Shelby Blythe Developmental control of chromatin structure & embryo pattern formation

Research Interests

At any moment, the developmental state of a cell is reflected directly in chromatin structure, and the organization of this structure changes rapidly during embryogenesis in response to developmental cues. Yet, the mechanistic underpinnings of these transitions in chromatin structure, particularly in response to developmental signals, is poorly understood. My laboratory uses the Drosophila embryo as a model system to study the mechanisms that establish the chromatin architecture of pluripotent embryonic cells from an unpatterned ground state. Our goal is to understand both the molecular determinants for specification of ‘active’ versus ‘repressed’ chromatin, and also how developmental signals provide information to alter chromatin states over time. We combine the power of Drosophila genetics with genomic methods for interrogating chromatin accessibility and occupancy, in addition to developing confocal imaging approaches for quantitative assessment of chromatin state.

Current projects include measuring changes in chromatin accessibility status in the absence of all developmental patterning cues; functional studies on transcription factors such as Bicoid that are associated with chromatin modifying activities; genetic screening for mutants that disrupt the pluripotent chromatin state; and development of optical tools for direct assessment of local chromatin accessibility status in real time.

To see a full list of publications, click here to see Shelby Blythe's NCBI bibliography. Current and former IBiS students in blue.

Selected Publications

Lower-order methylation states underlie the maintenance and re-establishment of Polycomb modifications in Drosophila maternal to zygotic transition. Gonzaga-Saavedra N, Degen EA, Soluri IV, Croslyn C, Blythe SA. bioRxiv 2025.07.02.662854; doi: https://doi.org/10.1101/2025.07.25.666882.

Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition. Gonzaga-Saavedra N, Degen EA, Soluri I, Croslyn C, Blythe SA. bioRxiv 2025.07.02.662854; doi: https://doi.org/10.1101/2025.07.02.662854.

Bicoid-nucleosome competition and genome replication constrain concentration sensitive transcription. Degen EA, Croslyn C, Mangan N, Blythe SA. Accepted, in press at Cell Reports, preprint available at https://doi.org/10.1101/2024.12.10.627802.

Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression. Gaskill MM, Soluri IV, Branks AE, Boka AP, Stadler MR, Vietor K, Huang HS, Gibson TJ, Mukherjee A, Mir M, Blythe SA, and Harrison MM. Developmental Cell. 2023 July 20:online ahead of print.

Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. Soluri IV, Zumerling LM, Payan Parra OA, Clark EG, and Blythe SA. eLife. 2020 April 29;9:e53916.