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Table 1 Commonly used terminologies

From: Three-dimensional genome architecture and emerging technologies: looping in disease

Terminology Definition
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
  1. 3D three-dimensional, DHSs DNase I hypersensitive sites, HiC genome-wide chromatin conformation capture, FIREs frequently interacting regions, kb kilobases, PIRs promoter interacting regions, Temp temporarily phenotypic
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