilisation of stem-loop structures with AID hotspots in negatively supercoiled region can localise the hypermutable bases of both strands of DNA, to AID-mediated SHM.

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Acknowledgments

BD is supported by the Ontario Graduate Scholarship and The President Susan Mann Dissertation Scholarship. GEW is funded by The Arthritis Society. JW is funded by the Natural Sciences and Engineering Research Council of Canada (NSERC), the Canada Research Chairs program (CRC) and by Mprime. The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the quality of the paper.

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The authors declare no conflict of interest.

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Author notes

  1. Venkata R. Duvvuri

    Present address: Ontario Agency for Health Protection and Promotion, Toronto, ON, Canada

Authors and Affiliations

  1. School of Kinesiology & Health Science, Faculty of Health, York University, 4700 Keele Street, Toronto, ON, Canada, M3J 1P3

    Bhargavi Duvvuri & Gillian E. Wu

  2. Mprime Centre for Disease Modeling, York University, 4700 Keele Street, Toronto, ON, Canada, M3J 1P3

    Venkata R. Duvvuri & Jianhong Wu

  3. Mount Sinai Hospital, Toronto, ON, Canada

    Venkata R. Duvvuri

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  1. Bhargavi Duvvuri
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Correspondence to Bhargavi Duvvuri.

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Table S1

Structural state of bases C’s sand G’s by folding NTS and TS strands of germline IGHV3-23 gene sequence in ‘mfold’a (DOC 37 kb)

Table S2

Comparison of C’s in hot spots (WRC) on NTS and TS (DOC 32 kb)

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Duvvuri, B., Duvvuri, V.R., Wu, J. et al. Stabilised DNA secondary structures with increasing transcription localise hypermutable bases for somatic hypermutation in IGHV3-23. Immunogenetics 64, 481–496 (2012). https://doi.org/10.1007/s00251-012-0607-3

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