Biology subjects

Fraser, H. B.

Publications and source records attributed to Fraser, H. B..

At least 19 recordsLinked to original sources

bioRxiv2026

A human transcriptomic deletion links cortical expansion and cancer

Alternative splicing represents a major source of potential evolutionary novelty in protein sequence. Despite this, relatively few studies have investigated the functional impacts of human-specific alternative splicing. Here, we analyze RNA-sequencing data from nine iPSC-derived cell types and identify dozens of human transcriptomic conserved deletions (htCONDELs): evolutionary divergence in splicing that leads to the partial or full removal of conserved protein-coding sequence from the human transcriptome. We investigated one example in detail: an htCONDEL in the gene HMMR, which encodes a centrosomal protein that binds microtubules and regulates mitosis. We found that this htCONDEL, which produces a human-specific isoform lacking a conserved microtubule-binding domain, enables cells to flexibly divide with a broader range of mitotic spindle orientations in vitro. Introducing the human HMMR isoform into mice similarly alters the orientation of cell division in the developing neocortex and increases the production of outer radial glia-like cells, the expansion of which played an essential role in increasing human brain size. Combined with previous work implicating the same HMMR isoform in carcinoma progression, our results suggest that evolution of HMMR splicing in humans increased plasticity in cell division, potentially leading to tradeoffs between advantageous effects on brain development and deleterious effects on cancer risk later in life.

evolutionary biology↗

bioRxiv2026

Adaptive loss of function accelerated the evolution of ancient and modern human cognition

Methods to detect accelerated evolution have identified many genomic regions with unexpectedly rapid evolution in the human lineage-significantly more than in chimpanzees, our closest living relatives. However, these methods focus on accelerated sequence evolution of short non-coding regions, leaving open the questions of how to identify accelerated evolution of molecular function, as opposed to sequence, and whether accelerated evolution has shaped the human genome more broadly. Here, we introduce a new approach to detect accelerated evolution: Function Aware Statistical Test for Evolutionary Rates (FASTER). In contrast to previous methods, FASTER can detect not only accelerated evolution of sequence, but also of predicted function, and can be applied to any set of genomic regions. Applying this method to humans and chimpanzees, we identified protein-coding, untranslated (UTR), and non-coding regions with accelerated evolution of function. Across all these genomic levels, we consistently found more rapid evolution in conserved sites in the human lineage compared to chimpanzee, many of which are predicted to reduce protein stability or chromatin accessibility. Multiple lines of evidence suggest this human-acceleration was driven in part by positive selection on brain development and cognition which has continued to shape human evolution even in the past several thousand years. Collectively, these results demonstrate the power of genome-wide scans for the evolution of predicted function and specifically suggest that a higher rate of reduction in function-including widespread decreases in cis-regulatory activity-may have been an important driver of both ancient and recent human evolution.

genomics↗

bioRxiv2025

A framework to detect positive selection using variant effect predictions reveals widespread adaptive evolution of human neurons

Detecting positive selection is essential to understanding evolution. Many methods to detect positive selection use simple classifications of genetic variants (e.g. synonymous/nonsynonymous). Here, we propose that these methods can be considered special cases of a more general framework to detect positive selection with any variant effect prediction method. Using evolutionary conservation and deep learning-based variant effect predictions, we apply this framework genome-wide in the human lineage and identify positive selection on protein sequences of genes involved in brain and heart development, chromatin accessibility in binding sites of dozens of transcription factors, and non-coding substitutions in compact genomic regions with reinforcing cell type-specific effects on cis-regulatory activity. Consistently, the dominant theme was positive selection on genes regulating neuronal connectivity, suggesting that fine-scale changes in brain wiring were essential to the evolution of human cognition. Overall, this framework represents a powerful, versatile tool to investigate adaptive evolution across the tree of life.

genomics↗

bioRxiv2024

Massively parallel experimental interrogation of natural variants in ancient signaling pathways reveals both purifying selection and local adaptation

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and nearly neutral theories or whether they can commonly have large functional and fitness effects as proposed by the balance theory. We address this question by mapping the fitness effects of over 9,000 natural variants in the Ras/PKA and TOR/Sch9 pathways--key regulators of cell proliferation in eukaryotes--across four conditions in Saccharomyces cerevisiae. While most variants are neutral in our assay, [~]3,500 exhibited significant fitness effects. These non-neutral variants tend to be missense and to affect conserved, more densely packed, and less solvent-exposed protein regions. While some of these non-neutral variants are younger and rarer, and more often found in heterozygous states--consistent with purifying selection--a substantial fraction is present at high frequencies in the population, which is expected under balancing selection. Indeed, we find that variants with a positive fitness effect in our laboratory measurement show strong signs of local adaptation as they tend to be found specifically in domesticated strains isolated from human-made environments. Our findings support the view that while many common variants might be effectively neutral, a significant proportion have locally adaptive functional consequences and are driven into a subset of the population by local positive selection. This study highlights the potential to combine high-throughput precision genome editing with fitness measurements to explore natural genetic variation on a pathway-wide scale, thereby bridging the gap between population genetics and functional genomics to understand the nature of evolutionary forces in the wild.

evolutionary biology↗

bioRxiv2024

A general principle governing neuronal evolution reveals a human-accelerated neuron type potentially underlying the high prevalence of autism in humans

The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons--layer 2/3 intratelencephalic excitatory neurons--has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In sum, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.

neuroscience↗

bioRxiv2023

Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells

Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells--the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell type-specific cis-regulatory changes. We find that cell type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.

evolutionary biology↗

bioRxiv2022

Chromatin activity identifies differential gene regulation across human ancestries

Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. To address this, we devised an approach to search for lineage-specific selection on chromatin activity, transcription factor binding, and chromosomal looping--critical steps in transcriptional regulation. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, we find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, we show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. Overall, our study indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This work provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species.

genomics↗

bioRxiv2022

Evolution of spatial and temporal cis-regulatory divergence between marine and freshwater sticklebacks

Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are enriched in genomic regions associated with marine-freshwater divergence, supporting an important role for cis-regulatory differences in adaptive evolution of sticklebacks. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes and supports a fundamental role for cis-regulatory changes in rapid adaptation to new environments.

evolutionary biology↗

bioRxiv2022

Allele-specific expression reveals genetic drivers of tissue regeneration in mice

In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, "super-healer" MRL mice have the unusual ability to regenerate ear punch wounds, yet the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we use allele-specific gene expression to identify cis-regulatory variation associated with ear regeneration. Analyzing three major wound cell populations, we identified extensive strain- and tissue- specific cis-regulatory divergence associated with differences in healing outcomes. Genes with cis-regulatory differences specifically in fibroblasts were associated with wound healing phenotypes and pathways, and were enriched near genetic markers associated with ear-healing in a genetic cross. Finally, we demonstrated that one of these genes, Cfh, could be applied ectopically to accelerate wound repair and induce regeneration in typically fibrotic wounds. Overall, our results provide insight into the molecular drivers of regeneration in MRL mice with potential clinical implications.

genomics↗

bioRxiv2022

Gene-by-environment interactions are pervasive among natural genetic variants

Gene-by-Environment (GxE) interactions are fundamental to understanding fitness landscapes and evolution, but have been difficult to identify at the single-nucleotide level, precluding understanding of their prevalence and molecular mechanisms. Most examples involving natural genetic variants exist at the level of entire genomes, e.g. measurement of microbial strain growth across environments, or loci encompassing many variants identified by quantitative trait loci mapping. Here, we introduce CRISPEY- BAR, a high-throughput precision-editing strategy, and use it to map base-pair resolution GxE interactions impacting yeast growth under stress conditions. First, we used CRISPEY-BAR to uncover 338 variants with fitness effects within QTLs previously mapped in different environments. We then measured 1432 ergosterol pathway variants from diverse lineages across six environments, identifying 205 natural variants affecting fitness measured in all six conditions, of which 93.7% showed GxE interactions. Finally, we examine pleiotropic cis-regulatory variants suggesting molecular mechanisms of GxE interaction. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions, while also demonstrating high- throughput genome editing as an effective means for investigating this complexity.

genomics↗

bioRxiv2022

Widespread epistasis among beneficial genetic variants revealed by high-throughput genome editing

Genetic interactions occur when a variants phenotypic effect is altered by variation at other genomic loci. Also known as epistasis, these interactions shape the genetic architecture of complex traits and modify phenotypes across genetic backgrounds. However, the factors associated with their occurrence remain poorly understood. To investigate this, we employed high-throughput genome editing to measure the fitness effects of 1,826 naturally polymorphic variants in four genetically diverse strains of Saccharomyces cerevisiae. About 31% of variants affect fitness in a common laboratory environment, of which 24% have strain-specific fitness effects indicative of epistasis. We found that beneficial variants are more likely to exhibit genetic interactions, and that genetic interactions are depleted among variants at higher allele frequencies. In addition, we demonstrate that these epistatic interactions for fitness can be mediated by specific traits such as flocculation ability. This work suggests that adaptive evolution from standing variation will often involve trade-offs where a variant is only beneficial in some genetic backgrounds, potentially explaining why many beneficial variants remain polymorphic. In sum, we provide a framework to understand the factors influencing epistasis in natural genetic variants with single-nucleotide resolution, revealing widespread epistasis among beneficial variants.

genomics↗

bioRxiv2022

Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits

Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis-regulatory changes underlying adaptation. However, it remains difficult to identify genes most likely to explain species-specific traits. Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that have constrained cis- regulation within species yet show divergence between species. Applying this strategy to data from human-chimpanzee hybrid cortical spheroids, we identify signatures of lineage-specific selection on genes related to cellular proliferation, speech, and glucose metabolism. We also highlight cis-regulatory divergence in CUX1 and EDNRB that may shape the unique trajectory of human brain development.

evolutionary biology↗

bioRxiv2021

Transcriptome diversity is a systematic source of bias in RNA-sequencing data

BackgroundRNA sequencing has been widely used as an essential tool to probe gene expression. While standard practices have been established to analyze RNA-seq data, it is still challenging to detect and remove artifactual signals. Several factors such as sex, age, and sequencing technology have been found to bias these estimates. Probabilistic estimation of expression residuals (PEER) has been used to account for some systematic effects, but it has remained challenging to interpret these PEER factors. ResultsHere we show that transcriptome diversity - a simple metric based on Shannon entropy - explains a large portion of variability in gene expression, and is a major factor detected by PEER. We then show that transcriptome diversity has significant associations with multiple technical and biological variables across diverse organisms and datasets. This prevalent confounding factor provides a simple explanation for a major source of systematic biases in gene expression estimates. ConclusionsOur results show that transcriptome diversity is a metric that captures a systematic bias in RNA-seq and is the strongest known factor encoded in PEER covariates.

genomics↗

bioRxiv2021

Bacterial retrons enable precise gene editing in human cells

Retrons are bacterial genetic elements involved in anti-phage defense. They have the unique ability to reverse transcribe RNA into multicopy single-stranded DNA (msDNA) that remains covalently linked to their template RNA. Retrons coupled with CRISPR-Cas9 in yeast have been shown to improve editing efficiency of precise genome editing via homology-directed repair (HDR). HDR editing efficiency has been limited by challenges associated with delivering extracellular donor DNA encoding the desired mutation. In this study, we tested the ability of retrons to produce msDNA as donor DNA and facilitate HDR by tethering msDNA to guide RNA in HEK293T and K562 cells. Through heterologous reconstitution of retrons from multiple bacterial species with the CRISPR-Cas9 system, we demonstrated HDR rates of up to 11.3%. Overall, our findings represent the first step in extending retron-based precise gene editing to human cells.

bioengineering↗

bioRxiv2020

The cis-regulatory effects of modern human-specific variants

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.

evolutionary biology↗

bioRxiv2020

Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci

BackgroundTo investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we have created a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells (HCASMC). ResultsTo this end, we have used a pooling approach with HCASMC lines to map regulatory variation that mediates binding of the CAD associated transcription factor TCF21 with ChIPseq studies (bQTLs), variation that regulates chromatin accessibility with ATACseq studies (caQTLs), and chromosomal looping with HiC methods (clQTLs). We show significant overlap of the QTLs, and their relationship to smooth muscle specific genes and the binding of smooth muscle transcription factors. Further, we use multiple analyses to show that these QTLs are highly associated with CAD GWAS loci and correlated to lead SNPs in these loci where they show allelic effects. We have verified with genome editing that identified functional variants can regulate both chromatin accessibility and chromosomal looping, providing new insights into functional mechanisms regulating chromatin state and chromosomal structure. Finally, we directly link the disease associated TGF{beta}1-SMAD3 pathway to the CAD associated FN1 gene through a response QTL that modulates both chromatin accessibility and chromosomal looping. ConclusionsTogether, these studies represent the most thorough mapping of multiple QTL types in a highly disease relevant primary cultured cell type, and provide novel insights into their functional overlap and mechanisms that underlie these genomic features and their relationship to disease risk.

genomics↗

bioRxiv2019

The somatic mutation landscape of the human body

Somatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet remain largely uncharacterized. To gain a better understanding of their distribution and functional impacts, we leveraged the genomic information contained in the transcriptome to uniformly call somatic mutations from over 7,500 tissue samples, representing 36 distinct tissues. This catalog, containing over 280,000 mutations, revealed a wide diversity of tissuespecific mutation profiles associated with gene expression levels and chromatin states. We found pervasive negative selection acting on missense and nonsense mutations, except for mutations previously observed in cancer samples, which were under positive selection and were highly enriched in many healthy tissues. These findings reveal fundamental patterns of tissue-specific somatic evolution and shed light on aging and the earliest stages of tumorigenesis.

genomics↗

bioRxiv2018

Fine-mapping cis-regulatory variants in diverse human populations

Genome-wide association studies (GWAS) are a powerful approach for connecting genotype to phenotype. Most GWAS hits are located in cis-regulatory regions, but the underlying causal variants and their molecular mechanisms remain unknown. To better understand human cis-regulatory variation, we mapped quantitative trait loci for chromatin accessibility (caQTLs)--a key step in cis-regulation--in 1000 individuals from 10 diverse populations. Most caQTLs were shared across populations, allowing us to leverage the genetic diversity to fine-map candidate causal regulatory variants, several thousand of which have been previously implicated in GWAS. In addition, many caQTLs that affect the expression of distal genes also alter the landscape of long-range chromosomal interactions, suggesting a mechanism for long-range expression QTLs. In sum, our results show that molecular QTL mapping integrated across diverse populations provides a high-resolution view of how worldwide human genetic variation affects chromatin accessibility, gene expression, and phenotype.

molecular biology↗