Table 2 Data types used for identification of candidate non-coding regions

ATAC-seq or DNase

Flags regions of open chromatin

Promoter / CRE

ENCODE; ROADMAP epigenomics

Promoter capture Hi-C

Links enhancer regions to promoters of target genes

CRE

Published datasets; 3D genome browser^a

Transient interactions that may not be needed for enhancer function

Hi-C

Define topologically associated domains (TADs)

TAD boundaries

Published datasets; 3D genome browser^a

Cap analysis gene expression (CAGE)

Marks the 5' cap of mRNA

Promoter / 5'UTR

FANTOM5

Alternative transcripts

CTCF ChIP-seq

Identifies regions bound by the insulator protein CTCF

TAD boundaries

ENCODE; ROADMAP epigenomics

Transcription factor ChIP-seq

Identifies regions bound by specific transcription factors

Promoter / CRE

ENCODE; ROADMAP epigenomics

H3K4Me

Histone modification found near enhancers

CRE

ENCODE; ROADMAP epigenomics

H3K4Me3

Histone modification found near promoters

Promoter

ENCODE; ROADMAP epigenomics

H3K27Ac

Histone modification found at active regulatory elements

Promoter / CRE

ENCODE; ROADMAP epigenomics

Expression quantitative trait loci (eQTLs)

Identifies variants that are associated with changes in gene expression

Promoter / CRE

GTEx; eqtlgen.org

Experimental perturbation

Demonstrates an impact of altering/deleting all or part an element on gene expression

Promoter / CRE

Published data

Assays may not be representative of endogenous situation

Northern blot, RT-qPCR, RNA sequencing and microarrays

Detection of miRNAs

miRNAs

miRBase; published datasets

Multiple approaches

Experimentally validated miRNA–target interactions

miRNA targets

miRTarBase; published datasets

Bisulphite sequencing

Detects methylated DNA and allows identification of differentially methylated regions

Promoter / upstream gene regions

ENCODE; ROADMAP epigenomics

RNA Pol II ChIP-seq

Detection of poised polymerase II

Promoter

ENCODE; ROADMAP epigenomics