About

Zeba Wunderlich is an Associate Professor whose research focuses on understanding the architecture, robustness, and evolvability of gene regulatory networks through the study of regulatory DNA. Her lab investigates how the tasks performed by gene regulatory networks influence their structure and function, using the Drosophila early embryonic patterning system and the Drosophila innate immune response as model systems. The research combines imaging-based and genomic measurements of gene expression with statistical and physically-based computational models to explore gene regulatory network function. The lab also leverages naturally occurring sequence variation between individuals and species to study how changes in regulatory DNA affect transcriptional regulation. Zeba Wunderlich holds a PhD in Biophysics from Harvard University and a BA in Molecular Biology & Biochemistry and Statistics from Rutgers University.

Research topics

• Biology
• Genetics
• Computer Science
• Computational biology
• Cell biology
• Psychology
• Molecular biology
• Evolutionary biology

Selected publications

• Epithelial cell competition is promoted by signaling from immune cells

  Nature Communications · 2025-04-18 · 2 citations

  articleOpen access

  In epithelial tissues, juxtaposition of cells of different phenotypes can trigger cell competition, a process whereby one type of cell drives death and extrusion of another. During growth and homeostasis, cell competition is thought to serve a quality control function, eliminating cells that are "less fit". Tissues may also attack and eliminate newly arising tumor cells, exploiting mechanisms shared with other instances of cell competition, but that differ, reportedly, in the involvement of the immune system. Whereas immune cells have been shown to play a direct role in killing tumor cells, this has not been observed in other cases of cell competition, suggesting that tissues recognize and handle cancer cells differently. Here, we challenge this view, showing that, in the fruit fly Drosophila, innate immune cells play similar roles in cell killing during classical cell competition as in eliminating tumors. These findings suggest that immune suppression of cancer may exploit the same mechanisms as are involved in promoting phenotypic uniformity among epithelial cells.

  PublisherOA PDFDOI

• Comparison of activities of transcription factor NF-κB from two jellyfish models

  Comparative Immunology Reports · 2025-06-17 · 1 citations

  articleOpen access

  • The immune transcription factor NF-κB pathway is present in jellyfish. • Activities and regulation of two jellyfish NF-κB proteins are compared and contrasted. • Alphafold3-based structures of jellyfish NF-κB proteins are generated. • Expression of NF-κB mRNA is characterized through development and in single cell analysis. Herein, transcription factor Nuclear Factor-kappaB (NF-κB) is characterized as the downstream effector of putative innate immune signaling pathways from two model jellyfish, Aurelia aurita ( Aa ) and Clytia hemisphaerica ( Ch ). Both jellyfish NF-κB proteins consist primarily of the N-terminal DNA-binding/dimerization domain, and they lack the C-terminal ankyrin repeat inhibitory domain found in vertebrate NF-κB proteins. Both jellyfish NF-κB proteins bind to a consensus mammalian NF-κB binding site, and their AlphaFold3-predicted structures on DNA are similar to that of mouse NF-κB p50. Neither Aa - nor Ch -NF-κB activated transcription of an NF-κB-site reporter gene in human cells; however, Aa -NF-κB did activate transcription from a GAL4-site reporter gene in yeast, whereas Ch -NF-κB did not. Aa - and Ch -NF-κB were both constitutively located in the nucleus when expressed in vertebrate cells. Homologs of IκB-like proteins from both species interacted with their corresponding NF-κB proteins in co-immunoprecipitation assays in HEK 293T cells. These IκB-like proteins influenced the subcellular localization of their cognate NF-κB proteins in vertebrate cells, and their ankyrin repeat domains were predicted to interact with Ch -NF-κB in a manner similar to mammalian IκB and NF-κB. RNA-sequencing data from Ch animals indicate that Ch -NF-κB is expressed at high levels in early developmental stages, when Ch -IκB expression is low, suggesting that active Ch -NF-κB controls an early developmental process. In contrast, in adult animals the expression of Ch -IκB is high, suggesting that Ch -NF-κB requires a signal in order to become active. Overall, these results provide comparative information on the structure, activity, and mRNA expression of jellyfish NF-κB pathway proteins among jellyfish, and they suggest roles for NF-κB in developing and adult jellyfish.

  PublisherDOI

• Comparison of Activities of Transcription Factor NF-κB from Two Jellyfish Models

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-22

  preprintOpen access

  Abstract Herein, transcription factor Nuclear Factor-kappaB (NF-κB) is characterized as the downstream effector of putative innate immune signaling pathways from two model jellyfish, Aurelia aurita ( Aa ) and Clytia hemisphaerica ( Ch ). Both jellyfish NF-κB proteins consist primarily of the N-terminal DNA-binding/dimerization domain, and they lack the C-terminal ankyrin repeat inhibitory domain found in vertebrate NF-κB proteins. Both jellyfish NF-κB proteins bind to a consensus mammalian NF-κB binding site, and their AlphaFold3-predicted structures on DNA are similar to that of mouse NF-κB p50. Neither Aa - nor Ch -NF-κB activated transcription of an NF-κB-site reporter gene in human cells; however, Aa -NF-κB did activate transcription from a GAL4-site reporter gene in yeast, whereas Ch -NF-κB did not. Aa - and Ch -NF-κB were both constitutively located in the nucleus when expressed in vertebrate cells. Homologs of IκB-like proteins from both species interacted with their corresponding NF-κB proteins in co-immunoprecipitation assays in HEK 293T cells. These IκB-like proteins influenced the subcellular localization of their cognate NF-κB proteins in vertebrate cells, and their ankyrin repeat domains were predicted to interact with Ch -NF-κB in a manner similar to mammalian IκB and NF-κB. RNA-sequencing data from Ch animals indicate that Ch -NF-κB is expressed at high levels in early developmental stages, when Ch -IκB expression is low, suggesting that active Ch -NF-κB controls an early developmental process. In contrast, in adult animals the expression of Ch -IκB is high, suggesting that Ch -NF-κB requires a signal in order to become active. Overall, these results provide comparative information on the structure, activity, and mRNA expression of jellyfish NF-κB pathway proteins among jellyfish, and they suggest roles for NF-κB in developing and adult jellyfish.

  PublisherOA PDFDOI

• Heterogeneous NF-κB activation and enhancer features shape transcription in Drosophila immunity

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-19

  preprintOpen accessSenior authorCorresponding

  Conserved NF-κB signaling pathways shape immune responses in animals. In mammals, NF-κB activation patterns and downstream transcription vary with stimulus, cell type, and stochastic differences among identically treated cells. Whether animals without adaptive immunity exhibit similar heterogeneity or rely on distinct immune strategies remains unknown. We engineered Drosophila melanogaster S2* reporter cells as an immune-responsive model to monitor the dynamics of an NF-κB transcription factor, Relish, and downstream transcription in single, living cells. Following immune stimulation, Relish exhibits diverse nuclear localization dynamics that fall into distinct categories, with both the fraction of responsive cells and their activation speed rising with stimulus dose. Pre-stimulus features, including Relish nuclear fraction, predict a cell's responsiveness to stimulation. Simultaneous measurement of Relish and downstream transcription revealed that the probability of transcriptional bursts from immune-responsive enhancers correlates with Relish nuclear fraction. The number of NF-κB binding sites tunes transcriptional activity among immune enhancers. Our study uncovers heterogeneity in NF-κB activation and target gene expression within Drosophila, illustrating how dynamic NF-κB behavior and enhancer architecture tune gene regulation.

  PublisherOA PDFDOI

• A genome-wide survey reveals a diverse array of enhancers coordinate the <i>Drosophila</i> innate immune response

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-24

  preprintOpen accessSenior authorCorresponding

  Abstract To defend against microbes, animals regulate a complex immune response. The Drosophila innate immune system deploys a large transcriptional induction of signaling proteins, anti-microbial effectors, and other critical immune factors. This transcriptional response is encoded in enhancers, cis -regulatory sequences that modulate gene expression by binding transcription factors (TFs). While enhancers and transcription factor binding sites (TFBS) have been identified for several immune responsive genes in Drosophila , most enhancers that regulate immune-induced genes are unknown. By identifying enhancers, we can understand how their composition controls expression and contributes to infection outcome. We employed STARR-seq (Self Transcribing Active Regulatory-Region sequencing) in a hemocyte-like cell line to identify immune-specific enhancers across the D. melanogaster genome and performed ATAC-seq in hemocytes extracted from adult flies to assess the chromatin state of these enhancers before and after immune stimulus. We identified thousands of enhancers responsive to IMD stimulation, one of the two primary immune signaling pathways in Drosophila . As expected, immune enhancers are enriched for motifs of Relish, an NF-κB factor, and Kay/Jra, a bZip heterodimer pair, involved in the Imd and JNK pathways respectively, compared to enhancers active in unstimulated cells. However, when grouping enhancers by their target gene’s expression timing or functional role or by the enhancers’ chromatin accessibility pre- or post-stimulus, different groups of TFBS motifs are enriched, suggesting distinct regulatory logic for different parts of the immune response. Identification and characterization of the diverse array of enhancers that regulate the innate immune response expands our understanding of how animals fight infections.

  PublisherOA PDFDOI

• Comparison of Activities of Transcription Factor Nf-Κb from Two Jellyfish Models

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Beyond the heat shock pathway: Heat stress responses in Drosophila development

  Developmental Biology · 2024-11-16 · 3 citations

  reviewOpen accessSenior author

  Heat stress has broad effects on an organism and is an inevitable part of life. Embryos face a particular challenge when faced with heat stress - the intricate molecular processes that pattern the embryo can all be affected by heat, and the embryo lacks some of the strategies that adults can use to manage or avoid heat stress. We use Drosophila melanogaster as a model, as insects are capable of developing normally under a wide range of temperatures and are exposed to daily temperature swings as they develop. Research has focused on the heat shock pathway and the transcription of heat shock proteins as the main response to heat and heat damage. This review explores embryonic heat responses beyond the heat shock pathway. We examine the effects of heat from a biochemical standpoint, as well as highlighting other mechanisms of heat stress regulation, such as miRNA activity or other signaling pathways. We discuss how different elements of the heat stress response must be coordinated across the embryo to enable development under a wide range of temperatures. Studying heat stress in Drosophila melanogaster can be a powerful lens into how developmental systems ensure robustness to environmental factors.

  PublisherDOI

• Drosophila immune priming to Enterococcus faecalis relies on immune tolerance rather than resistance

  PLoS Pathogens · 2023-08-11 · 26 citations

  articleOpen accessSenior authorCorresponding

  Innate immune priming increases an organism's survival of a second infection after an initial, non-lethal infection. We used Drosophila melanogaster and an insect-derived strain of Enterococcus faecalis to study transcriptional control of priming. In contrast to other pathogens, the enhanced survival in primed animals does not correlate with decreased E. faecalis load. Further analysis shows that primed organisms tolerate, rather than resist infection. Using RNA-seq of immune tissues, we found many genes were upregulated in only primed flies, suggesting a distinct transcriptional program in response to initial and secondary infections. In contrast, few genes continuously express throughout the experiment or more efficiently re-activate upon reinfection. Priming experiments in immune deficient mutants revealed Imd is largely dispensable for responding to a single infection but needed to fully prime. Together, this indicates the fly's innate immune response is plastic-differing in immune strategy, transcriptional program, and pathway use depending on infection history.

  PublisherDOI

• Shadow enhancers mediate trade-offs between transcriptional noise and fidelity

  PLoS Computational Biology · 2023-05-19 · 5 citations

  articleOpen accessCorresponding

  Enhancers are stretches of regulatory DNA that bind transcription factors (TFs) and regulate the expression of a target gene. Shadow enhancers are two or more enhancers that regulate the same target gene in space and time and are associated with most animal developmental genes. These multi-enhancer systems can drive more consistent transcription than single enhancer systems. Nevertheless, it remains unclear why shadow enhancer TF binding sites are distributed across multiple enhancers rather than within a single large enhancer. Here, we use a computational approach to study systems with varying numbers of TF binding sites and enhancers. We employ chemical reaction networks with stochastic dynamics to determine the trends in transcriptional noise and fidelity, two key performance objectives of enhancers. This reveals that while additive shadow enhancers do not differ in noise and fidelity from their single enhancer counterparts, sub- and superadditive shadow enhancers have noise and fidelity trade-offs not available to single enhancers. We also use our computational approach to compare the duplication and splitting of a single enhancer as mechanisms for the generation of shadow enhancers and find that the duplication of enhancers can decrease noise and increase fidelity, although at the metabolic cost of increased RNA production. A saturation mechanism for enhancer interactions similarly improves on both of these metrics. Taken together, this work highlights that shadow enhancer systems may exist for several reasons: genetic drift or the tuning of key functions of enhancers, including transcription fidelity, noise and output.

  PublisherDOI

• Longitudinal monitoring of individual infection progression in Drosophila melanogaster

  iScience · 2022-10-17 · 1 citations

  articleOpen accessSenior authorCorresponding

  over time.

  PublisherDOI

Recent grants

• NIH Grant R00HD073191

  NIH · $745k · 2020

• Mechanisms of shadow enhancer robustness during development

  NIH · $2.7M · 2018–2029

• Uncovering the regulatory DNA logic of the Drosophila innate immune response

  NSF · $1000k · 2020–2022

• NIH Grant K99HD073191

  NIH · $258k · 2015

Frequent coauthors

• Angela H. DePace

  Harvard University

  75 shared

• Meghan D. J. Bragdon

  Boston University

  62 shared

• Javier Estrada

  45 shared

• Ben J. Vincent

  Center for Systems Biology

  31 shared

• Leonid A. Mirny

  Dana-Farber Cancer Institute

  29 shared

• Max V. Staller

  Chan Zuckerberg Initiative (United States)

  25 shared

• Francheska López-Rivera

  Boston VA Research Institute

  19 shared

• Kelly B. Eckenrode

  Harvard University

  18 shared

Labs

• Wunderlich LabPI