Three-dimensional genome structures of single diploid human cells

Abstract

Three-dimensional genome structures play a key role in gene regulation and cell functions. Characterization of genome structures necessitates single-cell measurements. This has been achieved for haploid cells but has remained a challenge for diploid cells. We developed a single-cell chromatin conformation capture method, termed Dip-C, that combines a transposon-based whole-genome amplification method to detect many chromatin contacts, called META (multiplex end-tagging amplification), and an algorithm to impute the two chromosome haplotypes linked by each contact. We reconstructed the genome structures of single diploid human cells from a lymphoblastoid cell line and from primary blood cells with high spatial resolution, locating specific single-nucleotide and copy number variations in the nucleus. The two alleles of imprinted loci and the two X chromosomes were structurally different. Cells of different types displayed statistically distinct genome structures. Such structural cell typing is crucial for understanding cell functions.

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

“…PCR, sequencing) to map pairs of loci that spatially interact in the nucleus 1, 19 . The general principles underlying these techniques can be modified to target specific nuclear proteins by immunoprecipitation (ChIA-PET 20 , HiChIP 21 ) or specific loci using nucleic acid hybridization enrichment(ChiC 22 ), and they can be adapted to study single-cell samples 23,24 . Most notably, Hi-C enables unbiased mapping of active (A) and inactive (B) chromatin compartments, TADs, cohesin loops, and enhancer-promoter interactions among the billions of interacting locus pairs in these genome-wide contact maps.…”

The multi‐faceted regulation of nuclear tRNA gene transcription

“…With the use of novel technics such as Hi‐C, the resolution of chromatin conformation and location is now possible at the single cell level in human and even down to the single gene level in A. thaliana . Regions of the genome that frequently physically interact with each other termed Topologically Associating Domains (TADs) have been described in the genomes of many organisms such as human , fruit fly , budding yeast , and plants . Transcription may be further influenced by an additional level of location complexity where these structures preferentially occupy areas around the nuclear center or periphery called chromosome territories .…”

“…With the use of novel technics such as Hi-C, the resolution of chromatin conformation and location is now possible at the single cell level in human (93) and even down to the single gene level in A. thaliana (94). Regions of the genome that frequently physically interact with each other termed Topologically Associating Domains (TADs) have been described in the genomes of many organisms such as human (93), fruit fly (95), budding yeast (96), and plants (97).…”

RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids

“…Such a simple one-step tagmentation reaction has been proved to greatly simplify the experimental process, shorten the time and lower the cost. Tn5-tagmentation has also been used for chromatin accessibility detection, high-accuracy single-cell wholegenome sequencing, and chromatin interaction studies [27][28][29][30][31]. For RNA-seq, the RNA transcripts have to undergo reverse transcription and second strand synthesis, before the Tn5 tagmentation of the resulting dsDNA [32,33].…”