Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases

Abstract

Genome-wide association studies (GWAS) have mapped over 90% of disease- and quantitative-trait-associated variants within the non-coding genome. Non-coding regulatory DNA (e.g., promoters and enhancers) and RNA (e.g., 5' and 3' UTRs and splice sites) are essential in regulating temporal and tissue-specific gene expressions. Non-coding variants can potentially impact the phenotype of an organism by altering the molecular recognition of the cis-regulatory elements, leading to gene dysregulation. However, determining causality between non-coding variants, gene regulation, and human disease has remained challenging. Experimental and computational methods have been developed to understand the molecular mechanism involved in non-coding variant interference at the transcriptional and post-transcriptional levels. This review discusses recent approaches to evaluating disease-associated single-nucleotide variants (SNVs) and determines their impact on transcription factor (TF) binding, gene expression, chromatin conformation, post-transcriptional regulation, and translation.

Keywords: RNA processing; gene regulation; massively parallel reporter assay; non-coding variants; transcription factors.

Fig. 1.. Non-coding variants can alter transcription factor (TF)–DNA binding activity, transcriptional machinery recruitment, and gene expression.

(A) TFs bind to regulatory DNA (e.g., promoters and enhancers) and recruit transcriptional machinery to initiate gene expression. (B) Non-coding variants can change TF–DNA binding affinities, altering transcriptional complex recruitment and gene expression. Changes in TF–DNA binding affinities are represented by equilibrium arrows. Changes in gene expression are represented by a black (decrease) and orange (increase) arrow.

Fig. 2.. Non-coding variants can alter Cis-regulatory element (CRE) interactome.

(A) TFs facilitate promoter–enhancer interactions by forming topologically associating domains (TADs) to regulate gene expression. (B) Non-coding variants can alter TAD boundaries and CRE interactions that regulate gene expression. Changes in gene expression are represented by an orange (increase) and black (decrease) arrow.

Fig. 3.. Non-coding variants can disrupt mRNA processing and translation initiation.

(A) mRNA interactions with RNA-binding proteins and ribosomes are needed for processing (e.g., splicing and adenylation) and translation initiation, respectively. (B) Non-coding variants can alter splice and polyadenylation sites needed for stable mRNA processing and expression of functional protein isoforms. mRNA variants can create translation sites that compete with the main open reading frame (mORF). PAS, polyadenylation sites.