  Motivation Gene transcription requires the orchestrated binding of various
proteins to the promoter of a gene. The binding times and binding order of
proteins allow to draw conclusions about the proteins' exact function in the
recruitment process. Time-resolved ChIP experiments are being used to analyze
the order of protein binding for these processes. However, these ChIP signals
do not represent the exact protein binding patterns. Results We show that for
promoter complexes that follow sequential recruitment dynamics the ChIP signal
can be understood as a convoluted signal and propose the application of
deconvolution methods to recover the protein binding patterns from experimental
ChIP time-series. We analyze the suitability of four deconvolution methods: two
non-blind deconvolution methods, Wiener deconvolution and Lucy-Richardson
deconvolution, and two blind deconvolution methods, blind Lucy-Richardson
deconvolution and binary blind deconvolution. We apply these methods to infer
the protein binding pattern from ChIP time-series for the pS2 gene.
