Biology subjects

Edgerton, S. J.

Publications and source records attributed to Edgerton, S. J..

3 recordsLinked to original sources

bioRxiv2026

Identification of transgene insertion sites via short- and long-read whole genome sequencing.

Transgenic mouse lines are essential to uncover organ or system level genotype-phenotype relationships. The generation of such lines via transgene addition may lead to the insertion into unknown genomic loci potentially leading not only to the disruption of native genes but also attenuation of transgene expression. Additionally, this often results in the inability to determine transgene zygosity which in turn complicates breeding and interpretation of experimental results. In this study we present two whole genome sequencing based pipelines that allow the identification and genotyping of even complex multi transgenic inserts. As they use widely available reagents and bioinformatic tools, they can easily be applied to develop genotyping strategies in potentially any species.

molecular biology↗

bioRxiv2025

CUT&TIME captures the history of open chromatin indeveloping neurons

Chromatin structure plays a central role in defining cell identity by regulating gene expression. During development, shifts in chromatin structure facilitate changes in gene expression needed to specify distinct cell types. To understand how changes in chromatin structure influence the developmental trajectory of neural progenitor cells, we developed CUT&TIME, a technique that uses a hyperactive 6-methyl adenosine (6mA) methyltransferase pulsed in living cells to map historical chromatin accessibility genome-wide in single cells. We show that CUT&TIME produces a record of the chromatin landscape during neurogenesis in the developing retina, specifically as neural progenitors produce the major projection neuron type, retinal ganglion cells (RGCs). We further show that this method is compatible with single cell profiling technologies, which allows us to visualize and capture the diversity of chromatin states that produce RGCs. Additionally, we identify changes in promoter accessibility associated with the transition from progenitor to RGC. Together, these data demonstrate that CUT&TIME captures a historical record of chromatin structure, which can be used to identify early changes in accessibility associated with cell-fate commitment.

developmental biology↗

bioRxiv2024

Ciliary marginal zone of the developing human retina maintains retinal progenitor cells until late gestational stages

Non-mammalian vertebrates maintain a proliferative stem cell population at the far periphery of their retina called the ciliary marginal zone (CMZ), which gives rise to all retinal cell types and contributes to retinal regeneration upon injury. Humans do not maintain a proliferative CMZ into adulthood; however, it is not known how long in development this region continues to generate new neurons. Here, we identify a population of cells in the far peripheral retina of the fetal human that continues to proliferate long after the rest of the retina is quiescent. Single cell RNA-sequencing and EdU tracing at late time points in development reveal that this region has features of the non-mammalian CMZ, including the capacity to produce both early and late born cell types at late developmental stages, and a longer cell cycle than more centrally located retinal progenitor cells (RPCs). Moreover, while more central RPCs exit the cell cycle with the addition of a TGF{beta}-inhibitor, we show that early RPCs within the CMZ do not. These findings define the late stages of neurogenesis in human retinal development, and present a unique model system to study the fetal CMZ in humans.

developmental biology↗