Reconstructing protein binding patterns from ChIP time-series

TL;DR

This paper presents a method to recover precise protein binding patterns from ChIP time-series data by applying deconvolution techniques, addressing the challenge of convoluted signals in time-resolved gene regulation studies.

Contribution

It introduces the application of four deconvolution methods to interpret ChIP time-series data for sequential protein recruitment in gene regulation.

Findings

Wiener and Lucy-Richardson deconvolutions are suitable for non-blind scenarios.

Blind deconvolution methods can recover binding patterns without prior knowledge.

Application to pS2 gene data demonstrates the effectiveness of the proposed approach.

Abstract

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.