Biology subjects

Mouri, K.

Publications and source records attributed to Mouri, K..

5 recordsLinked to original sources

bioRxiv2024

Functional dissection of complex and molecular trait variants at single nucleotide resolution

Identifying the causal variants and mechanisms that drive complex traits and diseases remains a core problem in human genetics. The majority of these variants have individually weak effects and lie in non-coding gene-regulatory elements where we lack a complete understanding of how single nucleotide alterations modulate transcriptional processes to affect human phenotypes. To address this, we measured the activity of 221,412 trait-associated variants that had been statistically fine-mapped using a Massively Parallel Reporter Assay (MPRA) in 5 diverse cell-types. We show that MPRA is able to discriminate between likely causal variants and controls, identifying 12,025 regulatory variants with high precision. Although the effects of these variants largely agree with orthogonal measures of function, only 69% can plausibly be explained by the disruption of a known transcription factor (TF) binding motif. We dissect the mechanisms of 136 variants using saturation mutagenesis and assign impacted TFs for 91% of variants without a clear canonical mechanism. Finally, we provide evidence that epistasis is prevalent for variants in close proximity and identify multiple functional variants on the same haplotype at a small, but important, subset of trait-associated loci. Overall, our study provides a systematic functional characterization of likely causal common variants underlying complex and molecular human traits, enabling new insights into the regulatory grammar underlying disease risk.

genetics↗

bioRxiv2023

Machine-guided design of synthetic cell type-specific cis-regulatory elements

Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.

synthetic biology↗

bioRxiv2022

Do males know? Evidence-driven rainmaking of male bonobos to meet fertile phase of females

In most mammals, female sexual receptivity (estrus) closely coincides with ovulation, providing males with precise fertility signals. However, in some anthropoid primates living in multi-male societies, females display extended receptivity along with exaggerated sexual swellings that probabilistically indicate ovulation. This raises the question about how males successfully time mating, particularly when ovulation is difficult to predict from such cues as seen in bonobos. To address this question, we combined daily variation in swelling size, hormonal profiles, and male mating behaviors. By estimating day-specific ovulation probabilities relative to the onset of the maximal swelling phase and detumescence, we also examined how male efforts correlate with female fertility. Our results revealed that while ovulation probability was widely distributed and difficult to predict when aligned with the onset of the swelling phase, male behavior was closely aligned with the conception probability. Males concentrated mating efforts late in the phase and stopped after detumescence. High-ranking males intervened in copulations involving females with higher conception probabilities, specifically those with maximal swelling and older infants. When multiple females exhibited maximal swelling, males preferentially followed females whose maximal swelling started earlier and who had older infants. Male-male aggression increased when there were more females with maximal swelling. However, this tendency was reversed when male party size exceeded the average. Importantly, our results revealed that the low predictability of ovulation is best explained by inter- and intra-individual variation in the length of maximal swelling phase, rather than ovulation occurring randomly within that phase in bonobos. Males effectively manage such a noisy signal by prioritizing late-phase ovulatory cues and integrating reproductive history, thereby extracting usable timing information. This behavioral mechanism helps explain the persistence of conspicuous yet noisy ovulatory signals in bonobos. Since males are capable of inferring ovulation timing even under noisy conditions, selection may not favor highly precise female signals. Instead, it shifts more of the time and energy costs onto males, allowing conspicuous female traits to be maintained.

animal behavior and cognition↗

bioRxiv2022

Whole genome functional characterization of RE1 silencers using a modified massively parallel reporter assay

Both upregulation and downregulation by cis-regulatory elements help establish precise gene expression. Our understanding of how elements repress transcriptional activity is far more limited than activating elements. To address this gap, we characterized RE1, a group of transcriptional silencers bound by REST, on a genome-wide scale using an modified massively parallel reporter assay (MPRAduo). MPRAduo empirically defined a minimal binding strength of REST required for silencing (REST m-value), above which multiple cofactors colocalize and act to directly silence transcription. We identified 1,500 human variants that alter RE1 silencing and found their effect sizes are predictable when they overlap with REST binding sites above the m-value. In addition, we demonstrate that non-canonical REST binding motifs exhibit silencer function only if they precisely align two half sites with specific spacer length. Our results show mechanistic insights into RE1 silencer which allows us to predict its activity and effect of variants on RE1, providing a paradigm for performing genome-wide functional characterization of transcription factors binding sites.

genomics↗

bioRxiv2021

Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells

Genome-wide association studies have uncovered hundreds of autoimmune disease-associated loci; however, the causal genetic variant(s) within each locus are mostly unknown. Here, we perform high-throughput allele-specific reporter assays to prioritize disease-associated variants for five autoimmune diseases. By examining variants that both promote allele-specific reporter expression and are located in accessible chromatin, we identify 60 putatively causal variants that enrich for statistically fine-mapped variants by up to 57.8-fold. We introduced the risk allele of a prioritized variant (rs72928038) into a human T cell line and deleted the orthologous sequence in mice, both resulting in reduced BACH2 expression. Naive CD8 T cells from mice containing the deletion had reduced expression of genes that suppress activation and maintain stemness. Our results represent an example of an effective approach for prioritizing variants and studying their physiologically relevant effects.

genetics↗