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Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships

ABSTRACT: Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships

PROVIDER: PRJNA516680 | ENA |

REPOSITORIES: ENA

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Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships.

Project description:Technological improvements enable single-cell epigenetic analyses of organ development. We reasoned that high-resolution single-cell chromatin accessibility mapping would provide needed insight into the epigenetic reprogramming and transcriptional regulators involved in normal mammary gland development. Here, we provide a single-cell resource of chromatin accessibility for murine mammary development from the peak of fetal mammary stem cell (fMaSC) functional activity in late embryogenesis to the differentiation of adult basal and luminal cells. We find that the chromatin landscape within individual cells predicts both gene accessibility and transcription factor activity. The ability of single-cell chromatin profiling to separate E18 fetal mammary cells into clusters exhibiting basal-like and luminal-like chromatin features is noteworthy. Such distinctions were not evident in analyses of droplet-based single-cell transcriptomic data. We present a web application as a scientific resource for facilitating future analyses of the gene regulatory networks involved in mammary development.

| S-EPMC6887110 | biostudies-literature

Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships

Project description:We perfromed single-nucleus ATAC-seq (snATAC-seq) on normal mammary epithelial cells

2019-09-01 | GSE125523 | GEO

Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity

Project description:Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity

| PRJNA478444 | ENA

Mammary gland

Project description:Goat Mammary gland RNA-Seq (DGE)

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Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ATAC-seq]

Project description:Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ATAC-seq]

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Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ChIP-seq]

Project description:Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ChIP-seq]

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Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [RNA-seq]

Project description:Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [RNA-seq]

| PRJNA478445 | ENA

Epigenetic and Transcriptomic Profiling of Mammary Gland Development and Tumor Models Disclose Regulators of Cell State Plasticity.

Project description:Cell state reprogramming during tumor progression complicates accurate diagnosis, compromises therapeutic effectiveness, and fuels metastatic dissemination. We used chromatin accessibility assays and transcriptional profiling during mammary development as an agnostic approach to identify factors that mediate cancer cell state interconversions. We show that fetal and adult basal cells share epigenetic features consistent with multi-lineage differentiation potential. We find that DNA-binding motifs for SOX transcription factors are enriched in chromatin that is accessible in stem/progenitor cells and inaccessible in differentiated cells. In both mouse and human tumors, SOX10 expression correlates with stem/progenitor identity, dedifferentiation, and invasive characteristics. Strikingly, we demonstrate that SOX10 binds to genes that regulate neural crest cell identity, and that SOX10-positive tumor cells exhibit neural crest cell features.

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Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development

Project description:Single cell analysis of the mouse mammary gland from embryonic to adult stages using 10X Chromium platform.

2018-08-07 | GSE111113 | GEO

microRNA expression during ovine adult mammary gland development

Project description:The mammary gland undergoes extensive remodeling between the begin- ning of pregnancy and lactation; this involves cellular processes including cell proliferation, differentiation, and apoptosis, all of which are under the control of numerous regulators. To unravel the role played by miRNA, we describe here 47 new ovine miRNA cloned from mammary gland in early pregnancy displaying strong similari- ties with those already identified in the cow, human, or mouse. A microarray study of miRNA variations in the adult ovine mammary gland during pregnancy and lactation showed that 100 miRNA are regulated according to three principal patterns of expression: a de- crease in early pregnancy, a peak at midpregnancy, or an increase throughout late pregnancy and lactation. One miRNA displaying each pattern (miR-21, miR-205, and miR-200b) was analyzed by qRT- PCR. Variations in expression were confirmed for all three miRNA. Using in situ hybridization, we detected both miR-21 and miR-200 in luminal mammary epithelial cells when expressed, whereas miR-205 was expressed in basal cells during the first half of pregnancy and then in luminal cells during the second half. We therefore conclude that miR-21 is strongly expressed in the luminal cells of the normal mammary gland during early pregnancy when extensive cell prolif- eration occurs. In addition, we show that miR-205 and miR-200 are coexpressed in luminal cells, but only during the second half of pregnancy. These two miRNA may cooperate to maintain epithelial status by repressing an EMT-like program, to achieve and preserve the secretory phenotype of mammary epithelial cells. 5 samples for sheep and 5 samples for mouse

2013-01-04 | E-GEOD-32654 | biostudies-arrayexpress

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