Biology subjects

Tavazoie, S.

Publications and source records attributed to Tavazoie, S..

15 recordsLinked to original sources

bioRxiv2025

Noise-driven morphogenesis independent of transcriptional regulatory programs

Development is widely understood as a deterministic process driven by transcriptional programs that specify cell fate and orchestrate morphogenesis. However, this view overlooks pervasive stochasticity in gene expression, often considered an obstacle to reliable tissue patterning. Here, we introduce stochastic tuning-driven morphogenesis (STM), an alternative conceptualization of development in which noisy gene expression is not a nuisance but the primary driving force--guiding cell fates toward optimal multicellular configurations by a trial-and-error process analogous to reinforcement learning. STM operates independently of fixed transcriptional programs, instead relying on convergence of sensory information into signaling hubs, which by reinforcing random transcriptional changes, prospectively and contextually fine-tune gene expression along key developmental milestones. STM offers a fundamentally different view of development--one in which stochastic gene expression enables real-time optimization of gene expression toward multicellular objectives, implementing a self-organizing process that is inherently resistant to molecular and environmental fluctuations.

developmental biology↗

bioRxiv2025

Adaptation by stochastic tuning of gene expression in mammalian cells

Cells often face environmental challenges for which they lack pre-programmed regulatory responses. We have previously shown that yeast cells can, nevertheless, adapt to such unfamiliar conditions by a phenomenon we have termed stochastic tuning. In this process, cells use gene expression noise to randomly change the expression of individual genes and actively reinforce those changes that improve the overall health of the cell. Here, we provide experimental evidence for stochastic tuning in human cells adapting to the lethal chemotherapeutic agent methotrexate. As in yeast, the tuning process is not driven by mutations and is reversible upon removal of methotrexate challenge. We show that stochastic tuning is a conserved eukaryotic mechanism of cellular adaptation, and potentially a key factor in the phenomenon of cancer cell plasticity underlying chemotherapy resistance.

systems biology↗

bioRxiv2025

Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis

Transfer RNAs (tRNAs), once viewed as static adaptors in translation, are now recognized as dynamic regulators of gene expression. While recent studies have illuminated roles for tRNA stability, the upstream mechanisms governing tRNA transcription remain poorly understood. To address this gap, we generated the EXpression atlas of tRNA (EXTRNA), a high-resolution tRNA expression dataset spanning 24 cell lines across 9 human tissues. EXTRNA revealed both tissue-type-specific expression programs ("tRNAomes") and unexpected intra-tissue heterogeneity across breast cancer samples. Integrating EXTRNA with computational network analysis and data from other publicly available datasets, we identified Zinc Finger ZZ-Type And EF-Hand Domain Containing 1 (ZZEF1) as the first sequence-specific transcription factor of a particular tRNA. ZZEF1 promoted tRNA-LysUUU transcription by partnering with the ATP-dependent chromatin remodeler Chromodomain Helicase DNA Binding Protein 6 (CHD6), enhancing chromatin accessibility at tRNA-Lys-TTT-3 loci. ZZEF1 deficiency reduced tRNA-LysUUU abundance, decreased the translational efficiency of AAR codon-enriched mRNAs--including the tumor suppressor Serine/Threonine Kinase 3 (STK3)--and promoted metastatic progression in breast cancer in vivo. Together, our findings establish a previously unrecognized mechanism for RNA polymerase III-mediated tRNA transcription and define a regulatory circuit linking chromatin remodeling, codon-specific translation, and tumor suppression. More broadly, this work introduces a framework for dissecting the regulatory logic of the tRNAome and highlights tRNA expression control as a promising avenue for therapeutic intervention.

genomics↗

bioRxiv2024

The genetic landscape of antibiotic sensitivity in Staphylococcus aureus

A comprehensive genetic landscape of antibiotic sensitivity in Staphylococcus aureus is lacking. Using ultra-dense CRISPR-interference libraries, we systematically quantified global gene fitness across ten antibiotics and uncovered hundreds of significant antibiotic-gene interactions. Essential genes dominated these interactions, a finding not revealed by transposon-based studies. Processes most vulnerable to transcriptional repression under antibiotic conditions included cell wall synthesis/cell division (CC), DNA replication/DNA recombination (DD), coenzyme A biosynthesis, and riboflavin metabolism. Network and genetic analyses further revealed novel synergistic genetic interactions (GIs) within these processes, including an extensive CC-DD subnetwork. Only a subset of CC-DD synergies was dependent on the cell division inhibitor SosA. Informed by these GIs, we identified multiple drug-drug combinations with potent synergistic activity against multidrug-resistant S. aureus. Our detailed profiling of drug-gene, gene-gene, and drug-drug interactions reveals novel functional relationships among essential genes and defines a vulnerability landscape to guide new drug target discovery and effective combination therapies.

systems biology↗

bioRxiv2024

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Recent research has indicated the presence of heterochromatin-like regions of extended protein occupancy and transcriptional silencing of bacterial genomes. We utilized an integrative approach to track chromatin structure and transcription in E. coli K-12 across a wide range of nutrient conditions. In the process, we identified multiple loci which act similarly to facultative heterochromatin in eukaryotes, normally silenced but permitting expression of genes under specific conditions. We also found a strong enrichment of small regulatory RNAs (sRNAs) among the set of differentially expressed transcripts during nutrient stress. Using a newly developed bioinformatic pipeline, the transcription factors regulating sRNA expression were bioinformatically predicted, with experimental follow-up revealing novel relationships for 36 sRNA-transcription factors candidates. Direct regulation of sRNA expression was confirmed by mutational analysis for five sRNAs of metabolic interest: IsrB, CsrB and CsrC, GcvB, and GadY. Our integrative analysis thus reveals additional layers of complexity in the nutrient stress response in E. coli and provides a framework for revealing similar poorly understood regulatory logic in other organisms.

systems biology↗

bioRxiv2023

Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells

Utilization of specific codons varies significantly across organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine restriction--a feature of tumor microenvironments--is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced a proteomic shift towards low arginine codon containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons--reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.

cancer biology↗

bioRxiv2022

Intracellular acidification is a hallmark of thymineless death in E. coli

Thymidine starvation causes rapid cell death. This enigmatic process known as thymineless death (TLD) is the underlying killing mechanism of diverse antimicrobial and antineoplastic drugs. Despite decades of investigation, we still lack a mechanistic understanding of the causal sequence of events that culminate in TLD. Here, we used a diverse set of unbiased approaches to systematically determine the genetic and regulatory underpinnings of TLD in Escherichia coli. In addition to discovering novel genes in previously implicated pathways, our studies revealed a critical and previously unknown role for intracellular acidification in TLD. We observed that a decrease in cytoplasmic pH is a robust early event in TLD across diverse genetic backgrounds. Furthermore, we show that acidification is a causal event in the death process, as chemical and genetic perturbations that increase intracellular pH substantially reduce killing. We also observe a decrease in intracellular pH in response to exposure to the antibiotic gentamicin, suggesting that intracellular acidification may be a common mechanistic step in the bactericidal effects of other antibiotics.

microbiology↗

bioRxiv2021

OxPhos Dysfunction Causes Hypermetabolism and Reduces Lifespan in Cells and in Patients with Mitochondrial Diseases

Patients with primary mitochondrial diseases present with fatigue and multi-system disease, are often lean, and die prematurely, but the mechanistic basis for this clinical picture remains unclear. Integrating data from 17 cohorts of patients with mitochondrial diseases (n=690), we find that clinical mitochondrial disorders increase resting energy expenditure, a state termed hypermetabolism. In a longitudinal cellular model of primary patient-derived fibroblasts from multiple donors, we show that genetic and pharmacological disruptions of oxidative phosphorylation (OxPhos) similarly trigger increased energy consumption in a cell-autonomous manner, despite near-normal OxPhos coupling efficiency. Hypermetabolism is associated with mtDNA instability, activation of the integrated stress response, increased extracellular secretion of age-related cytokines and metabokines including GDF15, as well as an accelerated rate of telomere erosion and epigenetic aging, and a reduced Hayflick limit. Together with these dynamic measures, we have generated a longitudinal RNASeq and DNA methylation resource dataset, which reveals conserved, energetically demanding, genome-wide recalibrations in response to OxPhos dysfunction. The increased energetic cost of living, or hypermetabolism, in cells and organisms with OxPhos defects has important biological and clinical implications.

cell biology↗

bioRxiv2021

A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of bound metabolic mRNAs

Stress-induced cleavage of transfer RNAs (tRNAs) into tRNA-derived fragments (tRFs) occurs across organisms from yeast to human, yet its mechanistic bases and pathological consequences remain poorly defined. By performing genome-wide small RNA profiling, we detected increased abundance of a Cysteine tRNA fragment (5-tRFCys) during breast cancer metastatic progression. 5-tRFCys is required for efficient breast cancer metastatic lung colonization and metastatic cell survival. We identified Nucleolin as the direct binding partner of 5-tRFCys. 5-tRFCys binding enhanced the stability of Nucleolins associated pro-metastatic transcripts encoding metabolic enzymes Mthfd1l and Pafah1b1. 5-tRFCys stabilized these transcripts by promoting Nucleolin oligomerization and the assembly of Nucleolin and its bound transcripts into a higher-order ribonucleoprotein complex. Our findings reveal that a tRF can promote oligomerization of an RNA binding protein into a stabilizing ribonucleoprotein complex containing specific target transcripts, thereby driving specific metabolic pathways underlying cancer progression.

cancer biology↗

bioRxiv2020

Molecular topography of an entire nervous system

Nervous systems are constructed from a deep repertoire of neuron types but the underlying gene expression programs that specify individual neuron identities are poorly understood. To address this deficit, we have produced an expression profile of all 302 neurons of the C. elegans nervous system that matches the single cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of [~]23 neuropeptide-encoding genes and [~]36 neuropeptide receptors thus pointing to an expansive "wireless" signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression across the nervous system and (2) reveal adhesion proteins with potential roles in synaptic specificity and process placement. These data are available at cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system.

neuroscience↗

bioRxiv2020

An inducible CRISPR-interference library for genetic interrogation of Saccharomyces cerevisiae biology

Genome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. Despite its dominance as a model eukaryote, a genome-wide CRISPRi library, optimized for targeting the Saccharomyces cerevisiae genome, has not been presented to date. We have generated a comprehensive, inducible CRISPRi library, based on spacer design rules optimized for yeast. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed parameters for optimal transcriptional repression, including upstream distance, nucleosomal occupancy, and strand bias. CRISPRi screens, using this library can identify genes and pathways with high precision and low false discovery rate across a variety of experimental conditions, enabling rapid and reliable genome-wide assessment of gene function and genetic interactions in S.cerevisiae.

systems biology↗

bioRxiv2020

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

Free-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein-DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (IPOD-HR), and present a pilot application to E. coli. We observe that the E. coli protein-DNA interactome organizes into two distinct prototypic features: (1) highly dynamic condition-dependent transcription factor occupancy, and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence-specificity models for the majority of active transcription factors. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria which are not amenable to routine genetic manipulation.

systems biology↗

bioRxiv2019

Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

Despite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotes has been hindered by their extremely low mRNA abundance, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a low-cost, high-throughput, prokaryotic scRNA-seq pipeline that overcomes these technical obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. PETRI-seq captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and low bias, with median capture rates >200 mRNAs/cell for exponentially growing E. coli. These characteristics enable robust discrimination of cell-states corresponding to different phases of growth. When applied to wild-type S. aureus, PETRI-seq revealed a rare sub-population of cells undergoing prophage induction. We anticipate broad utility of PETRI-seq in defining single-cell states and their dynamics in complex microbial communities.

systems biology↗

bioRxiv2018

A post-transcriptional regulatory code for mRNA stability during the zebrafish maternal-to-zygotic transition

Post-transcriptional regulation is crucial to shape gene expression. During the Maternal-to-Zygotic Transition (MZT), thousands of maternal transcripts are regulated upon fertilization and genome activation. Transcript stability can be influenced by cis-elements and trans-factors, but how these inputs are integrated to determine the overall mRNA stability is unclear. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. To identify cis-regulatory elements, we performed a massively parallel reporter assay for stability-influencing sequences, which revealed that 3-UTR poly-U motifs are associated with mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC and CUGC elements emerged as the main destabilizing motifs in the embryo, with miR-430 and AREs causing mRNA deadenylation in a genome activation-dependent manner. To identify the trans-factors interacting with these cis-elements, we comprehensively profiled RNA-protein interactions and their associated regulatory activities across the transcriptome during the MZT. We find that poly-U binding proteins are preferentially associated with 3-UTR sequences and stabilizing motifs, and that antagonistic sequence contexts for poly-C and poly-U binding proteins shape the binding landscape and magnitude of regulation across the transcriptome. Finally, we integrate these regulatory motifs into a machine learning model that accurately predicts the stability of mRNA reporters in vivo. Our findings reveal how mechanisms of post-transcriptional regulation are coordinated to direct changes in mRNA stability within the early zebrafish embryo.

genomics↗

bioRxiv2017

Cellular Adaptation Through Fitness-Directed Transcriptional Tuning

Cells adapt to changes in their environment through transcriptional responses that are hard-coded in their regulatory networks. Such dedicated pathways, however, may be inadequate for adaptation to novel or extreme environments. We propose the existence of a fitness optimization mechanism that tunes the global transcriptional output of a genome to match arbitrary external conditions in the absence of dedicated gene-regulatory networks. We provide evidence for the proposed tuning mechanism in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. We show that transcriptional tuning operates locally at individual gene promoters and its efficacy is modulated by genetic perturbations to chromatin modification machinery.

systems biology↗