Fine-Resolution Mapping of TF Binding and Chromatin Interactions

Jenia Gutin,Ronen Sadeh,Nitzan Bodenheimer,Daphna Joseph-Strauss,Avital Klein-Brill,Adi Alajem,Oren Ram,Nir Friedman

doi:10.1016/j.celrep.2018.02.052

Jenia Gutin, Ronen Sadeh + Show 6 more

Open Access

https://doi.org/10.1016/j.celrep.2018.02.052

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Journal: Cell Reports	Publication Date: Mar 1, 2018
Citations: 48	License type: cc-by

Affiliation: Hebrew University of Jerusalem

Abstract

SummaryTranscription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal −1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level.

Highlights

Binding of transcription factors (TFs) to specific DNA sequences is fundamental for regulation of transcription and chromatin structure
SLIM-chromatin immunoprecipitation (ChIP) Reconstructs Rules of REB1 Binding As a test case, we performed SLIM-ChIP to map Reb1 binding in Saccharomyces cerevisiae (Figure 1B)
We searched for sequence motifs enriched at SLIMChIP Reb1 peak centers (Experimental Procedures) recovering the consensus sequence motif (Figure 1C) that has been previously reported for Reb1 both in vivo and in vitro (Kasinathan et al, 2014; Liaw and Brandl, 1994; Rhee and Pugh, 2011)

Summary

Introduction

Binding of transcription factors (TFs) to specific DNA sequences is fundamental for regulation of transcription and chromatin structure. Our understanding of transcription factor binding in vivo is based on mapping their occupancy along the genome, mainly by chromatin immunoprecipitation (ChIP) (Solomon et al, 1988). Coupling of ChIP to next-generation sequencing technology allows genome-wide mapping of transcription factors in a single experiment (Mikkelsen et al, 2007). Typical ChIP protocols involve cross-linking of proteins to DNA prior to DNA shearing by sonication, immunoprecipitation with an antibody against the transcription factor of interest, release of bound DNA, and next-generation sequencing compatible library preparation. Drawbacks of standard ChIP-sequencing (ChIP-seq) assays are the requirement for large amounts of sample material and the relatively low resolution ($200– 500 bp) due to the size of DNA fragments generated by chromatin sonication. Most ChIP assays are not readily compatible with high-throughput practices, which limits the number of samples that can be processed simultaneously

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