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

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.

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

“…25 Such studies yielded the concept of 'active chromatin hubs', arguing that distant regulatory elements control the expression of tissuespecific genes, for example, the αand β-globin genes by the recruitment of promoters into a common complex [26][27][28] (for review, see Reference 24). The seminal invention of Hi-C 29-31 enabled the genome wide identification of the spatial proximity of regulatory sequences in cis and trans, [32][33][34][35][36][37][38] for technical explanations of Hi-C methodologies see References [39][40][41][42]. These studies support a complex dynamic 3D genomic networking of interacting DNA segments, 38,[43][44][45] (for review, see References 21,24,and 46).…”

Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub

“…Chromatin loops between neighboring clutches account for 5-to 10-kb contacts, and hierarchical loops account for 10-to 20-kb contacts.features on fiber contact morphology. Additionally, ChIP with paired-end tags data(44), circular chromosome conformation capture (4C), and a high-resolution Hi-C variant, Bridge Linker-Hi-C (BL-Hi-C), developed by Liang et al(45) show looping among HOXC10, HOXC9, and HOXC6 genes. Such contacts are evident in our HOXC fibers.…”

3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk Factors in Human T-Lineage Acute Lymphoblastic Leukemia

“…Hi-C was performed on one million cells/sample, according to the BL-Hi-C protocol 13 . Raw BL-Hi-C reads were processed by the in-house HiCpipe framework, which integrated several Hi-C analysis methods for to generate multiple features of the Hi-C data.…”

“…Recent whole-exome and RNA sequencing analyses of large T-ALL cohorts are focused on the coding region of the genome and have identified novel driver mutations, dysregulated transcription factors and pathways in T-ALLs 9–12 . To determine whether alterations in the 3D genome organization are associated with malignant transformation of T-ALL, we conducted BL-Hi-C 13 analysis using purified primary leukemic blasts from 18 newly diagnosed T-ALL patients, including 8 early T-cell precursor ALL (ETP ALL) and 10 non-ETP ALL, two clinical subtypes of T-ALL, as well as normal T cells from 4 healthy volunteers (Supplementary Fig. 1a).…”