Loss-of-function tolerance of enhancers in the human genome

Abstract

Previous studies have surveyed the potential impact of loss-of-function (LoF) variants and identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to losing enhancers has not yet been evaluated. Here we present the catalog of LoF-tolerant enhancers using structural variants from whole-genome sequences. Using a conservative approach, we estimate that individual human genomes possess at least 28 LoF-tolerant enhancers on average. We assessed the properties of LoF-tolerant enhancers in a unified regulatory network constructed by integrating tissue-specific enhancers and gene-gene interactions. We find that LoF-tolerant enhancers tend to be more tissue-specific and regulate fewer and more dispensable genes relative to other enhancers. They are enriched in immune-related cells while enhancers with low LoF-tolerance are enriched in kidney and brain/neuronal stem cells. We developed a supervised learning approach to predict the LoFtolerance of all enhancers, which achieved an area under the receiver operating characteristics curve (AUROC) of 98%. We predict 3,519 more enhancers would be likely tolerant to LoF and 129 enhancers that would have low LoF-tolerance. Our predictions are supported by a known set of disease enhancers and novel deletions from PacBio sequencing. The LoF-tolerance scores provided here will serve as an important reference for disease studies. Author summaryEnhancers are elements where transcription factors bind and regulate the expression of protein-coding genes. Although multiple previous studies have focused on which genes can tolerate loss-of-function (LoF), none has systematically evaluated the tolerance of all enhancers in the human genome to LoF. Individual studies have shown a broad range of phenotypic effects of enhancer LoF. The phenotypic effects of enhancer LoF likely fall into a spectrum where deletion of LoF-tolerant enhancers would not elicit substantial phenotypic impact, while some enhancers are likely to cause fitness defects when deleted. Here PLOS GENETICSPLOS Genetics | https://doi.

Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation

“…Fourth, most studies of LoF mutations have focused on variations in coding regions; however, a mutation in the promoter or UTR could also affect gene expression ( Yang et al., 2018 ; Niu et al., 2019 ; Xu et al., 2020 ). Synthetic biology can offer interesting insights into the beneficial effects of regulator loss.…”

Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance

“…When we plotted the median pLI of genes linked to DAEs, or to nDAEs, genes linked to DAEs scored significantly higher (Figure 2F). Finally, a recent study determined loss-of-function tolerance scores for non-coding sequences, by using machine learning and structural variants from whole genome sequencing, including homozygous enhancer deletions [50]. Using this analysis, we observed that DAEs were more likely to be intolerant to loss-of-function, whereas nDAEs were more often tolerant to loss-of-function (Figure 2G).…”

“…To determine whether different DNA sequence features distinguish different enhancer groups and whether there is any association between these features and functional prediction, we considered the following features: (i) the non-coding essential regulation (ncER) score (https://github.com/TelentiLab/ncER_datasets/; updated 06-03-2019) [43]; (ii) GC content, as determined by the GCcontent R packages based on BSgenome.Hsapiens.UCSC.hg19 (version 1.4.3); (iii) conservation score for each enhancer, as derived from the gscores R packages based on phastCons100way.UCSC.hg19 (version 3.7.2) [44]; (iv) Orion scores [47]; (v) CADD scores [48]; (vi) Haploinsufficiency scores [50] and (vii) probability of loss-of-function intolerance (pLI) score [49]. The overlaps between DNA sequence features and enhancer coordinates were defined using intersectBed.…”

The Nestin neural enhancer is essential for normal levels of endogenous Nestin in neuroprogenitors but is not required for embryo development

“…A study of single conserved limb enhancers showed that 90% of these had no impact on cognate gene expression (21), as well as highly conserved ß-globin enhancers (22). Computational analyses have predicted that most (96%) of enhancers within the genome are tolerant to LoF mutations, and that many essential genes will have a degree of enhancer redundancy (23). In the vast majority of examples, deletion of a single conserved enhancer element has no impact on cognate gene expression (21, 22).…”