Biology subjects

Grimm, S. A.

Publications and source records attributed to Grimm, S. A..

18 recordsLinked to original sources

bioRxiv2026

Short-term methionine starvation induces de novo diurnal oscillations of hepatic m6A RNA methylation

Dietary methionine restriction has been shown to improve metabolic health and treat multiple diseases. Methionine metabolism regulates transmethylation reactions, including N6-methyladenosine (m6A) RNA methylation, by modulating the availability of S-adenosyl methionine (SAM). Both m6A RNA methylation and methionine metabolism are involved in the regulation of the circadian clock. However, it remains unclear whether dietary methionine influences circadian rhythms through the regulation of m6A RNA modification. In this study, we investigated the effects of short-term methionine deprivation on the diurnal oscillations of m6A RNA methylation in the mouse liver. We found that a methionine-deficient (MD) diet reprogrammed the cyclic expression patterns of m6A writers, erasers, and readers. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that the MD diet induced de novo diurnal m6A oscillations in genes associated with RNA processing, protein translation, protein ubiquitination, and mTORC1 signaling pathways. RNA-seq and quantitative proteomics analyses demonstrated that MD-induced changes in m6A RNA levels were linked to alterations in mRNA and protein abundance. We observed that dynamic m6A RNA methylation of the transcripts encoding two key enzymes, MAT2A and CBS, helps maintain methionine homeostasis in response to methionine starvation. These findings identify m6A RNA methylation as a key mechanism linking methionine metabolism to circadian regulation.

molecular biology↗

bioRxiv2026

Aging restricts colorectal tumor growth by epigenetically silencing developmental gene programs

The incidence of early-onset colorectal cancer (CRC) has risen sharply in recent decades1, yet the biological basis underlying the distinct behavior of tumors arising in young versus aged tissues remains poorly understood. Here we show that aging reprograms the epigenetic landscape of the colon, restricting colon tumor growth through stable silencing of developmental and fetal gene programs. We find that colon tumors arising in aged mice are intrinsically less proliferative than those arising in young animals. Multi-omic profiling of normal colon and colon tumors reveals that aging drives DNA hypermethylation, loss of Polycomb-associated chromatin states, and reduced chromatin accessibility at a defined set of developmental genes that are bivalent (marked by both H3K27me3 and H3K4 methylation), transcriptionally active in colon tumors from young animals and repressed in both tumors and normal tissue from old animals. Among the genes most strongly repressed in old animals is Tacstd2 (Trop2), a regulator of fetal intestinal programs and epithelial stemness. Pharmacologic inhibition of DNA methylation reactivates the aging-silenced gene network in organoids from old animals, whereas genetic disruption of Tacstd2 suppresses growth and developmental transcriptional programs in young tumor organoids. TACSTD2, fetal gene signatures, and the aging-associated bivalent gene program are likewise repressed in late-onset vs. early-onset human colorectal cancers. Collectively, these findings identify age-associated epigenetic silencing of developmental gene programs as a causal mechanism that constrains colorectal tumor growth and provide a mechanistic framework for understanding the distinct biology of early-onset colorectal cancer.

cancer biology↗

bioRxiv2026

Methionine Deprivation-induced Reprogramming of Hepatic Rhythms Is Mediated by Glucocorticoid Receptor

The circadian clock tightly interacts with cellular metabolism, and nutritional challenges can profoundly remodel its function. Dietary methionine restriction has been shown to improve metabolic health and extend lifespan. However, whether and how dietary methionine restriction impacts the circadian clock is unclear. Here, we demonstrate that methionine deprivation (MD) in the mouse induces alterations in multiple signaling systems, inducing rhythmic biological events in liver that are entrained by feeding time rather than day/light cycles. Alteration in growth factor signaling leads to loss of activation of a pioneer transcription factor, STAT5, which normally directs rhythmic chromatin localization of the glucocorticoid receptor (GR). Loss of active STAT5 leads to reprogramming of the epigenome and of the GR-directed transcriptome in a manner abolished by liver-specific deletion of GR. These results demonstrate that dietary methionine restriction remodels the circadian biological program directed by glucocorticoid receptor.

genomics↗

bioRxiv2026

GLIS3 is a key regulator of astrocyte differentiation in human neural stem cells

Astrocytes play a key role in neuronal homeostasis and in various neural disorders. The generation of astrocytes from neural progenitor cells (NPCs) and its functions are under a complex control of several signaling networks and transcription factors. In this study, we demonstrate that the transcription factor, GLIS similar 3 (GLIS3), which has been implicated in several neurodegenerative diseases, is highly expressed in astrocytes, and is required for the efficient differentiation of human NPCs into astrocytes. Loss of GLIS3 function greatly impairs astrocytes differentiation, resulting in reduced expression of astrocyte markers, whereas expression of exogenous GLIS3 restores the induction of astrocyte specific genes indicating a critical role for GLIS3 in astrocyte differentiation. Integrated transcriptomic and cistromic analyses revealed that GLIS3 directly regulates the transcription of several astrocyte-associated genes, including GFAP, SLC1A2, NFIA, and ATF3, in coordination with lineage-determining factors, such as STAT3, NFIA, and SOX9. We hypothesize that GLIS3 dysfunction disrupts this transcriptional network thereby contributing to astrocyte-associated neurological disorders. Identification of GLIS3 as a key regulator of astrocyte differentiation and gene expression will advance our understanding of its role in neurodegenerative diseases and may provide a new therapeutic target.

developmental biology↗

bioRxiv2026

Neonatal diethylstilbestrol exposure disrupts uterine epithelial apical-basal polarity and partial EMT state

The developing female reproductive tract is highly sensitive to external hormonal stimulation, which can result in infertility and gynecologic diseases. To determine the underlying mechanisms, we used a mouse model to test the immediate, cell type-specific effects of neonatal exposure to the estrogenic chemical, diethylstilbestrol (DES), on the developing uterus. We found that control uterine epithelium is in a partial epithelial-mesenchymal transition state that is lost following DES exposure. This is accompanied by evidence of premature differentiation including altered apical-basal cell polarity and absence of the Lgr5+ epithelial stem cell population required for uterine gland formation. Cell-cell communication between epithelial and mesenchymal cells is restructured, and Wnt signaling is persistently reduced. The DES-exposed uterine mesenchyme has early signs of fibrosis through increased deposition of extracellular matrix collagen.Mechanistically, DES exposure causes cell type-specific changes in chromatin accessibility and gene expression, most prominently in epithelial cells. These changes can be explained in part by cell-specific alterations in chromatin looping at enhancer regions in concert with alterations in ER binding. These findings suggest that reprogramming cell type-specific differentiation trajectories and extracellular matrix characteristics underlie the long-term phenotypic effects of developmental exposure to estrogenic endocrine disrupting chemicals. These changes lead to functional impairment of adult tissues and increased cancer risk. Significance StatementUterine development is strongly impacted by brief exposure to estrogenic endocrine disruptors, but it is unclear why development is such a sensitive time point. This study employed multiomic analysis to identify cell type-specific uterine developmental trajectories in neonatal mice exposed to the estrogenic chemical, diethylstilbestrol, and compared these to controls. Control epithelium was under the influence of carefully orchestrated Wnt/{beta}-catenin signaling and was in a partial epithelial-to-mesenchymal transition state. DES exposure repressed Wnt/{beta}-catenin signaling and drove the epithelium toward full differentiation, resulting in the loss of both epithelial stem cells and normal apical-basal polarity. These changes provide an explanation for how endocrine disruptors can divert intrinsically programmed developmental trajectories to alter adult organ function.

developmental biology↗

bioRxiv2026

Identification of distinct functions of GLIS3 in β-cell generation critical to prevention of neonatal diabetes

GLIS3 plays a critical role in pancreatic {beta} cells and diabetes, being one of only a few genes implicated in Type 1, Type 2, and Gestational diabetes. In addition to {beta} cells, GLIS3 is expressed embryonically in bipotent and proendocrine progenitor cells, suggesting a role in endocrine lineage development in mice. We hypothesize that GLIS3 is playing important roles in endocrine development as well as during {beta} cell differentiation. We utilized single cell RNA-sequencing at three different timepoints (embryonic day (e)13.5, e15.5, and e18.5) and single nucleus (sn)ATAC-sequencing at e15.5 in both wild type (WT) and Glis3 Knockout (Glis3KO) mouse embryos. This analysis revealed that the numbers of bipotent, proendocrine progenitor, and all subsequent endocrine cells were proportionately reduced in Glis3KO mice. Additionally, loss of GLIS3 function generates a unique subpopulation of cells that fail to upregulate Ins2 transcription and downregulate expression of several ribosomal and oxidative phosphorylation genes normally repressed during pre{beta} to {beta} cell differentiation. Our study therefore shows that GLIS3 regulates two distinct stages: the embryonic generation/differentiation of bipotent cells and the differentiation of pre{beta} to {beta} cells. Dysregulation of these two stages provides a causal mechanism for the development of neonatal diabetes in GLIS3-deficiency.

developmental biology↗

bioRxiv2025

Discovery and performance of DNA methylation panels for cancer detection and classification in blood

Examining DNA in a liquid biopsy for non-invasive cancer detection relies on identifying dilute signal in a high background. This study aims to identify DNA methylation biomarkers for multi-cancer detection. Utilizing large tissue datasets, we apply novel search algorithms to discover confined biomarker panels capable of distinguishing tumor from normal and determining the tissue of origin. We explore the applicability to blood-based testing using targeted methylation sequencing followed by machine learning classification. We present an 8-marker panel, which successfully predicts tumors across 14 types with a 91% average sensitivity, maintaining a low false positive rate (< 0.04%). Additionally, a panel of 39 CpG sites exhibits accuracies ranging from 69% to 98% for identifying tissue of origin. When tested on 114 patient plasma samples (colon, liver, pancreatic, prostate, and stomach cancer), the 8-marker panel obtains an AUC of 0.78 with a 78% sensitivity among 32 early-stage patients (stage I-II), and 60% overall. Using the 39-marker panel in a multi-class classification model selecting only the best match, 54% of tumor samples were on average correctly assigned to the tissue of origin, and up to 80% when allowing more inclusive criteria. Using a limited set of biomarkers, our work contributes to advancing non-invasive cancer diagnostics.

cancer biology↗

bioRxiv2025

Glycogen metabolism in mouse embryonic Sertoli cells sustains the germ line through the lactate shuttle

Metabolites are key regulators of cell fate decisions, epigenetic remodeling, and lineage commitment. While genetic pathways governing testis differentiation are well studied, the role of metabolism remains poorly understood. In this study, we investigated a transient, male-specific accumulation of glycogen in supporting (Sertoli) cells of embryonic testis in mice. Although glycogen metabolism was dispensable for Sertoli cell differentiation, its disruption led to reduced lactate production and impaired PGCs ability to colonize the newly forming testis cords. Inhibiting lactate transport further revealed a critical metabolic coupling between Sertoli and germ cells during early testis development. Surprisingly, external lactate or glucose supplementation failed to rescue the germ cell phenotype. These findings suggest that glycogen accumulation supports a critical developmental window in which both Sertoli and germ cells are metabolically constrained and unable to rely on external carbon sources. This highlights a sensitive period during testicular development where nutrient scarcity could have long-term consequences for fertility.

developmental biology↗

bioRxiv2023

Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4

Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here we determine the roles of CHD4 to enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility at transcription factor binding sites; its depletion leads to altered motif scanning and redistribution of transcription factors to sites not previously occupied. During GATA3-mediated cellular reprogramming, CHD4 activity is necessary to prevent inappropriate chromatin opening and enhancer licensing. Mechanistically, CHD4 competes with transcription factor-DNA interaction by promoting nucleosome positioning over binding motifs. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents inappropriate gene expression by editing binding site selection by transcription factors.

genomics↗

bioRxiv2022

Contribution of the Wolffian duct mesenchyme to the formation of the female reproductive tract

The female reproductive tract develops from its embryonic precursor, the Mullerian duct. In close proximity to the Mullerian duct lies the precursor for the male reproductive tract, the Wolffian duct, which is eliminated in the female embryo during sexual differentiation. We discovered that a component of the Wolffian duct, its mesenchyme, is not eliminated after sexual differentiation. Instead, the Wolffian duct mesenchyme underwent changes in transcriptome and chromatin accessibility from male tract to female tract identity, and became a unique mesenchymal population in the female reproductive tract with localization and transcriptome distinct from the mesenchyme derived from the Mullerian duct. Partial ablation of the Wolffian duct mesenchyme stunted the growth of the fetal female reproductive tract. These findings reveal a new fetal origin of mesenchymal tissues for female reproductive tract formation and reshape our understanding of sexual differentiation of reproductive tracts. Significance statementA female embryo initially possesses both the primitive female and male reproductive tracts, also known as the Mullerian and Wolffian duct. During sexual differentiation, the female eliminates the Wolffian duct and maintains the Mullerian duct that eventually differentiates into the female reproductive tract organs. However, in this paper, we show the female embryo retains mesenchymal cells surrounding the Wolffian duct for its reproductive tract formation. When incorporated into the female reproductive tract organs, the Wolffian duct mesenchyme shows unique anatomical localization and transcriptome and plays critical roles in female reproductive tract growth. This discovery provides new insights into female reproductive tract development and advances our understanding of sexual differentiation of reproductive tracts.

developmental biology↗

bioRxiv2021

CUT&Tag-BS: an efficient and low-cost method for simultaneous profiling of histone modification and DNA methylation

It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic localization of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS shows similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further reveals that H3K4me1-marked regions are mostly CpG-poor, lack methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenarios with precious biological samples.

genomics↗

bioRxiv2021

GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans

Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open- angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, is the major cause of elevated IOP. Here, we demonstrate that mice deficient in the Kruppel- like zinc finger transcriptional factor GLI-similar-1 (GLIS1) develop chronically elevated IOP. Magnetic resonance imaging and histopathological analysis reveal that deficiency in GLIS1 expression induces progressive degeneration of the TM, leading to inefficient AqH drainage from the anterior chamber and elevated IOP. Transcriptome and cistrome analyses identified several glaucoma- and extracellular matrix-associated genes as direct transcriptional targets of GLIS1. We also identified a significant association between GLIS1 variant rs941125 and glaucoma in humans (P=4.73x10-6), further supporting a role for GLIS1 into glaucoma etiology. Our study identifies GLIS1 as a critical regulator of TM function and maintenance, AqH dynamics, and IOP.

molecular biology↗

bioRxiv2021

Low-input ATAC&mRNA-Seq: a simple and robust method for simultaneous dual-omics profiling with low cell number

Deciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. Single-cell multi-omics technologies have been developed for concurrent profiling of chromatin accessibility and gene expression. However, multi-omics profiling of low-input bulk samples remains challenging. Therefore, we developed low-input ATAC&mRNA-seq, a simple and robust method for studying the role of chromatin structure in gene regulation in a single experiment with thousands of cells, to maximize insights from limited input material by obtaining ATAC-seq and mRNA-seq data simultaneously from the same cells with data quality comparable to conventional mono-omics assays. Integrative data analysis revealed similar strong association between promoter accessibility and gene expression using the data of low-input ATAC&mRNA-seq as using single-assay data, underscoring the accuracy and reliability of our dual-omics assay to generate both data types simultaneously with just thousands of cells. We envision our method to be widely applied in many biological disciplines with limited materials.

genomics↗

bioRxiv2020

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals crucial and distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.

genetics↗

bioRxiv2020

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.

genetics↗

bioRxiv2019

GATA3 mutation disrupts a functional network governed by estrogen receptor, FOXA1 and GATA3

Estrogen receptors (ER) are part of the nuclear receptor superfamily of transcription factors and are activated by the steroid hormone 17{beta}-estradiol. ER forms a regulatory network in conjunction with other transcription factors, such as FOXA1 and GATA3. GATA3 has been identified as one of the most frequently mutated genes in breast cancer and is capable of specifying chromatin localization of FOXA1 and ER. How GATA3 mutations impact this transcriptional network is unknown. Here we investigate the function of one of the recurrent patient-derived GATA3 mutations (R330fs) on this regulatory network. Genomic analysis indicates that the R330fs mutant can disrupt the cooperative action of ER, FOXA1, and GATA3, and induce a change in chromatin localization of these factors. Relocalization of ER and FOXA1 is associated with altered chromatin architecture, which leads to differential gene expression in GATA3 mutant cells. These results suggest an active role for GATA3 mutants in ER positive breast tumors.

genomics↗

bioRxiv2019

RUNX1 safeguards the identity of the fetal ovary through an interplay with FOXL2

Sex determination of the gonads begins with fate specification of gonadal supporting cells into either ovarian granulosa cells or testicular Sertoli cells. This process of fate specification hinges on a balance of transcriptional control. We discovered that expression of the transcription factor RUNX1 is enriched in the fetal ovary in rainbow trout, turtle, mouse, goat and human. In the mouse, RUNX1 marks the supporting cell lineage and becomes granulosa cell-specific as the gonads differentiate. RUNX1 plays complementary/redundant roles with FOXL2 to maintain fetal granulosa cell identity, and combined loss of RUNX1 and FOXL2 results in masculinization of the fetal ovaries. At the chromatin level, RUNX1 occupancy overlaps partially with FOXL2 occupancy in the fetal ovary, suggesting that RUNX1 and FOXL2 target a common set of genes. These findings identify RUNX1, with an ovary-biased pattern conserved across species, as a novel regulator in securing the identity of ovarian supporting cells and the ovary.

developmental biology↗

bioRxiv2017

A class of GATA3 mutation reprograms the breast cancertranscriptional network through gain and loss of function

GATA3 is frequently mutated in breast cancer; these mutations are widely presumed to be loss of function. Here, we address molecular alterations downstream of a novel class of GATA3 mutations, revealing both gain and loss of function. Mutation of one allele of GATA3 led to loss of binding and decreased expression at a subset of genes, including Progesterone Receptor. At other loci, associated with epithelial to mesenchymal transition, gain of binding at a novel sequence motif correlated with increased gene expression. These results demonstrate that not all GATA3 mutations are equivalent and that these mutations impact breast cancer through gain and loss of function.

cell biology↗