Massively parallel discovery of human-specific substitutions that alter enhancer activity

Uebbing, Severin; Gockley, Jake; Reilly, Steven K.; Kocher, Acadia A.; Geller, Evan; Gandotra, Neeru; Scharfe, Curt; Cotney, Justin; Noonan, James P.

doi:10.1073/pnas.2007049118

Cited by 83 publications

(109 citation statements)

References 48 publications

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“…In line with the fact that our data was not pre-filtered for putative regulatory regions, the proportion of active sequences we observed tends to be slightly lower than these previous studies. However, the magnitude of differential activity, as well as the fraction of differentially active sequences out of the active sequences was similar to previous studies 16, 28–31, 84–86 . At the same time, we were capable of measuring regulatory activity in regions that would otherwise be excluded by filtering for a specific set of marks.…”

Section: Discussionsupporting

confidence: 89%

“…With the exception of highly repetitive regions, which were removed from our library for technical reasons, the sequences we selected included all known modern human-derived fixed or nearly fixed variants (see Methods). Conversely, previous reporter assays and MPRAs on human intra- or inter-species variation used biased sets of variants by selecting sequences with putative regulatory function (e.g., eQTLs 28 , TF binding sites 16 , ChIP-seq peaks 29 , or TSSs 84 ) and/or regions showing particularly rapid evolution (e.g., human accelerated regions 30, 31, 85, 86 ). In line with the fact that our data was not pre-filtered for putative regulatory regions, the proportion of active sequences we observed tends to be slightly lower than these previous studies.…”

Section: Discussionmentioning

confidence: 99%

“…By cloning a candidate regulatory sequence downstream to a short transcribable sequence-based barcode, thousands of sequences and variants can be tested for regulatory activity in parallel. Thus, MPRA is an effective high-throughput tool to identify variants underlying divergent regulation, especially in organisms where experimental options are limited 28–31 . Here, we conducted a lentivirus-based MPRA (lentiMPRA 32 ) on the 14,042 fixed or nearly fixed single-nucleotide variants that emerged along the modern human lineage.…”

Section: Introductionmentioning

confidence: 99%

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Thecis-regulatory effects of modern human-specific variants

Weiss

Harshman

Inoue

et al. 2020

Preprint

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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, 1,791 (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.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Thecis-regulatory effects of modern human-specific variants

Weiss

Harshman

Inoue

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Consistent with other MPRA studies 4! (Tewhey et al 2016, Ulirsch et al 2016Uebbing et al 2021), most active sequences showed 5! relatively small effects, with only 17.1% of active sequences showing a LFC greater than 2 6!…”

Section: !mentioning

confidence: 97%

Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

Jagoda

Marnetto

Montinaro

et al. 2021

Preprint

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Individuals infected with the SARS-CoV-2 virus present with a wide variety of phenotypes ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe COVID-19 phenotype. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the severe COVID-19 phenotype. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform an locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify 4 introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. These variants likely drive the locus impact on severity by putatively modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.

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“…1C and Table S2). To study the evolutionary and functional impact of non-coding regulatory elements, we interrogated molecular signatures from genes associated with regions with human-specific substitutions (20,29,30) (fig. S3E and Table S3).…”

Section: Phenotypic and Molecular Adaptations Reveal Metabolic Human Acceleration Domainsmentioning

confidence: 99%

Metabolic resilience is encoded in genome plasticity

Agudelo

Tuyéras

Llinares

et al. 2021

Preprint

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Metabolism plays a central role in evolution, as resource conservation is a selective pressure for fitness and survival. Resource-driven adaptations offer a good model to study evolutionary innovation more broadly. It remains unknown how resource-driven optimization of genome function integrates chromatin architecture with transcriptional phase transitions. Here we show that tuning of genome architecture and heterotypic transcriptional condensates mediate resilience to nutrient limitation. Network genomic integration of phenotypic, structural, and functional relationships reveals that fat tissue promotes organismal adaptations through metabolic acceleration chromatin domains and heterotypic PGC1A condensates. We find evolutionary innovation in several dimensions; low conservation of amino acid residues within protein disorder regions, nonrandom chromatin location of metabolic acceleration domains, condensate-chromatin stability through cis-regulatory archoring and encoding of genome plasticity in radial chromatin organization. We show that environmental tuning of these adaptations leads to fasting endurance, through efficient nuclear compartmentalization of lipid metabolic regions, and, locally, human-specific burst kinetics of lipid cycling genes. This process reduces oxidative stress, and fatty-acid mediated cellular acidification, enabling endurance of condensate chromatin conformations. Comparative genomics of genetic and diet perturbations reveal mammalian convergence of phenotype and structural relationships, along with loss of transcriptional control by diet-induced obesity. Further, we find that radial transcriptional organization is encoded in functional divergence of metabolic disease variant-hubs, heterotypic condensate composition, and evolutionary tuned protein residues sensing metabolic variation. During fuel restriction, these features license the formation of large heterotypic condensates that buffer proton excess, and shift viscoelasticity for condensate endurance. This mechanism maintains physiological pH, reduces pH-resilient inflammatory gene programs, and enables genome plasticity through transcriptionally driven cell-specific chromatin contacts. In vivo manipulation of this circuit promotes fasting-like adaptations with heterotypic nuclear compartments, metabolic and cell-specific homeostasis. In sum, we uncover here a general principle by which transcription uses environmental fluctuations for genome function, and demonstrate how resource conservation optimizes transcriptional self-organization through robust feedback integrators, highlighting obesity as an inhibitor of genome plasticity relevant for many diseases.

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Massively parallel discovery of human-specific substitutions that alter enhancer activity

Cited by 83 publications

References 48 publications

Thecis-regulatory effects of modern human-specific variants

Thecis-regulatory effects of modern human-specific variants

Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

Metabolic resilience is encoded in genome plasticity

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