Multiplex Chromatin Interaction Analysis with Single-Molecule Precision

Abstract

We describe a microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision. In multiplex chromatin interaction analysis (multi-ChIA), individual chromatin complexes are partitioned into droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts. Thus, multi -ChIA has the unprecedented ability to uncover multiplex chromatin interactions at single -molecule level, which has been impossible using previous methods that rely on analyzing pairwise contacts via proximity ligation. We demonstrate that multiplex chromatin interactions predominantly contribute to topologically associated domains, and clusters of gene promoters and enhancers provide a fundamental topological framework for co-transcriptional regulation.Genomes of higher organisms from fly to human are known to be extensively folded into chromosomal territories within the three-dimensional (3D) nuclear space 1 . Advanced long-range chromatin interaction

Women’s contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization

“…Also, new methods have been developed to overcome the limitation of most proximity-ligation methods that can only detect pair-wise interactions as they rely on the physical ligation of neighbouring fragments-ends. Recent techniques, such as SPRITE (Split-Pool Recognition of Interactions by Tag Extension) and ChIA-Drop (Chromatin Interaction Analysis via Droplet-based and barcode-linked sequencing), can detect multiway interactions by performing a physical separation of interacting domains (in wells or in droplets, respectively) followed by pooled-tagging and sequencing (Quinodoz et al, 2018;Zheng et al, 2019). The identification of multi-way interactions and complex contacts will be particularly relevant to delve deeper into chromatin topology and supercoiling.…”

Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape

“…These were more clearly confirmed by subsequent studies. For example, self-interacting domains were redefined by Micro-C under loop extrusion, which was defined in a future study as a transcription reeling-in model by ChIA-Drop [68]. Benefitting from Micro-C technology, scientists have discovered many new structures.…”

An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton (Gossypium spp.)

“…In the nuclei of multicellular eukaryotes, chromatin forms hierarchical three-dimensional (3D) structures on top of its linear conformation (Ouyang et al, 2020b). With the development of chromosome conformation capture (3C) methods (Louwers et al, 2009;Hakim and Misteli, 2012;Jamge et al, 2017;Hua et al, 2021), functional structures have been revealed at various genomic scales, including chromatin territories, A/B compartments, topologically associating domains (TADs), and chromatin loops (Meaburn and Misteli, 2007;Lieberman-Aiden et al, 2009;Dixon et al, 2012;Grob and Grossniklaus, 2017;Zheng et al, 2019). From territory to loop, the detection resolution required increases in order (Rodriguez-Granados et al, 2016).…”