Biology subjects

Schulz, M.

Publications and source records attributed to Schulz, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Prediction and evaluation of Split-ORFs using Ribo-seq data

Split Open Reading frames (Split-ORFs) occur in transcripts containing at least two open reading frames, each encoding a part of the same full-length protein. These multiple open reading frames arise from alternatively spliced transcript isoforms. Understanding which genes make Split-ORFs, and in which cell types and under which conditions, would generate new insights into gene regulation. We previously published the Split-ORF pipeline, a computational tool that predicts candidate Split-ORFs from transcript sequences. Here, we present a new and improved version of the Split-ORF pipeline adding modules to analyze Ribo-seq data, calculate regions unique to the Split-ORF candidates, quantitatively assess Ribo-seq coverage in these regions, and perform candidate prioritization. Using this pipeline, we predicted more than 14,000 candidate Split-ORF transcripts from alternatively spliced human transcripts containing premature termination codons or retained introns. Hundreds of candidate Split-ORFs show significant Ribo-seq coverage across diverse cell types and diseases in at least one of the Split-ORFs, and 120 transcripts in both Split-ORFs. The candidate Split-ORF genes with significant Ribo-seq coverage are enriched for RNA-binding and RNA-processing functions and the majority of them encode RNA-binding proteins.

bioinformatics↗

bioRxiv2026

Auditory Attention Implements Complementary but Independent Cortical Mechanisms of Enhancement and Suppression

In noisy environments, goal-directed behavior requires the brain to prioritize task-relevant sound and to suppress distraction. While mechanisms of proactive attention in the presence of foreknowledge about targets and distractors are well-characterized, the neural dynamics governing reactive auditory attention in the absence of foreknowledge remain less understood. To fill this gap, we recorded the electroencephalogram (EEG) from N = 34 participants performing an auditory search task. Participants identified an amplitude-modulated spoken target number amid distractor numbers of varying salience. Presenting stimuli from three spatial locations enabled isolation of lateralized electrophysiological responses to targets and distractors. We quantified selection of targets versus distractors by continuously tracking participants cursor movements on a virtual response pad. Behaviorally, the target-directedness of cursor movements (i.e., towardness) increased for target repetitions (positive priming) and decreased when the target was a distractor from the previous trial (negative priming), indicating respective enhancement and suppression. Neurally, lateral targets evoked an N2ac component reflecting reactive enhancement. Importantly, we here demonstrate for the first time in an auditory attention task that distracting sounds evoke an auditory distractor positivity (PD) component. Target enhancement and distractor suppression were largely independent: their neural and behavioral markers were not significantly correlated and they originated from distinct cortical sources. Furthermore, shorter N2ac-but not PD-latencies related to higher towardness. By dissociating neural signatures and behavioral relevance of enhancement and suppression, our findings refine biased-competition models of attention, demonstrating that reactive selection relies on separable mechanisms rather than a single competitive gain process. Significance statementEveryday listening requires the rapid selection of relevant sounds and ignoring distraction, even when there is no prior knowledge of what will be heard. Here, we reveal the neural mechanisms that enable such reactive auditory attention. Combining electroencephalography with continuous measures of behavior, we show that target enhancement and distractor suppression are supported by distinct neural processes, indexed by the N2ac and the auditory PD component. These processes are largely independent, with only enhancement predicting behavior. This dissociation challenges unitary accounts of attentional selection and instead supports models in which separable mechanisms of enhancement and suppression operate in parallel. Our findings provide a mechanistic framework for understanding how the human brain flexibly prioritizes information in complex listening environments.

neuroscience↗

bioRxiv2025

OVEREXPRESSION OF TUMORPROTECTIVE CLUSTERIN PREVENTS EXHAUSTION OF TRANSGENIC T CELLS

1T cell therapies, such as chimeric antigen receptor (CAR) T cells and T cell receptor (TCR) transgenic (tg) T cells, are a promising approach in the treatment of solid malignancies but are limited by T cell exhaustion caused by chronic antigen stimulation. Clusterin (CLU) is a chaperone protein known to protect both normal and malignant cells, from metabolic stress and reactive oxygen species (ROS). In this study, we investigated whether overexpression (OE) of CLU in TCRtg T cells and CAR-T cells respectively can reduce exhaustion induced by chronic antigen stimulation and enhance T cell functionality against Ewing sarcoma (EwS). Among other cytoprotective genes, we found that CLU was significantly downregulated in dysfunctional tumor infiltrating lymphocytes. Therefore, we engineered EwS-directed TCRtg T cells targeting a Chondromodulin-1 (Chm1)-derived peptide and GD2 CAR-T cells to overexpress CLU. We show here that CLU is downregulated in T cells following activation by tumor cells. CLU-overexpressing T cells exhibit decreased expression of exhaustion markers (PD1, LAG3) and reduced apoptosis after repetitive stimulation. These cells demonstrated improved infiltration into tumor spheroids and maintained functionality under hypoxic conditions. In vivo, CLU-overexpressing T cells showed enhanced persistence and a trend towards reduced tumor growth. Mechanistically, proteomic analysis suggested that reduced ribosomal activity might delay T cell exhaustion, implicating metabolic reprogramming. In conclusion, CLU OE in tg T cells enhances their persistence and functionality by mitigating exhaustion, possibly through modulation of ribosomal activity and metabolic pathways. This strategy holds potential for improving adoptive T cell therapies against solid tumors.

immunology↗

bioRxiv2025

Altered sperm DNA methylation in overweight men associates with transposable element regulation of paternal origins of risk in children

The occurrence of childhood neurodevelopmental disorders has been steadily increasing for decades yet we have little understanding of modes of inheritance implicated in these diseases. Epidemiology studies have revealed an association between an elevated paternal BMI and an increased risk for autism in children, suggesting non-genetic modes of inheritance may be involved. Epigenetic marks, like DNA methylation at cytosines, are especially susceptible to environmental, diet and lifestyle changes. Yet, whether a mans BMI influences the sperm methylome and potentially impacts offspring development remains unresolved. Using MethylC capture (MCC)-sequencing, we identified over 38 000 differentially methylated CpGs (DMCs) in the sperm of men with an elevated BMI, with many occurring in regions that were enriched for neural gene and disease ontologies. Differentially methylated regions (DMRs) were enriched at transposable elements that can act as active enhancers during human zygotic genome activation, and at gene promoters for early lineage specification. These results suggest that sperm methylome alterations that are linked to an elevated BMI may influence key embryonic transcriptional process, notably those associated with trophectoderm and placental development.

developmental biology↗

bioRxiv2024

Exploration of novel biomarkers for neurodegenerative diseases using proteomic analysis and ligand-binding assays

Neurodegenerative diseases are a major cause of morbidity and mortality world-wide, and their public health burden continues to increase. There is an urgent need to develop reliable and sensitive biomarkers to aid the timely diagnosis, disease progression monitoring, and therapeutic development for neurodegenerative disorders. Proteomic screening strategies, including antibody microarrays, are a powerful tool for biomarker discovery, but their findings should be confirmed using quantitative assays. The current study explored the feasibility of combining an exploratory proteomic strategy and confirmatory ligand-binding assays to screen for and validate biomarker candidates for neurodegenerative disorders. It analyzed cerebrospinal fluid (CSF) and plasma samples from patients with Alzheimers disease, Parkinsons disease, and multiple sclerosis and healthy controls. The screening antibody microarray identified differentially expressed proteins between patients with neurodegenerative diseases and healthy controls. Quantitative ligand-binding assays confirmed that cluster of differentiation 14 (CD14) levels were elevated in CSF of patients with Alzheimers disease, whereas osteopontin levels were increased in CSF of patients with Parkinsons disease. The current study demonstrated the utility of combining an exploratory proteomic approach and quantitative ligandbinding assays to identify biomarker candidates for neurodegenerative disorders. To further validate and expand these findings, large-scale analyses using well characterized samples should be conducted.

neuroscience↗

bioRxiv2024

Modulation of the ATP-adenosine signaling axis combined with radiotherapy facilitates anti-cancer immunity in brain metastasis

The immunosuppressive microenvironment in the brain poses a major limitation to successful therapy for brain metastases. Here we report that blockade of the ATP-to-adenosine-converting enzymes CD39 and CD73 and the adenosine receptor A2AR in combination with radiotherapy attenuates tumor progression in a breast-to-brain metastasis model by facilitating anti-cancer immunity. Immunophenotyping revealed loss of exhausted T cells and higher abundance of anti-cancer effector T cell populations. This effect was accompanied by a decrease of immunosuppressive lipid-laden macrophages and an expansion of CD14CD33high macrophages associated with antigen presentation. Analyses of human brain metastases samples supports a role of the ATP-adenosine signaling axis in modulating tumor inflammation and identified expression of CD39 and adenosine deaminase as predictive markers for patient survival and/or immune infiltration. Our findings demonstrate that the adenosine axis represents a druggable pathway to achieve local immunomodulation and treatment response, opening a new therapeutic avenue for brain metastases patients.

cancer biology↗

bioRxiv2024

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking thus far. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five genome-wide profiling protocols. As an evaluation reference, we employed highly quantitative locus-specific measurements from our preceding benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and several comprehensive metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To facilitate the sustainability of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and seamlessly expandable to future software.

bioinformatics↗

bioRxiv2024

CRISPR-inhibition screen for lncRNAs linked to melanoma growth and metastasis

Melanoma being one of the most common and deadliest skin cancers, has been rising since the past decade. Patients at advanced stages of the disease have very poor prognoses, as opposed to at the earlier stages. Nowadays the standard-of-care of advanced melanoma is resection followed by immune checkpoint inhibition based immunotherapy. However, a substantial proportion of patients either do not respond or develop resistances. This underscores a need for novel approaches and therapeutic targets as well as a better understanding of the mechanisms of melanoma pathogenesis. Long non-coding RNAs (lncRNAs) comprise a poorly characterized class of functional players and promising targets in promoting malignancy. Certain lncRNAs have been identified to play integral roles in melanoma progression and drug resistances, however systematic screens to uncover novel functional lncRNAs are scarce. Here, we profile differentially expressed lncRNAs in patient derived short-term metastatic cultures and BRAF-MEK-inhibition resistant cells. We conduct a focused growth-related CRISPR-inhibition screen of overexpressed lncRNAs, validate and functionally characterize lncRNA hits with respect to cellular growth, invasive capacities and apoptosis in vitro as well as the transcriptomic impact of our lead candidate the novel lncRNA XLOC_030781. In sum, we extend the current knowledge of ncRNAs and their potential relevance on melanoma. SignificancePreviously considered as transcriptional noise, lncRNAs have emerged as novel players in regulating many cellular aspects in health and disease including melanoma. However, the number and as well as the extent of functional significance of most lncRNAs remains elusive. We provide a comprehensive strategy to identify functionally relevant lncRNAs in melanoma by combining expression profiling with CRISPR-inhibition growths screens lowering the experimental effort. We also provide a larger resource of differentially expressed lncRNAs with potential implications in melanoma growth and invasion. Our results broaden the characterized of lncRNAs as potential targets for future therapeutic applications.

cancer biology↗

bioRxiv2024

Long non-coding RNAs direct the SWI/SNF complex to cell-specific enhancers

The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control1. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression2. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state2-5. It does so while retaining the ability to respond dynamically to cellular signals4. However, the mechanisms that guide SWI/SNF to specific genomic targets have remained elusive. Here we demonstrate that trans-acting long non-coding RNAs (lncRNAs) direct the SWI/SNF complex to cell type-specific enhancers. SWI/SNF preferentially binds lncRNAs and these predominantly bind DNA targets in trans. Together they localize to enhancers, many of which are cell type-specific. Knockdown of SWI/SNF- and enhancer-bound lncRNAs causes the genome-wide redistribution of SWI/SNF away from enhancers and a concomitant differential expression of spatially connected target genes. These lncRNA-SWI/SNF-enhancer networks support an enhancer hub model of SWI/SNF genomic targeting. Our findings reveal a competitive recruitment of SWI/SNF by lncRNAs which provide a specific and dynamic layer of control in chromatin accessibility and gene expression.

molecular biology↗

bioRxiv2024

Comparative venom analysis between melanistic and normally-colored phenotypes of the common adder (Vipera berus)

1Snake venom is an ecologically-relevant functional trait directly linked with a snakes fitness and survival, facilitating predation and defense. Snake venom variation occurs at all taxonomic levels, but the study of variation at intraspecific level is still in its early stages. The common adder (Vipera berus) exhibits considerable variation in color phenotypes across its distribution range. Melanistic (fully black) individuals are the subject of myths and fairytales, and in German folklore such "hell adders" are considered more toxic than their normally-colored conspecifics. However, these claims have never been formally tested. Here, we provide the first comparative analysis of venoms from melanistic and normally-colored common adders. Specifically, we compared the venom profiles by SDS-PAGE and RP-HPLC, and tested the protease, phospholipase A2 and cytotoxic activities of the venoms of both phenotypes. Phospholipase A2 activity was similar in both phenotypes, whereas general protease activity was higher in the melanistic venom, which was also more cytotoxic at two concentrations (6.25 and 12.5 {micro}g/ml). These minor differences between the venoms of melanistic and normally-colored adders are unlikely to be of clinical relevance in the context of human envenomation. In light of our results, the claim that melanistic adders produce more toxic venom than their normally-colored conspecifics appears rooted entirely in folklore.

molecular biology↗

bioRxiv2023

Tripartite interactions of PKA catalytic subunit and C-terminal domains of cardiac Ca2+ channel modulate its β-adrenergic regulation

The adrenergic nervous system augments cardiac contraction by increasing the activity of L-type voltage-gated CaV1.2 channels. Dysregulation of this process is linked to severe cardiac dysfunctions. The signaling cascade involves activation of {beta}-adrenergic receptors, elevation of cAMP levels, separation of protein kinase A (PKA) regulatory subunit (PKAR) from catalytic subunit (PKAC), and phosphorylation of the inhibitory protein Rad leading to increased Ca2+ influx. In cardiomyocytes, the core subunit of CaV1.2 (1C) exists in two forms: full-length (FL) or proteolytically processed (truncated), lacking the distal C-terminus (dCT). Specificity and efficiency in the cascade are believed to emanate from unique protein-protein interactions, such as anchoring PKA (via PKAR) to 1C by A-kinase anchoring proteins (AKAPs). However, most AKAPs do not interact with the truncated 1C, and their role in {beta}AR regulation of cardiac CaV1.2 remains unclear. Here we show that PKAC, independently of PKAR or AKAPs, directly interacts with 1C at two domains in 1C-CT: the proximal and distal C-terminal regulatory domains (PCRD and DCRD), which also interact with each other. Furthermore, we find that DCRD competes with PCRD and reduces its interaction with PKAC. The physiological consequences of these complex interactions are incompletely understood; our data suggest that they may fine-tune the {beta}AR regulation of CaV1.2. We propose that the newly discovered interactions take part in governing colocalization of regulatory proteins within the {beta}AR-CaV1.2 multimolecular signaling complexes in cardiomyocytes.

biochemistry↗

bioRxiv2023

Functional expression of a Mo-dependent formate dehydrogenase in Escherichia coli under aerobic conditions

BackgroundOxygen tolerant complex metal-dependent formate dehydrogenases hold potential for biotechnological applications. Principle FindingsIn this work, we report the functional expression of the complex, molybdenum-dependent soluble formate dehydrogenase encoded by the fdsGBACD operon from Cupriavidus necator (CnFDH) in Escherichia coli. Expression of the operon from plasmids or from a copy integrated in the chromosome enabled growth of an energy-auxotrophic selection strain on formate as sole energy source under aerobic conditions. Growth could be accelerated in turbidostat, leading to a drop of the generation time of 1 hour. While no mutation was found in the operon of evolved isolates, genome sequencing revealed non-synonymous point mutations in the gene focA coding for a bidirectional formate transporter carried in all isolates sequenced. Reverting the mutations led to a drop in the growth rate demonstrating the focA mutation as principle target of continuous culture adaptation. SignificanceA member of the oxygen-tolerant subclass of complex FDH showed stable formate oxidation activity when expressed in the heterologous host E. coli, a model organism of biotechnology. The integration of the operon in the chromosome offers the possibility of structure/function studies and activity enhancements through in vivo mutagenesis, which can also be applied to CO2 reduction in appropriate selection hosts.

bioengineering↗

bioRxiv2023

DNA methylation shapes the Polycomb landscape during the exit from naïve pluripotency

In mammals, 5 methyl-cytosine (5mC) and Polycomb Repressive Complex 2 (PRC2)-deposited histone 3 lysine 27 trimethylation (H3K27me3) are generally mutually exclusive at CpG-rich regions. As mouse embryonic stem cells exit the naive pluripotent state, there is a massive gain of 5mC coincident with a restriction of broad H3K27me3 to 5mC-free, CpG-rich regions. To formally assess how 5mC shapes the H3K27me3 landscape, we profiled the epigenome of naive and differentiated cells in the presence and absence of the DNA methylation machinery. Surprisingly, we found that 5mC accumulation is not required to restrict most H3K27me3 domains. We went on to show that this 5mC-independent H3K27me3 restriction is mediated by aberrant expression of the PRC2 antagonist Ezhip. At the regions where 5mC appears to genuinely supplant H3K27me3, we identified 68 candidate genes that appeared to require 5mC deposition and/or H3K27me3 depletion for their activation in differentiated cells. Employing site-directed epigenome editing to directly modulate 5mC levels, we demonstrated that 5mC deposition is sufficient to antagonize H3K27me3 deposition and confer gene activation at individual candidates. Altogether, we systematically measured the antagonistic interplay between 5mC and H3K27me3 in a system that recapitulates early embryonic dynamics. Our results suggest that H3K27me3 restraint depends on 5mC, both directly and indirectly. This study also reveals a non-canonical role of 5mC in gene activation, which may be important not only for normal development but also for cancer progression, as oncogenic cells frequently exhibit dynamic replacement of 5mC for H3K27me3 and vice versa.

molecular biology↗

bioRxiv2023

CVD-associated SNPs with regulatory potential drive pathologic non-coding RNA expression

BackgroundCardiovascular diseases (CVDs) are the leading cause of death worldwide. Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) appearing in non-coding genomic regions in CVDs. The SNPs may alter gene expression by modifying transcription factor (TF) binding sites and lead to functional consequences in cardiovascular traits or diseases. To understand the underlying molecular mechanisms, it is crucial to identify which variations are involved and how they affect TF binding. MethodsThe SNEEP (SNP exploration and analysis using epigenomics data) pipeline was used to identify regulatory SNPs, which alter the binding behavior of TFs and link GWAS SNPs to their potential target genes for six CVDs. The human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs), monoculture cardiac organoids (MCOs) and self-organized cardiac organoids (SCOs) were used in the study. Gene expression, cardiomyocyte size and cardiac contractility were assessed. ResultsBy using our integrative computational pipeline, we identified 1905 regulatory SNPs in CVD GWAS data. These were associated with hundreds of genes, half of them non-coding RNAs (ncRNAs), suggesting novel CVD genes. We experimentally tested 40 CVD-associated non-coding RNAs, among them RP11-98F14.11, RPL23AP92, IGBP1P1, and CTD-2383I20.1, which were upregulated in hiPSC-CMs, MCOs and SCOs under hypoxic conditions. Further experiments showed that IGBP1P1 depletion rescued expression of hypertrophic marker genes, reduced hypoxia-induced cardiomyocyte size and improved hypoxia-reduced cardiac contractility in hiPSC-CMs and MCOs. ConclusionsIGBP1P1 is a novel ncRNA with key regulatory functions in modulating cardiomyocyte size and cardiac function in our disease models. Our data suggest ncRNA IGBP1P1 as a potential therapeutic target to improve cardiac function in CVDs.

genomics↗

bioRxiv2023

Multi-omics analysis identifies LBX1 and NHLH1 as central regulators of human midbrain dopaminergic neuron differentiation

Midbrain dopaminergic neurons (mDANs) control voluntary movement, cognition, and reward behavior under physiological conditions and are implicated in human diseases such as Parkinsons disease (PD). Many transcription factors (TFs) controlling human mDAN differentiation during development have been described, but much of the regulatory landscape remains undefined. Using a tyrosine hydroxylase (TH) iPSC reporter line, we have generated time series transcriptomic and epigenomic profiles of purified mDANs during differentiation. Integrative analysis predicted novel central regulators of mDAN differentiation and super-enhancers were used to prioritize key TFs. We find LBX1, NHLH1 and NR2F1/2 to be necessary for mDAN differentiation and show that overexpression of either LBX1 or NHLH1 can also improve mDAN specification. NHLH1 is necessary for the induction of neuronal miR-124, while LBX1 regulates cholesterol biosynthesis, possibly through mTOR signaling. Consistently, rapamycin treatment led to an inhibition of mDAN differentiation. Thus, our work reveals novel regulators of human mDAN differentiation.

genomics↗

bioRxiv2022

Habitat quality, not patch isolation, drives distribution and abundance of two light-demanding butterflies in fragmented coppice landscapes

Coppice forests are socio-ecological systems especially rich in biodiversity. They have been transformed into high forest and abandoned across large areas of Europe over the past 200 years. Coppice loss is likely an important driver of insect declines. It is currently unclear whether habitat quality or decreasing connectivity of the remaining fragments is more important for the survival of insect populations. We related the abundance of two coppice-attached butterflies of conservation concern, Satyrium ilicis and Melitaea athalia, to indicators of habitat quality and habitat connectivity. We estimated butterfly densities using Distance Sampling along a successional gradient (time since last cut: 1-9 years; N = 130 plots) across one of the largest remaining simple oak-birch coppice landscapes in Central Europe. Both species reached abundance peaks within four to six years after the last cut, declining rapidly in abundance with subsequent succession. We found no evidence that coupe size, coppice availability and patch (= coupe) connectivity were related to the density of the species. Besides stand age, the cover of larval foodplants explained predicted butterfly densities well. Only Satyrium ilicis benefitted from high Red Deer densities. Implications for insect conservation: Our results suggest that habitat quality and sufficient availability of coppice of suitable age matters more than coupe size and fragmentation within a traditional managed coppice landscape. Coppice restoration aiming at the study species should ensure a shifting mosaic of successional habitat to provide a large availability of resprouting oak stools and blueberry vegetation that holds dense Melampyrum pratense stands.

ecology↗

bioRxiv2022

DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation

Somatic DNA methylation is established early during mammalian development, as embryonic cells transition from naive to primed pluripotency. This precedes the emergence of the three somatic germ layers, but also the segregation of the germline that undergoes genome-wide DNA demethylation after specification. While DNA methylation is essential for embryogenesis, the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Using culture modeling of cellular transitions, we found that DNA methylation-free embryonic stem cells (ESCs) with a triple DNA methyltransferase knockout (TKO) normally progressed through the continuum of pluripotency states, but demonstrated skewed differentiation abilities towards neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells (PGCLCs), even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that the neural and germline lineages are linked by a similar enhancer dynamics during priming, defined by common sets of methyl-sensitive transcription factors that fail to be decommissioned in absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of preferred differentiation route during early development.

developmental biology↗

bioRxiv2022

Gal1 repression memory in budding yeast

Cells must continuously adapt to changing environments and, thus, have evolved mechanisms allowing them to respond to repeated stimuli. For example, faster gene induction upon a repeated stimulus aids adaptation - a process known as reinduction memory. However, whether such a memory exists for gene repression is unclear. Here, we studied gene repression across repeated carbon source shifts in over 2,500 single Saccharomyces cerevisiae cells. By monitoring the expression of a carbon source-responsive gene, galactokinase 1 (Gal1), and mathematical modeling, we discovered repression memory at the population and single-cell level. Using a repressor model to estimate single-cell repression parameters, we show that repression memory is due to a shortened repression delay, the estimated time gap between carbon source shift and Gal1 expression termination, upon the repeated carbon source shift. Additionally, we show that cells lacking Elp6 display a gain-of-repression-memory phenotype characterized by a stronger decrease in repression delay between two consecutive carbon source shifts. Collectively, our study provides the first quantitative description of repression memory in single cells.

systems biology↗