The cis-regulatory effects of modern human-specific variants

Abstract

The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.

Multiple Causal Variants Underlie Genetic Associations in Humans

“…They have been used to screen potential regulatory elements in diverse cellular contexts, as well as for saturation mutagenesis or tiling along individual regulatory regions of interest (9)(10)(11)(12)(13). Beyond regulatory function, MPRAs have also been increasingly applied to assay the differential effects of allelic sequence pairs representing natural human variation, focused on variants that are human-specific or are lead variants of signals in GWAS or expression quantitative trait loci (eQTL) (14)(15)(16). However, despite increases in throughput no prior work has systematically dissected linked haplotype blocks in humans to assess the distribution of causal alleles; previous studies either targeted only variants with the strongest associative p-values with respect to particular phenotypes and/or applied extensive prior filtering to reduce library size for sensitive cell types (14,15,17,18).…”

Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells

“…Our work here is the first MPRA study to specifically investigate archaically introgressed alleles and we hope that the contribution of this data set to this growing list of emVars in human populations aids in future evolutionary studies. Notably, we find that a smaller percentage of the variants within active elements are emVars in our introgressed set (11.5%) compared with 30% of variants in active elements from human-accelerated regions (HARs) and human gain enhancers (HGEs) ( Uebbing et al 2021 ), and 30% and 25% of human fixed differences tested in osteoblasts and neural progenitor cells, respectively ( Weiss et al 2021 ). However, in this latter study the authors did identify only 9% emVars in embryonic stem cells.…”

“…We detected 8.2% of emVars had an absolute expression modulation LFC greater than 2. In comparison, Weiss et al (2021) detected 0–1.8% of fixed difference alleles had this strong of effect, whereas Tewhey et al (2016) found 5.5% of tested eQTLs and Uebbing et al found 16.8% of alleles in HARs and HGEs had this at least this strong of an effect. Whether this is due to the nature of positively selected introgressed alleles perhaps being selected for relatively strong effects relative to other types of variants, should be explored.…”

“…MPRA experiments are becoming a new tool in the effort to use genetics to understand evolutionary questions. For example, MPRAs have been conducted looking at the effects of fixed differences between humans and Neanderthals/Denisovans ( Weiss et al 2021 ) as well as regions of the human genome that have been largely diverged since the split from chimpanzees ( Uebbing et al 2021 ). These studies have produced rich data sets for additional research and have produced interesting findings, such as the finding that variants that are fixed between humans and Neanderthals/Denisovans are enriched for functionality in the vocal tract ( Weiss et al 2021 ).…”

“…For example, MPRAs have been conducted looking at the effects of fixed differences between humans and Neanderthals/Denisovans ( Weiss et al 2021 ) as well as regions of the human genome that have been largely diverged since the split from chimpanzees ( Uebbing et al 2021 ). These studies have produced rich data sets for additional research and have produced interesting findings, such as the finding that variants that are fixed between humans and Neanderthals/Denisovans are enriched for functionality in the vocal tract ( Weiss et al 2021 ). Our work here is the first MPRA study to specifically investigate archaically introgressed alleles and we hope that the contribution of this data set to this growing list of emVars in human populations aids in future evolutionary studies.…”