Biology subjects

Ehrenreich, I. M.

Publications and source records attributed to Ehrenreich, I. M..

6 recordsLinked to original sources

bioRxiv2026

A novel reaction-diffusion architecture for engineering self-organized patterns in mammalian cells

Reaction-diffusion circuits generate self-organized spatial patterns through local activation and long-range inhibition, but synthetic implementations in mammalian cells have been limited by the differential-diffusion requirement. Here, we introduce a novel architecture, juxtacrine activation with paracrine inhibition (JAPI), where the activator propagates through cell-cell contacts rather than diffusion. We demonstrate mathematically and numerically that JAPI accesses the same patterning regimes as classical diffusion-based circuits with one fewer free parameter. We then engineer compact synNotch-based JAPI circuits in mammalian fibroblasts and demonstrate their sufficiency for self-organized patterning through tunable, size-limited signal propagation. Functionalized to spatially control morphogen secretion, these circuits perturb feather bud formation on adjacent embryonic chicken epidermis. Finally, we develop a library-based approach to explore coupled, dual-JAPI circuits with tunable cross-inhibition, enabling programmable interactions between patterns and access to a broad morphospace of spatial states. Together, JAPI provides a compact, modular platform for programming self-organized multicellular patterning. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/727552v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fae8c9org.highwire.dtl.DTLVardef@c8eddborg.highwire.dtl.DTLVardef@177d08corg.highwire.dtl.DTLVardef@11cc952_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Synthetic collinearization of a chromosome segment enables genetic dissection of incompatibility between distant genera

Reproductive barriers and genomic structural differences hinder genetic analysis between highly divergent organisms. Here, we examined whether these challenges can be overcome by collinearization, the synthesis of chromosomes that retain the native gene content and organization of a host organism while incorporating the DNA sequences of another organism. We applied collinearization to Kluyveromyces marxianus, a yeast species that is both distantly related to and has a distinct genome structure from the model yeast Saccharomyces cerevisiae. We generated a [~]35-kb K. marxianus DNA segment that was collinear with one-sixth of a S. cerevisiae chromosome and contained 17 protein-coding genes. Although this synthetic chromosome segment successfully substituted for its native counterpart in an S. cerevisiae cell, it imposed a significant growth cost due to the incompatibility of two K. marxianus proteins with the host proteome. We predicted the disrupted protein-protein interactions using AlphaFold and alleviated their cost by supplementing orthologous protein partners from K. marxianus. Furthermore, we completely eliminated the growth cost by replacing the two incompatible K. marxianus genes with their S. cerevisiae orthologs. These findings demonstrate that collinearization can facilitate the creation of chimeric genomes to dissect the genetic basis of incompatibility and traits between organisms that cannot naturally hybridize. They also suggest that hundreds of genetic incompatibilities exist between S. cerevisiae and K. marxianus, reflecting disrupted protein-protein interactions that may be predictable in silico.

synthetic biology↗

bioRxiv2025

Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness

Global epistasis is a phenomenon in which the effects of genetic perturbations depend on the fitness of the individuals in which they occur. In populations with natural genetic variation, global epistasis arises from interactions between perturbations and polymorphic loci that are mediated by fitness. To investigate the prevalence and characteristics of loci involved in these interactions in the budding yeast Saccharomyces cerevisiae, we used combinatorial DNA barcode sequencing to measure the fitness of 169 cross progeny (segregants) subjected to 8,126 CRISPRi perturbations across two environments. Global epistasis was evident in these data, with more fit segregants within each environment exhibiting greater sensitivity to genetic perturbations than less fit segregants. We dissected the genetic basis of this global epistasis by scanning the genome for loci whose effects covary with CRISPRi-induced reductions in population fitness. This approach identified 58 loci that interact with fitness, most of which exhibited larger effects in the absence of genetic perturbations. In aggregate, these loci explained the observed global epistasis in each environment and demonstrated that the loci contributing to global epistasis largely overlap with those influencing fitness in unperturbed conditions.

genetics↗

bioRxiv2020

Genetic architecture of a mutation's expressivity and penetrance

Genetic background often influences the phenotypic consequences of mutations, resulting in variable expressivity. How standing genetic variants collectively cause this phenomenon is not fully understood. Here, we comprehensively identify loci in a budding yeast cross that impact the growth of individuals carrying a spontaneous missense mutation in the nuclear-encoded mitochondrial ribosomal gene MRP20. Initial results suggested that a single large effect locus influences the mutations expressivity, with one allele causing inviability in mutants. However, further experiments revealed this simplicity was an illusion. In fact, many additional loci shape the mutations expressivity, collectively leading to a wide spectrum of mutational responses. These results exemplify how complex combinations of alleles can produce a diversity of qualitative and quantitative responses to the same mutation.

genetics↗

bioRxiv2018

Unraveling the layers of cryptic genetic variation in a yeast gene regulatory network

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic variation underlying a Saccharomyces cerevisiae colony phenotype that is typically suppressed in a cross. Mapping of the traits genetic basis after induction by three different genetic perturbations identifies 21 total loci. The perturbations largely uncover distinct loci, and strongly influence additivity, epistasis, and genotype-environment interaction among these loci. Only a single locus-- the coding region of the cell surface gene FLO11--is common to all three perturbations. While the remaining loci mostly influence FLO11 transcription in cis or trans, we detect loci in different pathways and sub-pathways in the presence of each perturbation. Our work shows that complex gene regulatory networks can harbor multiple layers of cryptic variation, each of which may only be visible in highly specific genotypic and environmental contexts.\n\nArticle SummaryThe extent and regulation of cryptic genetic variation within populations is not fully understood. To address these questions, we comprehensively dissect the genetic basis of a budding yeast colony trait following its induction by three different genetic perturbations. In total, we identify 21 distinct loci, most of which show phenotypic effects that depend on particular perturbations, other segregating loci, and temperature. We find that nearly all involved loci participate in a common gene regulatory network (GRN). Thus, our work demonstrates the large amount of cryptic variation underlying a single trait and ties the visibility of this variation to GRN activity.

genetics↗

bioRxiv2017

The stress-inducible peroxidase TSA2 enables Chromosome IV duplication to be conditionally beneficial in Saccharomyces cerevisiae

Although chromosomal duplications are often deleterious, in some cases they enhance cells abilities to tolerate specific genetic or environmental challenges. Identifying the genes that cause particular chromosomal duplications to confer these conditionally beneficial effects can improve our understanding of the genetic and molecular mechanisms that enable certain aneuploidies to persist in cell populations and contribute to disease and evolution. Here, we perform a screen for spontaneous mutations that improve the tolerance of haploid Saccharomyces cerevisiae to hydrogen peroxide. Chromosome IV duplication is the most frequent mutation, as well as the only change in chromosomal copy number, seen in the screen. Using a genetic mapping strategy that involves systematically deleting segments of a duplicated chromosome, we show that the Chromosome IV duplications effect is largely due to the generation of a second copy of the stress-inducible cytoplasmic thioredoxin peroxidase TSA2. This finding is consistent with a growing literature indicating that the conditionally beneficial effects of chromosomal duplications tend to reflect the contributions of small numbers of genes that enhance tolerance to specific stresses when their copy number is increased.\n\nArticle summaryChanges in karyotype play an important role in evolution and health. Although these aneuploidization events are usually deleterious, in some instances they show conditionally beneficial effects by enabling cells to tolerate specific mutations or environmental stresses. The mechanisms underlying these protective effects of aneuploidization are not fully understood. To provide insights into this problem, we identify and characterize a conditionally beneficial chromosomal duplication that makes haploid yeast more tolerant to oxidative stress. We determine that the effect of the chromosomal duplication on oxidative stress tolerance is largely explained by duplication of a single stress-inducible gene.

genetics↗