Biology subjects

Grow, E. J.

Publications and source records attributed to Grow, E. J..

6 recordsLinked to original sources

bioRxiv2026

ECHOS enables spatial epigenome profiling at subcellular resolution

Biological structures and the epigenome are intertwined. For example, complex tissues are often the combined products of various groups of spatially patterned cell types with distinct epigenetic states. Furthermore, chromatin at various subnuclear locations within a cell often differ in their epigenetic properties. Thus, a systematic understanding of the relationship between the epigenome and its spatial distribution across biological scales would inform tissue and cellular functions as well as gene regulatory mechanisms. Yet, spatially resolved epigenome profiling--particularly at subcellular resolution--remains technically challenging. Here, we present Epigenetic CUT&Tag via High-resolution Optical Selection (ECHOS), a platform that combines high-resolution imaging and high-throughput sequencing to enable precise, spatially targeted epigenetic profiling across biological scales. At the cellular scale, ECHOS generates high-quality DNA-binding protein and histone modification datasets that show strong concordances with datasets from ChIP-seq and CUT&Tag experiments. Further optimization of ECHOS (ECHOS+) enables the characterization of the histone modification landscape of chromatin at the sub-micron resolution. Using ECHOS+, we revealed distinct gene regulatory logics at different layers of human ectocervical epithelium. We also showed that micronuclei--small nucleus-like structures formed by mitotic errors--exhibited a different epigenetic state from the same chromosome regions on the intact nuclei. Finally, we found that human aging altered the epigenetic state of the inactive X chromosome located in a subcellular nuclear structure called the Barr body, which may contribute to genes escaping X chromosome inactivation during female aging. Together, ECHOS and ECHOS+ represent a scalable and generalizable framework for spatial epigenomic analyses, with broad potential applications in various domains of biology.

genetics↗

bioRxiv2026

Spindle pole proteins confine chromosomes to ensure their expulsion during female meiosis

Animal oocytes undergo highly asymmetric divisions to expel excess copies of their genome into compact cells called polar bodies. This requires tight clustering and cortical positioning of meiotic chromosomes, yet the mechanism remains incompletely understood. Using C. elegans oocytes, we found that the meiotic spindle pole protein ZYG-9/ch-TOG delocalizes from microtubules to spread along the surface of chromosomes and prevent their dispersal in meiotic anaphase. This effect was more pronounced in the absence of the spindle, where ZYG-9 formed into a micron-scale droplet that enveloped all chromosomes. Purified ZYG-9 was sufficient to bind DNA and coat reconstituted chromatin. Mutations that perturb ZYG-9-DNA binding impaired chromosome packaging into polar bodies, resulting in oocytes carrying extra chromosomes and reduced fertility. We propose that liquid-like assemblies of spindle pole proteins are repurposed as surface-acting glue to tightly package meiotic chromosomes into polar bodies, thus ensuring oocytes have the correct genome copy number.

cell biology↗

bioRxiv2024

Mapping Chromatin Interactions of ZBP1 and ADAR Z-Alpha Domains: A ChIP-Seq Based Comparison

The DNA double helix typically exists in the canonical B-form conformation, but this structure often can adopt the unique alternative form known as Z-DNA. In Z-DNA, the DNA helix winds to the left in a zigzag pattern instead of the right-handed B-DNA form. Z-DNA is thought to play a key role in transcription, but it is unclear whether is a positive or negative regulator of RNA polymerase activity. Additionally, several studies have shown how Z-DNA contributes to DNA damage or genome instability. However, the precise role of Z-DNA in the genome remains unclear. To address this question, we mapped Z-DNA using a ChIP-Seq assay with two Z-DNA biosensors: Zaa-Zbp1, comprised of a dimerized Z-alpha Z-DNA binding domains from Z-DNA binding protein 1 (Zbp1), and Zaa-Adar1, comprised of dimerized Z-alpha domains from Adenosine deaminase acting on RNA 1 (Adar1). We found that these Zaa probes possessed similar binding profiles when analyzed with motif analysis, but gene ontology analysis revealed that these Z-alpha domains bound to heterogeneous genes, with Zaa-Zbp1 most strongly binding to genes in the RHOQ-GTPase pathway and Zaa-Adar1 binding to genes involved in the M phase of the cell cycle.

genomics↗

bioRxiv2023

Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation

Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating [~]84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.

developmental biology↗

bioRxiv2023

Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program

The embryonic transcription factor DUX regulates chromatin opening and gene expression in totipotent cleavage-stage mouse embryos, and its expression in embryonic stem cells promotes their conversion to 2-cell embryo-like cells (2CLCs) with extraembryonic potential. However, little is known regarding which domains within mouse DUX interact with particular chromatin and transcription regulators. Here, we reveal that the C-terminus of mouse DUX contains five uncharacterized [~]100 amino acid (aa) repeats followed by an acidic 14 amino acid tail. Unexpectedly, structure-function approaches classify two repeats as active and three as inactive in cleavage/2CLC transcription program enhancement, with differences narrowed to a key 6 amino acid section. Our proximity dependent biotin ligation (BioID) approach identified factors selectively associated with active DUX repeat derivatives (including the 14aa tail), including transcription and chromatin factors such as SWI/SNF (BAF) complex, as well as nucleolar factors that have been previously implicated in regulating the Dux locus. Finally, our mechanistic studies reveal cooperativity between DUX active repeats and the acidic tail in cofactor recruitment, DUX target opening, and transcription. Taken together, we provide several new insights into DUX structure-function, and mechanisms of chromatin and gene regulation.

developmental biology↗

bioRxiv2021

Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos

Transposable elements threaten genome stability, and the Piwi-piRNA system has evolved to silence transposons in the germline1-6. However, it remains largely unknown what mechanisms are utilized in early vertebrate embryos prior to germline establishment and ping-pong piRNA production. To address this, we first characterized small RNAs in early zebrafish embryos and detected abundant maternally-deposited, Ziwi-associated, antisense piRNAs that map largely to evolutionarily young long terminal repeat (LTR) retrotransposons. Notably, the focal establishment of the repressive modification H3K9me2/3 coincides with these young LTR elements, is deposited independent of transcription, and is required for LTR silencing. We find piRNAs highly enriched and maintained in primordial germ cells (PGCs), which display lower LTR expression than somatic cells. To examine the consequences of piRNA loss, we used reciprocal zebrafish-medaka hybrids, which display selective activation of LTRs that lack maternally-contributed targeting piRNAs. Thus, the Piwi-piRNA system actively antagonizes transposons in the soma and PGCs during early vertebrate embryogenesis.

developmental biology↗