About

Shelby Blythe, Ph.D., is a Principal Investigator at the Blythe Lab. The page lists her as a member and provides her title but does not include specific details about her research focus, background, or key contributions. Therefore, no additional biographical information is available from the provided text.

Research topics

• Genetics
• Biology
• Computational biology
• Cell biology

Selected publications

• Author response: Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

  2025-09-24

  peer-reviewOpen accessSenior author

  During zygotic genome activation (ZGA) in Drosophila, broad domains of Polycomb-modified chromatin are rapidly established across the genome. Here, we investigate the spatial and temporal dynamics by which Polycomb group (PcG) histone modifications, H3K27me3 and H2Aub, emerge during early embryogenesis. Using ChIP-seq and live imaging of CRISPR-engineered GFP-tagged PcG components, we show that PRC2-dependent H3K27me3 accumulates adjacent to a subset of E(z)-bound prospective Polycomb Response Elements (PREs) beginning in nuclear cycle 14 (NC14), with patterns indicative of nucleation followed by spreading. Surprisingly, PRE-binding factors Pho, Combgap, and GAGA-factor are excluded from interphase nuclei prior to NC10 despite nuclear localization of E(z) throughout early interphases. Loss-of-function studies further demonstrate that GAGA-factor is largely dispensable for PcG domain establishment, whereas the pioneer factor Zelda is required for proper deposition of H3K27me3 and H2Aub at a subset of Polycomb domains. The role of Zelda at Polycomb domains is context-dependent; a large subset of targets requires Zelda not for PcG factor recruitment, but instead to license a loaded PRE to deposit H3K27me3 and H2Aub. Our findings support a model where licensing of PcG domains is an initial step in the regulatory processes governing Polycomb-regulated developmental genes.

  PublisherDOI

• Lower-order methylation states underlie the maintenance and re-establishment of Polycomb modifications in <i>Drosophila</i> embryogenesis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-29

  preprintOpen accessSenior authorCorresponding

  SUMMARY Polycomb Group (PcG) proteins regulate the chromatin composition of an embryo by facilitating the mono, di, and tri-methylation of Histone H3 Lysine 27 (H3K27me1/2/3). For the zygote to inherit an H3K27 methylation blueprint from its mother, PcG-modified states established during oogenesis must persist through early embryogenesis until the onset of large-scale zygotic transcription (Zygotic Genome Activation, ZGA). However, questions have persisted regarding the relative contributions of two molecular mechanisms to the propagation of H3K27 methylation through early development: 1) allosteric regulation of the H3K27 methyltransferase Enhancer of Zeste (E(z)) by existing H3K27me2/3, and 2) nucleation of E(z) activity at chromatin by DNA binding factors. Here, we investigate how allostery and nucleation contribute to H3K27 methylation dynamics in early Drosophila embryogenesis by developing and experimentally validating a mathematical model. This model incorporates measurements of the nuclear concentration dynamics of E(z) and the Polycomb Response Element binding factor Pleiohomeotic (Pho), as well as the dilution of epigenetic modifications at DNA replication with the incorporation of histones to nascent chromatin. With stochastic simulations and in vivo experiments, we assert that allosteric regulation of E(z) maintains a PcG-imprint on maternal chromosomes in the form of lower-order H3K27 methylation states (H3K27me1/2), that de novo establishment of H3K27 methylation at paternal chromosomes relies on nucleation of E(z) activity by Pho, and that broad H3K27me3 domains at both maternal and paternal chromosomes are re-established at ZGA. This work provides a mechanistic explanation for the inheritance of Polycomb states in contexts of intense cellular proliferation.

  PublisherOA PDFDOI

• Rapid transcriptional response to a dynamic morphogen by time integration

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-09

  preprint

  Abstract During development, cells must interpret extracellular signals with speed and accuracy. While morphogen gradients pattern tissues, how cells respond to dynamic morphogens remains unclear. Here, we investigate how dorsal patterning in the Drosophila embryo is specified by a rapidly evolving BMP gradient. Using a live reporter of BMP pathway activity and nascent transcription reporters, we find that gene expression is best predicted by time integration of BMP signaling, rather than instantaneous levels. However, in sog mutant embryos with broad BMP activity, integration alone fails to predict gene expression outside the normal domain. We show that the transcription factor Zen lowers the signaling threshold required for activation, enabling integration to drive rapid transcriptional responses even at low BMP levels. Together, these results suggest that cells interpret dynamic morphogen signals through the combined action of temporal integration and spatial competence, providing a framework for robust pattern formation on fast developmental timescales.

  PublisherDOI

• Bicoid-nucleosome competition sets a concentration threshold for transcription constrained by genome replication

  Cell Reports · 2025-08-01

  articleOpen accessSenior author

  Transcription factors (TFs) regulate gene expression despite constraints from chromatin structure and the cell cycle. Here, we examine the concentration-dependent regulation of hunchback by the Bicoid morphogen through a combination of quantitative imaging, mathematical modeling, and epigenomics in Drosophila embryos. By live imaging of MS2 reporters, we find that, following mitosis, the timing of transcriptional activation driven by the hunchback P2 (hbP2) enhancer directly reflects Bicoid concentration. We build a stochastic model that can explain in vivo onset time distributions by accounting for both the competition between Bicoid and nucleosomes at hbP2 and a negative influence of DNA replication on transcriptional elongation. Experimental modulation of nucleosome stability alters onset time distributions and the posterior boundary of hunchback expression. We conclude that TF-nucleosome competition is the molecular mechanism whereby the Bicoid morphogen gradient specifies the posterior boundary of hunchback expression.

  PublisherOA PDFDOI

• Breaking anterior-posterior symmetry in the moth fly <i>Clogmia albipunctata</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-14 · 1 citations

  preprintOpen access

  Abstract Establishing the anterior-posterior (AP) body axis is a fundamental process during embryogenesis, and the fruit fly, Drosophila melanogaster , provides one of the best-known case studies. But for unknown reasons, different species of flies (Diptera) establish the AP axis through unrelated, structurally distinct anterior determinants (ADs). The AD of Drosophila, Bicoid (Bcd), initiates symmetry-breaking during nuclear cleavage cycles (NCs) when ubiquitous pioneer factors, such as Zelda (Zld), drive zygotic genome activation (ZGA) at the level chromatin accessibility by nucleosome depletion. While Bcd engages in a concentration-dependent competition with nucleosomes at the loci of a small set of transcription factor (TF) genes that are expressed in the anterior embryo, it remains unknown whether unrelated ADs of other fly species function in the same way and target homologous genes. We have examined the symmetry-breaking mechanism of a moth fly, Clogmia albipunctata , in which a maternally expressed transcript isoform of the pair-rule segmentation gene odd-paired serves as AD. We provide a de novo assembly and annotation of the Clogmia genome and describe how Clogmia’s orthologs of zelda ( Cal-zld ) and odd-paired ( Cal-opa ) affect chromatin accessibility and gene expression. Our results suggest direct roles of Cal-zld in opening and closing chromatin during nuclear cleavage cycles (NCs) and show that during the early phase of ZGA maternal Cal-opa activity promotes chromatin accessibility and anterior expression at Clogmia’s homeobrain and sloppy-paired loci. These genes are not known as key targets of Bcd but may serve a more widely conserved role in the initiation of anterior pattern formation given their early anterior expression and function in head development in insects. We conclude that the ADs of Drosophila and Clogmia differ in their target genes but share the mechanism of concentration-dependent nucleosome depletion.

  PublisherOA PDFDOI

• Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-03 · 2 citations

  preprintOpen accessSenior authorCorresponding

  , broad domains of Polycomb-modified chromatin are rapidly established across the genome. Here, we investigate the spatial and temporal dynamics by which Polycomb group (PcG) histone modifications, H3K27me3 and H2Aub, emerge during early embryogenesis. Using ChIP-seq and live imaging of CRISPR-engineered GFP-tagged PcG components, we show that PRC2-dependent H3K27me3 accumulates adjacent to a subset of E(z)-bound prospective Polycomb Response Elements (PREs) beginning in nuclear cycle 14 (NC14), with patterns indicative of nucleation followed by spreading. Surprisingly, PRE-binding factors Pho, Combgap, and GAGA-factor are excluded from interphase nuclei prior to NC10 despite nuclear localization of E(z) throughout early interphases. Loss-of-function studies further demonstrate that GAGA-factor is largely dispensable for PcG domain establishment, whereas the pioneer factor Zelda is required for proper deposition of H3K27me3 and H2Aub at a subset of Polycomb domains. The role of Zelda at Polycomb domains is context-dependent; a large subset of targets requires Zelda not for PcG factor recruitment, but instead to license a loaded PRE to deposit H3K27me3 and H2Aub. Our findings support a model where licensing of PcG domains is an initial step in the regulatory processes governing Polycomb-regulated developmental genes.

  PublisherOA PDFDOI

• Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

  eLife · 2025-09-24 · 1 citations

  preprintOpen accessSenior author

  Abstract During zygotic genome activation (ZGA) in Drosophila, broad domains of Polycomb-modified chromatin are rapidly established across the genome. Here, we investigate the spatial and temporal dynamics by which Polycomb group (PcG) histone modifications, H3K27me3 and H2Aub, emerge during early embryogenesis. Using ChIP-seq and live imaging of CRISPR-engineered GFP-tagged PcG components, we show that PRC2-dependent H3K27me3 accumulates adjacent to a subset of E(z)-bound prospective Polycomb Response Elements (PREs) beginning in nuclear cycle 14 (NC14), with patterns indicative of nucleation followed by spreading. Surprisingly, PRE-binding factors Pho, Combgap, and GAGA-factor are excluded from interphase nuclei prior to NC10 despite nuclear localization of E(z) throughout early interphases. Loss-of-function studies further demonstrate that GAGA-factor is largely dispensable for PcG domain establishment, whereas the pioneer factor Zelda is required for proper deposition of H3K27me3 and H2Aub at a subset of Polycomb domains. The role of Zelda at Polycomb domains is context-dependent; a large subset of targets requires Zelda not for PcG factor recruitment, but instead to license a loaded PRE to deposit H3K27me3 and H2Aub. Our findings support a model where licensing of PcG domains is an initial step in the regulatory processes governing Polycomb-regulated developmental genes.

  PublisherDOI

• Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

  eLife · 2025-09-24

  articleOpen accessSenior author

  Abstract During zygotic genome activation (ZGA) in Drosophila, broad domains of Polycomb-modified chromatin are rapidly established across the genome. Here, we investigate the spatial and temporal dynamics by which Polycomb group (PcG) histone modifications, H3K27me3 and H2Aub, emerge during early embryogenesis. Using ChIP-seq and live imaging of CRISPR-engineered GFP-tagged PcG components, we show that PRC2-dependent H3K27me3 accumulates adjacent to a subset of E(z)-bound prospective Polycomb Response Elements (PREs) beginning in nuclear cycle 14 (NC14), with patterns indicative of nucleation followed by spreading. Surprisingly, PRE-binding factors Pho, Combgap, and GAGA-factor are excluded from interphase nuclei prior to NC10 despite nuclear localization of E(z) throughout early interphases. Loss-of-function studies further demonstrate that GAGA-factor is largely dispensable for PcG domain establishment, whereas the pioneer factor Zelda is required for proper deposition of H3K27me3 and H2Aub at a subset of Polycomb domains. The role of Zelda at Polycomb domains is context-dependent; a large subset of targets requires Zelda not for PcG factor recruitment, but instead to license a loaded PRE to deposit H3K27me3 and H2Aub. Our findings support a model where licensing of PcG domains is an initial step in the regulatory processes governing Polycomb-regulated developmental genes.

  PublisherDOI

• Bicoid-nucleosome competition sets a concentration threshold for transcription constrained by genome replication

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-12 · 2 citations

  preprintOpen accessSenior authorCorresponding

  SUMMARY Transcription factors (TFs) regulate gene expression despite constraints from chromatin structure and the cell cycle. Here we examine the concentration-dependent regulation of hunchback by the Bicoid morphogen through a combination of quantitative imaging, mathematical modeling and epigenomics in Drosophila embryos. By live imaging of MS2 reporters, we find that, following mitosis, the timing of transcriptional activation driven by the hunchback P2 ( hb P2) enhancer directly reflects Bicoid concentration. We build a stochastic model that can explain in vivo onset time distributions by accounting for both the competition between Bicoid and nucleosomes at hb P2 and a negative influence of DNA replication on transcriptional elongation. Experimental modulation of nucleosome stability alters onset time distributions and the posterior boundary of hunchback expression. We conclude that TF-nucleosome competition is the molecular mechanism whereby the Bicoid morphogen gradient specifies the posterior boundary of hunchback expression.

  PublisherOA PDFDOI

• Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression

  Developmental Cell · 2023-07-20 · 29 citations

  articleOpen access
  PublisherOA PDFDOI

Recent grants

• Mechanisms for Measuring the Nucleocytoplasmic Ratio in Early Embryogenesis

  NIH · $163k · 2012–2015

Frequent coauthors

• Eric Wieschaus

  Princeton University

  27 shared

• Peter S. Klein

  University of Pennsylvania

  14 shared

• Colleen E Hannon

  Howard Hughes Medical Institute

  9 shared

• Yong-Jae Kwon

  Northwestern University

  6 shared

• Greg J. Beitel

  Northwestern University

  6 shared

• Joseph Q. Nguyen

  Northwestern University

  6 shared

• Kevin G. Nyberg

  Northwestern University

  6 shared

• Richard W. Carthew

  6 shared

Labs

• Blythe LabPI

Education

• Ph.D.

  University of Pennsylvania

  2009

Awards & honors

• Pew Scholar in the Biomedical Sciences, 2020