Table 1 Commonly used terminologies

Euchromatin

Chromatin that contains loosely packed nucleosomes. Usually represents transcriptionally active sites in the genome, including regulatory elements

Heterochromatin

Chromatin that is densely packed with nucleosomes. Usually represents transcriptionally silent site in the genome

DNase I hypersensitive sites (DHSs)

Nucleosome-free regions of chromatin that are mostly found at enhancers and promoters. Largely indicative of transcription factor binding

Enhancer elements

Enhancers are sequences of DNA that enhance gene expression by being bound by transcription factors and looping to interact with gene promoters. These elements are located on the same chromosome (cis-regulatory) and can be near promoters or megabases away

Super-enhancer

Group of multiple enhancers located within 12 kb of each other, which are bound by an array of transcription factors and marked by acetylation

Temp enhancer

A novel class of cis-regulatory elements whose disruption leads to temporary loss of target gene expression, which is eventually regained

Human-gained enhancer

Putative novel enhancer-like elements gained in the human lineage, discovered from brain Hi-C data

Purifying selection

Negative selection in which deleterious alleles are selectively removed through evolution

Gene desert

Large genomic regions that are devoid of genes, but may harbor many disease-causing variants and distal regulatory elements

Promoter interacting regions (PIRs)

PIRs are broadly defined as distal regulatory elements interacting with promoters via looping interactions

Frequently interacting regions (FIREs)

FIREs are regional groups of putative enhancer-like elements that interact with each other and many promoters

Population average ensemble structure

During Hi-C experiments in bulk, cells are present in multiple growth stages; thus, they exhibit multiple 3D architectural landscapes. In bulk Hi-C, different architectural landscapes are captured and this is called population average ensemble structure

Haplotype phasing

Deciphering haplotype block structures for polymorphic sites using genotype data. This is traditionally done computationally to determine if variants are on the same allele. Hi-C provides an experimental means of determining if variants reside on the same allele

Combinatorial indexing

Method that tags DNA within intact nuclei in each cell with successive rounds (combinatorial) of nucleic acid barcodes for adapting to different genomics application such as transcriptomics, Hi-C and chromatin accessibility for single-cell studies, without the need for isolating single cells physically