Transcription factors (TFs)	Proteins that bind specific target DNA sequences, located within enhancers or promoters, contributing to the regulation of RNA transcription of specific gene(s).
Promoter	DNA regulatory region typically present upstream of the transcription start site (TSS) of a gene. RNA polymerase recruitment at those loci triggers the transcription of the gene(s).
Enhancer	DNA element that modulates the transcription by binding TFs and bringing them in physical interaction with the cognate promoter(s) of gene(s). In contrast to promoters, enhancers act independently of the distance (up to hundreds of kilobases or even megabases) and orientation to the respective target gene(s). They are characterized by accessible chromatin devoid of nucleosomes and flanked by nucleosomes with specific histone modifications (H3K27ac and/or H3K4me1).
ChIP-seq	Chromatin immunoprecipitation followed by sequencing is a method for finding DNA–protein interactions by combining immunoprecipitation and DNA-sequencing. Can be applied to TF to validate their binding sites or to covalent histone modifications (e.g., H3K27 acetylation, H3K4 methylation) to identify putative regulatory regions—a process referred to as chromatin segmentation—and their differential activity.
RNA-seq	RNA-sequencing is a next-generation sequencing method that provides an overall unbiased quantification of RNA content, which can be refined by ribosomal RNA depletion or mRNA enrichment before cDNA synthesis, library preparation, and sequencing. The relative abundance of transcripts obtained constitute the input to evaluate differential gene expression between samples or conditions.
scRNA-seq	Single-cell RNA-sequencing; a technology that allows the gene expression analysis at single-cell resolution. Isolating individual cells, this technique highlights transcriptional differences between cells of the same biological sample, otherwise obscured using only the bulk RNA-seq analysis.
Hi-C	Hi-C is based on the chromosome conformation capture (3C) technology and it is used to detect, in a genome-wide manner, the chromatin interactions inside the nucleus. Chromatin is crosslinked with formaldehyde; the spatially close genomic fragments are ligated generating chimeric DNA fragments which are captured and identified by deep sequencing.
TAD	Topologically associate domains (TADs) are 3D chromosome structures, whose boundaries are relatively conserved while their internal conformation can change depending upon epigenetic marks and nucleosome structures. Within TADs, chromatin looping brings together regulatory element in close proximity (i.e., enhancers with promoters).
MPRA	Massively parallel reporter assay; method that provides a quantitative measurement of the activity of thousand potential DNA regulatory sequences in parallel. A library of candidate sequences cloned upstream of a promoter/reporter construct are transfected into a cellular model system and identified by deep sequencing.
STARR-seq	Self-transcribing active regulatory region sequencing; like MPRA, this technology assesses the activity of thousand potential regulatory regions, in a cellular model. Candidate sequences are cloned downstream of a promoter/reporter construct. Potential regulatory regions are self-transcribed and identified by RNA-seq to measure candidate regions’ activity.
CRISPR/Cas9	Clustered regularly interspaced short palindromic repeats. Cas9 is an endonuclease that can be directed to the target region by a synthetic guide RNA (sgRNA) complementary to the target causing a DNA strand break. A mutated version of Cas9 without endonuclease activity (dead or dCas9) if fused with activator or repressor domains can induce chromatin changes leading to inactivation (CRISPRi) or activation (CRISPRa) of the target regions.
GWAS	Genome-wide association study. It is an observational study of a set of genetic variants (genome-wide) in different individuals to see if any variant is associated with a specific trait. Variants are detected by microarray or whole-genome sequencing technology.
eQTL	Expression quantitative trait loci. Regions of DNA in which genetic variation is associated with variability in the expression of one or more genes.
DNase-seq	A method based on DNaseI hypersensitivity for identifying accessible regions of the genome.
ATAC-seq	Assay for transposase accessible chromatin; a method for identifying accessible regions of the genome, based on transposase activity.
WGCNA	Weighted gene co-expression network analysis identifies modules of genes which exhibit correlated patterns of gene expression across samples and often represent similar cell types. Trends in the network can be summarized by eigengenes or hub genes that are central to the network structure.