BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions

Zhengyu Liang,Yanjian Li,Guipeng Li,Zejun Wang,Yang Chen,Michael Q Zhang,Min-Ping Qian,Mohamed Nadhir Djekidel

doi:10.1038/s41467-017-01754-3

Abstract

In human cells, DNA is hierarchically organized and assembled with histones and DNA-binding proteins in three dimensions. Chromatin interactions play important roles in genome architecture and gene regulation, including robustness in the developmental stages and flexibility during the cell cycle. Here we propose in situ Hi-C method named Bridge Linker-Hi-C (BL-Hi-C) for capturing structural and regulatory chromatin interactions by restriction enzyme targeting and two-step proximity ligation. This method improves the sensitivity and specificity of active chromatin loop detection and can reveal the regulatory enhancer-promoter architecture better than conventional methods at a lower sequencing depth and with a simpler protocol. We demonstrate its utility with two well-studied developmental loci: the beta-globin and HOXC cluster regions.

Highlights

In human cells, DNA is hierarchically organized and assembled with histones and DNAbinding proteins in three dimensions
Based on the two-step ligation model (Supplementary Fig. 1b), DNA fragments originally brought together by specific protein complexes are preferentially ligated to biotin-labeled bridge linkers in the nuclei, when compared to non-protein-centric DNA fragments. This preference is significantly enhanced in two-step ligation compared with onestep ligation, as described by an ordinary differential equation (ODE) and illustrated by the simulation results (Methods and Supplementary Fig. 1c)
When we examined CTCF and RNAPII chromatin immunoprecipitation (ChIP)-seq peaks in chromatin interaction anchor regions, there were ~ 1.3–3.3-fold CTCF enrichment and ~ 2.0–5.4-fold RNAPII enrichment for Bridge Linker-High-throughput chromosome conformation capture (Hi-C) (BL-Hi-C) paired-end tags (PETs) compared to in situ Hi-C and HiChIP (Fig. 2a and Supplementary Fig. 2a)

Summary

Introduction

DNA is hierarchically organized and assembled with histones and DNAbinding proteins in three dimensions. A growing body of evidence has shown that architectural proteins and transcription factors play important roles in maintaining distal chromatin interactions and regulating the chromatin conformation on a much smaller scale[6,7,8,9]. To directly investigate this sophisticated structure, several variations of 3D genomics methods have been published[10,11,12,13,14,15,16,17,18]. This goal led to our BL-Hi-C method, which provides a new, to the best of our knowledge, strategy for the enrichment of proteincentric chromatin contacts

Methods

Results

Conclusion