Biology subjects

Morrison, A. J.

Publications and source records attributed to Morrison, A. J..

14 recordsLinked to original sources

bioRxiv2026

The Prion-Like Properties of the INO80 Chromatin Remodeler Regulate Metabolic Gene Expression

The INO80 chromatin-remodeling complex is a multi-subunit regulator of DNA-templated processes, yet the mechanisms that control remodeler function in vivo are not completely known. In this study, we report that the Ies6 subunit of the INO80 complex encodes a prion-like domain (PLD) within a larger region of predicted disorder. After transient inducible overexpression, both full-length Ies6 and the PLD domain alone aggregate in a manner that evades proteasome-mediated degradation, suggestive of prion-like behavior. Cytosolic aggregates are also visible with fluorescent microscopy following expression of the PLD alone. Loss of the protein chaperone Hsp70 increases Ies6 aggregation. In addition, deletion of ARP5, another INO80 subunit and binding partner of Ies6, also results in elevated protein aggregation. Finally, transcriptome analysis indicates that loss of PLD-mediated aggregation alters the expression of telomere-proximal and metabolic stress-responsive genes, including those involved in glucose starvation and respiratory programs, even under glucose-replete conditions. Together, these findings support a model in which Ies6 couples the INO80 complex to metabolic gene regulation via prion-like behavior, providing a potential new mechanism for tuning chromatin-based metabolic adaptation.

molecular biology↗

bioRxiv2026

Acetyl-CoA Synthetase 1 Regulates Global Histone Propionylation and Metabolic Stress Responses

Cells and organisms are often exposed to various metabolic environments that require adaptive responses for survival. One common way cells adapt to fluctuating nutrient environments is through regulated transcription of metabolic genes. Intermediary metabolites, such as acetyl-CoA, produced by metabolic pathways, serve as cofactors for histone post-translational modifications, which in turn regulate gene expression. However, increasing evidence shows that non-acetyl acyl-CoAs, such as propionyl-CoA, participate in gene regulation during metabolic stress. In this report, we find that histone propionylation functions as a global response to glucose starvation. Furthermore, we find that Acetyl-CoA Synthetase 1 (Acs1) binds chromatin and is the primary enzyme responsible for generating propionyl-CoA in the nucleus. Together, our findings reveal that Acs1-mediated histone propionylation constitutes a novel pathway for metabolic adaptation, linking nutrient availability to chromatin modification.

molecular biology↗

bioRxiv2024

p53 Regulates Nuclear Architecture to Reduce Carcinogen Sensitivity and Mutagenic Potential

The p53 tumor suppressor is an indispensable regulator of DNA damage responses that accelerates carcinogenesis when mutated. In this report, we uncover a new mechanism by which p53 maintains genomic integrity in the absence of canonical DNA damage response activation. Specifically, loss of p53 dramatically alters chromatin structure at the nuclear periphery, allowing increased transmission of an environmental carcinogen, ultraviolet (UV) radiation, into the nucleus. Genome-wide mapping of UV-induced DNA lesions in p53-deficient primary cells reveals elevated lesion abundance in regions corresponding to locations of high mutation burden in malignant melanomas. These findings uncover a novel role of p53 in the suppression of mutations that contribute to cancer and highlight the critical influence of nuclear architecture in regulating sensitivity to carcinogens. One-Sentence SummaryThe p53 tumor suppressor reduces carcinogen sensitivity and mutagenic potential by maintaining nuclear architecture.

cancer biology↗

bioRxiv2023

A pan-MHC reference graph with 246 fully contiguous phased sequences

The major histocompatibility complex (MHC) is a region of the human genome that is key to immune system function but sometimes refractory to genomic analyses due to extreme polymorphism and structural variation. We performed targeted long-read sequencing and de novo assembly of MHC to create 246 highly accurate, fully contiguous, and phased full-length sequences, mostly from data provided by the Human Pangenome Reference Consortium (HPRC). We identified alleles at high resolution across 39 loci including the class I and II HLA (human leukocyte antigen) genes, discovering 1,246 putative novel allele sequences. We identified copy number variation in the C4A and C4B genes and found significant linkage disequilibrium between C4A[~]C4B haplotypes and 14 MHC loci. We build our sequences into a novel "pan-MHC" reference graph, and we demonstrate that this improves the accuracy of short-read variant calling. Our haplotypes and graph contain significantly more population diversity than preexisting MHC sequences, thus improving the prospects for global health equity in this clinically important genomic region.

genomics↗

bioRxiv2023

Development and Validation of the Mentoring in Undergraduate Research Survey

Here we present the development and initial validation of the Mentoring in Undergraduate Research Survey (MURS) as a measure of a range of mentoring experienced by undergraduate science researchers. We drafted items based on qualitative research and refined the items through cognitive interviews and expert sorting. We used national dataset to evaluate the internal structure of the measure and a second national dataset to examine how responses on the MURS related to theoretically-relevant constructs and student characteristics. Our factor analytic results indicate seven lower order forms of mentoring experiences: abusive supervision, accessibility, career and technical support, psychosocial support, interpersonal mismatch, sexual harassment, and unfair treatment. These forms of mentoring mapped onto two higher-order factors: supportive and destructive mentoring experiences. Although most undergraduates reported experiencing supportive mentoring, some reported experiencing absence of supportive as well as destructive experiences. Undergraduates who experienced less supportive and more destructive mentoring also experienced lower scientific integration and a dampening of their beliefs about the value of research. The MURS should be useful for investigating the effects of mentoring experienced by undergraduate researchers and for testing interventions aimed at fostering supportive experiences and reducing or preventing destructive experiences and their impacts. Highlight summaryThis study presents the development and initial validation of the Mentoring in Undergraduate Research Survey, including evidence of its internal structure as well as convergent, discriminant, and predictive validity.

scientific communication and education↗

bioRxiv2022

An experimental demonstration of ensemble epistasis in the lac repressor

Epistatic, non-additive, interactions between mutations reveal the functional architecture of living systems, strongly shape evolution, and present a difficult challenge for bioengineers. Interpreting and modeling epistasis requires knowledge of the mechanisms that bring it about. We recently argued that "ensemble epistasis" could be a generic mechanism for epistasis between mutations introduced into a single macromolecule. Because proteins exist as ensembles of interconverting conformations, a mutation could induce epistasis by subtly altering ensemble composition and thus the effects of subsequent mutations. Here we show experimentally that the thermodynamic ensemble does indeed yield high magnitude epistasis in the lac repressor. We observed two- and three-way epistasis in DNA binding, with magnitudes as large or larger than the individual effects of mutations. This biophysical effect propagated to substantial epistasis in gene expression in vivo. As predicted in previous theoretical work, IPTG concentration tunes the magnitude of ensemble epistasis. Further, our observations could all be captured with a rigorous mathematical model of the lac repressor ensemble. Given that conformational ensembles are unavoidable features of macromolecules, we expect this is a ubiquitous and underappreciated cause of intramolecular epistasis.

biophysics↗

bioRxiv2022

Higher-order interactions shape microbial interactions as microbial community complexity increases

Non-pairwise interactions, or higher-order interactions (HOIs), in microbial communities have been claimed to explain the emergent features in microbiomes. Yet, the re-organization of microbial interactions between pairwise cultures and larger communities remains largely unexplored from a molecular perspective but is central to our understanding and further manipulation of microbial communities. Here, we used a bottom-up approach to investigate microbial interaction mechanisms from pairwise cultures up to 4-species communities from a simple microbiome (Hafnia alvei, Geotrichum candidum, Pencillium camemberti and Escherichia coli). Specifically, we characterized the interaction landscape for each species combination involving E. coli by identifying E. colis interaction-associated genes using an RB-TnSeq-based interaction assay. We observed a deep reorganization of the interaction-associated genes, with very few 2-species interactions conserved all the way up to a 4-species community and the emergence of multiple HOIs. We further used a quantitative genetics strategy to decipher how 2-species interactions were quantitatively conserved in higher community compositions. Epistasis-based analysis revealed that, of the interactions that are conserved at all levels of complexity, 82% follow an additive pattern. Altogether, we demonstrate the complex architecture of microbial interactions even within a simple microbiome, and provide a mechanistic and molecular explanation of HOIs.

microbiology↗

bioRxiv2021

Pharmacokinetics of long-term low-dose oral rapamycin in four healthy middle-aged companion dogs

ObjectiveTo determine the blood concentration and pharmacokinetic parameters of rapamycin in companion dogs following long-term, low-dose oral administration of rapamycin. AnimalsFour healthy, middle-aged, medium-to-large breed privately owned dogs participated. ProceduresAll dogs had been receiving oral rapamycin at a dose of 0.025 mg/kg on Monday, Wednesday, and Friday mornings for at least one month. An initial blood sample was collected prior to morning rapamycin administration, and samples were collected at 1, 2, 6, and 24 hours after rapamycin was given. Blood samples were transferred to blood spot collection cards, air-dried and stored at -80{degrees}C. Rapamycin concentrations were determined via HPLC/MS. All blood collections occurred on Wednesdays, so that the previous dose of rapamycin had taken place 48 hours prior to blood collection. ResultsFor all dogs, rapamycin Tmax was 2 hours. Median Cmax was 1.47 ng/ml (0.912 - 2.13), and the median AUC0-last was 15.7 ng*hr/mL (1.30 - 36.3). Due to sample size and timing, the only estimates related to elimination rate reported are for mean residence time with a median of 4.70 hrs (0.90 - 7.30). Conclusions and Clinical RelevanceA 0.025 mg/kg oral dose of rapamycin, administered three times a week, resulted in concentrations of rapamycin in the blood capable of being measured in ng/ml.

pharmacology and toxicology↗

bioRxiv2020

Ensemble epistasis: thermodynamic origins of non-additivity between mutations

Non-additivity between mutations--epistasis--profoundly shapes evolution. It can be difficult to understand its mechanistic origins. Here we show that "ensemble epistasis" is likely a universal feature of macromolecules. Using a simple analytical model, we found that epistasis arises when two conditions are met: 1) a macro-molecule populates at least three structures and 2) mutations have differential effects on a least two of the inactive structures. To explore the relative magnitude of ensemble epistasis, we performed a virtual deep-mutational scan of the allosteric Ca2+ signaling protein S100A4. We found that 27% of mutation pairs gave ensemble epistasis with a magnitude on the order of thermal fluctuations, 1 kT. We observed many forms of epistasis: magnitude, sign, and reciprocal sign epistasis. Depending on the effector concentration, the same mutation pair could even exhibit different forms of epistasis. The ubiquity of ensembles in biology and its pervasiveness in our dataset suggests that ensemble epistasis may be a universal mechanism of epistasis. Significance statementAddressing the mechanistic origins of evolutionary unpredictability is critical to understanding how mutations combine to determine phenotype. Here we lay the theoretical foundations and investigate the plausibility of a potentially universal mechanism of unpredictability in macromolecules. Macromolecules often adopt a set of interchanging structures, called a thermodynamic ensemble. Mutations can change the relative population of each structure, introducing unpredictability in the mapping between genotype and phenotype. The conditions under which we expect this to arise are common in macromolecules, suggesting that this form of unpredictability may be pervasive in evolution. We conclude that the thermodynamic ensemble bakes unpredictability into biology and that future attempts to address it might incorporate this mechanistic insight.

biophysics↗

bioRxiv2020

Endocardial/endothelial angiocrines regulate cardiomyocyte development and maturation and induce features of ventricular non-compaction

Non-compaction cardiomyopathy is a devastating genetic disease caused by insufficient consolidation of ventricular wall muscle that can result in inadequate cardiac performance. Despite being the third most common cardiomyopathy, the mechanisms underlying the disease, including the cell types involved, are poorly understood. We have previously shown that endothelial cell-specific deletion of the chromatin remodeler gene Ino80 results in defective coronary vessel development that leads to ventricular noncompaction in embryonic mouse hearts. Here, we used single-cell RNA-sequencing to characterize endothelial and endocardial defects in Ino80-deficient hearts. We observed a pathological endocardial cell population in the non-compacted hearts, and identified multiple dysregulated angiocrine factors that dramatically affected cardiomyocyte behavior. We identified Col15A1 as a coronary vessel-secreted angiocrine factor, downregulated by Ino80-deficiency, that functioned to promote cardiomyocyte proliferation. Furthermore, mutant endocardial and endothelial cells (ECs) upregulated expression of secreted factors, such as Tgfbi, Igfbp3, Isg15, and Adm, which decreased cardiomyocyte proliferation and increased maturation. These findings support a model where coronary ECs normally promote myocardial compaction through secreted factors, but that endocardial and ECs can secrete factors that contribute to non-compaction under pathological conditions.

developmental biology↗

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

Process-specific somatic mutation distributions vary with three-dimensional genome structure

Somatic mutations arise during the life history of a cell. Mutations occurring in cancer driver genes may ultimately lead to the development of clinically detectable disease. Nascent cancer lineages continue to acquire somatic mutations throughout the neoplastic process and during cancer evolution (Martincorena and Campbell, 2015). Extrinsic and endogenous mutagenic factors contribute to the accumulation of these somatic mutations (Zhang and Pellman, 2015). Understanding the underlying factors generating somatic mutations is crucial for developing potential preventive, therapeutic and clinical decisions. Earlier studies have revealed that DNA replication timing (Stamatoyannopoulos et al., 2009) and chromatin modifications (Schuster-Bockler and Lehner, 2012) are associated with variations in mutational density. What is unclear from these early studies, however, is whether all extrinsic and exogenous factors that drive somatic mutational processes share a similar relationship with chromatin state and structure. In order to understand the interplay between spatial genome organization and specific individual mutational processes, we report here a study of 3000 tumor-normal pair whole genome datasets from more than 40 different human cancer types. Our analyses revealed that different mutational processes lead to distinct somatic mutation distributions between chromatin folding domains. APOBEC- or MSI-related mutations are enriched in transcriptionally-active domains while mutations occurring due to tobacco-smoke, ultraviolet (UV) light exposure or a signature of unknown aetiology (signature 17) enrich predominantly in transcriptionally-inactive domains. Active mutational processes dictate the mutation distributions in cancer genomes, and we show that mutational distributions shift during cancer evolution upon mutational processes switch. Moreover, a dramatic instance of extreme chromatin structure in humans, that of the unique folding pattern of the inactive X-chromosome leads to distinct somatic mutation distribution on X chromosome in females compared to males in various cancer types. Overall, the interplay between three-dimensional genome organization and active mutational processes has a substantial influence on the large-scale mutation rate variations observed in human cancer.

genomics↗

bioRxiv2017

Conservation of specificity in two low-specificity proteins

S100 proteins bind linear peptide regions of target proteins and modulate their activity. The peptide binding interface, however, has remarkably low specificity and can interact with many target peptides. It is not clear if the interface discriminates targets in a biological context, or whether biological specificity is achieved exclusively through external factors such as subcellular localization. To discriminate these possibilities, we used an evolutionary biochemical approach to trace the evolution of paralogs S100A5 and S100A6. We first used isothermal titration calorimetry to study the binding of a collection of peptides with diverse sequence, hydrophobicity, and charge to human S100A5 and S100A6. These proteins bound distinct, but overlapping, sets of peptide targets. We then studied the peptide binding properties of S100A5 and S100A6 orthologs sampled from across five representative amniote species. We found that the pattern of binding specificity was conserved along all lineages, for the last 320 million years, despite the low specificity of each protein. We next used Ancestral Sequence Reconstruction to determine the binding specificity of the last common ancestor of the paralogs. We found the ancestor bound the whole set of peptides bound by modern S100A5 and S100A6 proteins, suggesting that paralog specificity evolved by subfunctionalization. To rule out the possibility that specificity is conserved because it is difficult to modify, we identified a single historical mutation that, when reverted in human S100A5, gave it the ability to bind an S100A6-specific peptide. These results indicate that there are strong evolutionary constraints on peptide binding specificity, and that, despite being able to bind a large number of targets, the specificity of S100 peptide interfaces is indeed important for the biology of these proteins.

biochemistry↗

bioRxiv2017

INO80 Chromatin Remodelling Coordinates Metabolic Homeostasis with Cell Division

Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the Yeast Metabolic Cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here we demonstrate that the INO80 chromatin-remodelling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin in order to restrict proliferation to metabolically optimal states.

molecular biology↗