Mutations in the noncoding genome

Abstract

Purpose of review Clinical diagnostic sequencing currently focuses on identifying causal mutations in the exome, where most disease-causing mutations are known to occur. The rest of the genome is mostly comprised of regulatory elements that control gene expression, but these have remained largely unexplored in clinical diagnostics due to the high cost of whole genome sequencing and interpretive challenges. The purpose of this review is to illustrate examples of diseases caused by mutations in regulatory elements and introduce the diagnostic potential for whole genome sequencing. Different classes of functional elements and chromatin structure are described to provide the clinician with a foundation for understanding the basis of these mutations. Recent Findings The utilization of whole genome sequence data, epigenomic maps and iPS cell technologies facilitated the discovery that mutations in the PTF1A enhancer can cause isolated pancreatic agenesis. High resolution array CGH, whole genome sequencing, maps of 3-D chromatin architecture, and mouse models generated using CRISPR-Cas were used to show that disruption of topological-associated domain (TAD) boundary elements cause limb defects. Structural variants that reposition enhancers in somatic cells have also been described in cancer. Summary While not ready for diagnostics, new technologies, epigenomic maps and improved knowledge of chromatin architecture will soon enable a better understanding and diagnostic solutions for currently unexplained genetic disorders.

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

“…A substantial fraction of such variants is thought to modulate cis-regulatory element function, and a number of examples of disease-associated non-coding mutations that ablate or change enhancer function or impact the folding of topological domains have been identified (reviewed in (Scacheri and Scacheri, 2015)). Indeed, genetic variation within the human population coupled with quantitative epigenomic approaches can be leveraged to link sequence changes to chromatin state divergence, both locally and distally within interacting chromosomal regions, providing an avenue for an interpretation of GWAS studies and future investigations of mechanisms underlying disease traits (Grubert et al, 2015; Waszak et al, 2015).…”

CRISPR/Cas9-Based Engineering of the Epigenome

“…Occurrence of these aberrant states is mainly caused by DNA mutations in non-coding regions (Scacheri and Scacheri, 2015) and deregulation of specific chromatin modifications. Currently, non-coding mutations are identified by whole genome sequencing and then traced to regulatory regions by overlapping patient-specific mutations with epigenetic marks typical of such regions.…”

“…For instance, congenital malformations have been associated with the disruption of TADs, which organize chromatin and constrain the regulatory interactions between enhancers and promoters (Scacheri and Scacheri, 2015). It is conceivable that previously unappreciated mutations occurring in gene deserts but associated with disease could be functioning in a similar way to disrupt chromatin organization.…”

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

“…Techniques to understand regulatory networks, including small RNAs, transcription factor cascades (e.g., ChIP-Seq, enhancer mapping), epigenetic marks, and chromatin structure (e.g., histone mapping, chromatin conformation capture, topological domain mapping), rely on a comprehensive understanding of the identity and position of both coding and noncoding DNA sequences (154)(155)(156). The perturbation of regulatory networks represents a particularly powerful way to invoke evolutionary change without the need to evolve novel genes (45).…”