Length of the hypermutation motif DGYW/WRCH in the focus of statistical limits. Implications for a double-motif or extended motif recognition models

Journal of Theoretical Biology
J Kubrycht, Karel Sigler

Abstract

The motif DGYW/WRCH (Mh) and its frequently discussed simplified derivative GYW/WRC (Mhs) are involved in immunoglobulin (Ig) hypermutation. Both these motifs appear to be markedly shorter than the corresponding conventionally predicted minima of valid sequence lengths (MVSL). The same conclusion concerning both Mh and Mhs can also be obtained in the combined case including a less strict semi-empirically defined w-value and one nucleotide length tolerance related to MVSL. Such disagreement indicates considerably low information content in Mh and Mhs when evaluating these motifs as alphabetical structures (words). This fact raises a question of actually recognized structures (presumably longer than Mh and Mhs). Interestingly, both Mh and Mhs dimers or pairs of closely located Mh or Mhs achieve confirmation of length validity in the case of w=0.05, suggesting thus double-motif recognition as one of statistically consistent explanations. This possibility is also in agreement with the results of our model sequence study of mRNA derived from variable Ig gene sequences (rIgV) with respect to the most frequently occurring structures formed by motif overlaps in all model sequence sets. On the other hand, additional superior occurrence ...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 6, 1998·Molecular Biology and Evolution·T Sitnikova, C Su
Aug 15, 1998·Nucleic Acids Research·Z ZhangS F Altschul
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Feb 24, 2001·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·M DiazN Klinman
Jan 10, 2003·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
May 19, 2004·Proceedings of the National Academy of Sciences of the United States of America·Kefang XieJoseph E Wedekind
May 12, 2006·The Journal of Biological Chemistry·Jishu WangTasuku Honjo
Oct 13, 2006·Journal of Molecular Evolution·Jaroslav KubrychtPetr Jezek

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Citations

Feb 12, 2010·Bioinformatics·Fabian A BuskeTimothy L Bailey

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