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

Jagoda, Evelyn; Xue, James R.; Reilly, Steven K.; Dannemann, Michael; Racimo, Fernando; Huerta‐Sánchez, Emilia; Sankararaman, Sriram; Kelso, Janet; Pagani, Luca; Sabeti, Pardis C.; Capellini, Terence D.

doi:10.1093/molbev/msab304

Cited by 30 publications

(21 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These include prediction models to impute unobserved differences in gene expression and 3D genome organization (43, 44); CRISPR-Cas9 editing of archaic alleles into human-derived stem cells (45, 46); and massively parallel reporter assays (MPRAs) to identify causal variants with cis-regulatory impacts on transcription (47–49). In particular, MPRAs have been applied to study modernspecific and adaptively introgressed variants (50–53). Most of these studies focused on transcriptional regulation even though post-transcriptional processes, such as RNA splicing regulation, are also important to human phenotypes and disease (54–57).…”

Section: Introductionmentioning

confidence: 99%

Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans

Rong

Christopher

Maguire

et al. 2022

Preprint

View full text Add to dashboard Cite

Humans co-existed and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,224 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 969 exonic splicing mutations (ESMs) that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than in Neanderthals. Adaptively introgressed variants were enriched for moderate effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a novel tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a novel Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide novel insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.

show abstract

Section: Introductionmentioning

confidence: 99%

Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans

Rong

Christopher

Maguire

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Although we are able to detect tissue- and allele-specific effects, there are still limitations in WhAMPRA’s in vivo technology. In contrast to the hundreds of enhancers we profile, current cell culture reporter assays can provide quantitative, cell line-specific information across thousands of enhancers 17,27,53 . Efficient transduction of tissue is likely the current limitation in the technology.…”

Section: Discussionmentioning

confidence: 99%

“…The ability to effectively deliver plasmid libraries of hundreds-to-thousands of candidate enhancers to cultured cells has allowed for detailed, quantitative descriptions of how subtle differences in genome sequence relate to differences in cell type-specific gene regulation. Studies have used reporter assay techniques to measure the effects of single nucleotide polymorphisms (SNPs) identified from expression quantitative trait loci studies (eQTLs) 19,20 , SNPs from genome-wide association studies (GWAS) [24][25][26] , and human lineage-specific mutations 27,28 . High-throughput reporter assays have also been adapted to study gene regulation in cultured neurons 18,29 .…”

Section: Main Textmentioning

confidence: 99%

Anin vivomassively parallel platform for deciphering tissue-specific regulatory function

Brown

Fox

Kaplow

et al. 2022

Preprint

View full text Add to dashboard Cite

Genetic studies are rapidly identifying non-protein-coding human disease-associated loci. Understanding the regulatory mechanisms underlying these loci remains a challenge because the causal variants and the tissues in which they act are often unclear. Massively parallel reporter assays (MPRAs) have the potential to link differences in genome sequence, including genetic variants, to tissue-specific regulatory function. Although MPRA and similar technologies have been widely adopted in cell culture, there have been several barriers to widespread use in animals. We overcome these challenges with a new whole-animal MPRA (WhAMPRA), where systemic intravenous AAV effectively transduces the plasmid MPRA library to mouse tissues. Our WhAMPRA approach revealed models of tissue-specific regulation that generally match machine learning model predictions. In addition, we measured the regulatory effects of disrupting MEF2C transcription factor binding sites and impacts of late onset Alzheimers disease-associated genetic variations. Overall, our WhAMPRA technology simultaneously determines the transcriptional functions of hundreds of enhancers in vivo across multiple tissues.

show abstract

“…Second, the eQTLGen trans-eQTL screen includes a link between two aSNPs in the STAT2 region and IFI16, a predicted target of STAT2 , adding an empirical example that is consistent with the TF target gene prediction for this TF. Third, a recent study that experimentally tested aSNPs for their regulatory potential to modulate gene expression identified aSNPs with such a potential and using CRISPR technologies demonstrated that three of the detected variants modified the expression of STAT2 in an immune cell line (Table S12, (Jagoda et al, 2021)).…”

Section: Discussionmentioning

confidence: 99%

Long-range regulatory effects of Neandertal DNA in modern humans

Yermakovich

Pankratov

Võsa

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The admixture between modern humans and Neandertals has resulted in ~2% of the genomes of present-day non-Africans still being composed of Neandertal DNA. Association studies have shown that introgressed DNA still significantly influences skin and hair traits, immunity and behavioral phenotypes in people today. Several of the phenotype-associated archaic variants had links to regulatory effects as well. In general, analyses of allele-specific expression, regulatory sequence composition and cis-eQTL have demonstrated a significant contribution of this introgressed DNA to the transcriptomic landscape in people today. However, little is known about the impact of Neandertal DNA on trans-eQTLs - long-range regulatory effects that have been shown to explain ~20% of expression variation. Here, we used blood eQTL results from >30,000 individuals from eQTLGen Consortium. The cohort size allowed for a robust identification of trans-eQTLs and in addition enabled quantifying the role of transcription factors (TF) in mediating long-range regulatory effects. In our study we used this information to (i) annotate trans-eQTLs that are linked to Neandertal variants and (ii) predict long-range regulatory effects that are induced by Neandertal DNA by screening for the predicted target genes of TFs that are cis-eQTLs linked to Neandertal variants. We show that both trans-eQTL-associated Neandertal variants and those predicted to have long-range regulatory effects affect genes in genomic regions devoid of Neandertal DNA. In addition, both types of variants included candidates for local adaptation and show associations with autoimmune disorders, a severe Covid-19 phenotype, blood cell type composition and anthropometric measures. Our results suggest that the regulatory reach of Neandertal DNA goes beyond the 40% of genomic sequence that it still covers in present-day non-Africans and that via this mechanism Neandertal DNA additionally influences the phenotypic variation in people today.

show abstract

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

Cited by 30 publications

References 86 publications

Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans

Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans

Anin vivomassively parallel platform for deciphering tissue-specific regulatory function

Long-range regulatory effects of Neandertal DNA in modern humans

Contact Info

Product

Resources

About