Biology subjects

Quiroz, E.

Publications and source records attributed to Quiroz, E..

4 recordsLinked to original sources

bioRxiv2024

Gene mobility elements mediate cell type specific genome organization and radial gene movement in vivo

ABSTRACTUnderstanding the level of genome organization that governs gene regulation remains a challenge despite advancements in chromatin profiling techniques. Cell type specific chromatin architectures may be obscured by averaging heterogeneous cell populations. Here we took a reductionist perspective, starting with the relocation of the hunchback gene to the nuclear lamina in Drosophila neuroblasts. We previously found that this event terminates competence to produce early-born neurons and is mediated by an intronic 250 base-pair element, which we term gene mobility element (GME). Here we found over 800 putative GMEs globally that are chromatin accessible and are Polycomb (PcG) target sites. GMEs appear to be distinct from PcG response elements, however, which are largely chromatin inaccessible in neuroblasts. Performing in situ Hi-C of purified neuroblasts, we found that GMEs form megabase-scale chromatin interactions, spanning multiple topologically associated domain borders, preferentially contacting other GMEs. These interactions are cell type and stage-specific. Notably, GMEs undergo developmentally- timed mobilization to/from the neuroblast nuclear lamina, and domain swapping a GFP reporter transgene intron with a GME relocates the transgene to the nuclear lamina in embryos. We propose that GMEs constitute a genome organizational framework and mediate gene-to-lamina mobilization during progenitor competence state transitions in vivo.

developmental biology↗

bioRxiv2024

Assessment of the Epigenomic Landscape in Human Myometrium at Term Pregnancy

The myometrium plays a critical role during pregnancy as it is responsible for both the structural integrity of the uterus and force generation at term. Emerging studies in mice indicate a dynamic change of the myometrial epigenome and transcriptome during pregnancy to ready the contractile machinery for parturition. However, the regulatory systems underlying myometrial gene expression patterns throughout gestation remain largely unknown. Here we investigated human term pregnant nonlabor myometrial biopsies for transcriptome, enhancer histone mark cistrome, and chromatin conformation pattern mapping. More than thirty-thousand putative enhancers with H3K27ac and H3K4me1 double positive marks were identified in the myometrium. Enriched transcription factor binding motifs include known myometrial regulators AP-1, STAT, NFkB, and PGR among others. Putative myometrial super enhancers are mostly colocalized with progesterone receptor occupying sites and preferentially associated with highly expressing genes, suggesting a conserved role of PGR in regulating the myometrial transcriptome between species. In human myometrial specimens, inferred PGR activities are positively correlated with phospholipase C like 2 (PLCL2) mRNA levels, supporting that PGR may act through this genomic region to promote PLCL2 expression. PGR overexpression facilitated PLCL2 gene expression in myometrial cells. Using CRISPR activation, we assessed the functionality of a PGR putative enhancer 35-kilobases upstream of the contractile-restrictive gene PLCL2. In summary, results of this study serve as a resource to study gene regulatory mechanisms in the human myometrium at the term pregnancy stage for further advancing womens health research.

cell biology↗

bioRxiv2023

Structure-function relationships of mucociliary clearance in the human airways

Mucociliary clearance is a vital defense mechanism of the human airways, protecting against harmful particles and infections. When this process fails, it contributes to respiratory diseases like chronic obstructive pulmonary disease (COPD) and asthma. While advances in single-cell transcriptomics have revealed the complexity of airway composition, much of what we know about how airway structure impacts clearance relies on animal studies. This limits our ability to create accurate human-based models of airway diseases. Here we show that the airways in female rats and in humans exhibit species-specific differences in the distribution of ciliated and secretory cells as well as in ciliary beat, resulting in significantly higher clearance effectiveness in humans. We further reveal that standard lab-grown cultures exhibit lower clearance effectiveness compared to human airways, and we identify the underlying structural differences. By combining diverse experiments and physics-based modeling, we establish universal benchmarks to assess human airway function, interpret preclinical models, and better understand disease-specific impairments in mucociliary clearance.

biophysics↗

bioRxiv2023

Caveolin-1 Autonomously Regulates Hippocampal Neurogenesis Via Mitochondrial Dynamics

Hippocampal neurogenesis plays instrumental roles in learning and memory. However, the mechanisms underlying neurogenesis are not fully understood. Here we show that the expression of Caveolin-1 (Cav-1), the principal component of caveolae, peaks in neural progenitor cells (NPCs) during neurogenesis. Using NestinCreERT2;Cav-1fl/fl male mice, and CRISPR-sham (Cav-1 Ctrl) and CRISPR/Cas9-edited (Cav-1 KO) human induced-pluripotent stem cells, we observed that Cav-1 deletion led to reduced stem cell proliferation and enhanced differentiation into neurons. This was manifested by increased neuronal dendritic tree surface area and enhanced mouse performance in contextual discrimination. Proteomic analysis revealed that Cav-1 plays a role in mitochondrial pathways in NPCs. Cav-1 localized to the mitochondria in NPCs and co-immunoprecipitated with mitofusion 2. Mitochondrial morphology was elongated in Cav-1 KO NPCs and the expression of mitofusion 2 was increased in mitochondrial fractions. Restoration of Cav-1 levels rescued elongated mitochondrial morphology and altered neuronal differentiation in Cav-1 KO NPCs. Together, this study identifies Cav-1 as a novel regulator of neurogenesis and -dependent learning and memory. Significance StatementThe hippocampal dentate gyrus (DG) orchestrates adult hippocampal neurogenesis (AHN). The precise mechanisms governing AHN remain elusive. Caveolin-1 regulates neurogenesis through mitochondrial fission-fusion process, suggesting Caveolin-1 as a novel regulator of AHN and underscoring the impact of AHN on cognition.

neuroscience↗