Abstract
BackgroundChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. It is known that the targeted motifs in most cases can be found at the peak centers. A high resolution mapping of ChIP-seq peaks could in principle allow the fine mapping of the protein constituents within protein complexes, but the current ChIP-seq analysis pipelines do not target the basepair resolution strand specific mapping of peak summits.ResultsThe approach proposed here is based on i) locating regions that are bound by a sufficient number of proteins constituting a complex; ii) determining the position of the underlying motif using either a direct or a de novo motif search approach; and iii) determining the exact location of the peak summits with respect to the binding motif in a strand specific manner. We applied this method for analyzing the CTCF/cohesin complex, which holds together DNA loops. The relative positions of the constituents of the complex were determined with one-basepair estimated accuracy. Mapping the positions on a 3D model of DNA made it possible to deduce the approximate local topology of the complex that allowed us to predict how the CTCF/cohesin complex locks the DNA loops. As the positioning of the proteins was not compatible with previous models of loop closure, we proposed a plausible “double embrace” model in which the DNA loop is held together by two adjacent cohesin rings in such a way that the ring anchored by CTCF to one DNA duplex encircles the other DNA double helix and vice versa.ConclusionsA motif-centered, strand specific analysis of ChIP-seq data improves the accuracy of determining peak positions. If a genome contains a large number of binding sites for a given protein complex, such as transcription factor heterodimers or transcription factor/cofactor complexes, the relative position of the constituent proteins on the DNA can be established with an accuracy that allow one to deduce the local topology of the protein complex. The proposed high resolution mapping approach of ChIP-seq data is applicable for detecting the contact topology of DNA-binding protein complexes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2940-7) contains supplementary material, which is available to authorized users.
Highlights
ChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide
The summit-based high-resolution ChIP-seq analysis shows a characteristic shift pattern between the DNA contact points of CCCTC-binding factor (CTCF), STAG1/2, Double-strand-break repair protein rad21 homolog (RAD21) and SMC1/3 proteins The high-resolution mapping approach proposed here seeks to extend the conventional analyses in two respects
If we mapped the contact points of co-localizing DNA-binding proteins, we could define an average distance between them. Underlying these considerations was the assumption that the fine positional shifts that may exist between the contact points of cohesin proteins (CTCF, RAD21, SMC1/3 and STAG1/2) may reflect the 3D position of the components within the complex
Summary
ChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. The tripartite cohesin ring itself consists of RAD21, SMC1 and SMC3 proteins [3, 4] and is believed to anchor to DNA via STAG1/2 and CTCF [5,6,7,8,9,10,11,12]. The cohesin ring is large enough to embrace two sister chromatids, but this connection is believed to be topological rather than sequence specific, such as in the case of chromatin loop formation [3]. Models suggested in current studies [22, 24] consistently depict the ring in a distal position with respect to the loop and the anchoring CTCF molecules. As far as we are aware, there are no experimental data available that directly support this view
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