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

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

PROVIDER: PRJNA478444 | ENA |

REPOSITORIES: ENA

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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.

| S-EPMC6152943 | biostudies-literature

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]

| PRJNA478338 | ENA

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]

| PRJNA478343 | ENA

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:This SuperSeries is composed of the SubSeries listed below.

2018-06-29 | GSE116386 | GEO

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

Project description:We performed RNA-seq on normal mammary cell populations and mouse mammary tumor cell populations

2018-06-29 | GSE116385 | GEO

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

Project description:We performed H3K27ac ChIP-seq on normal mammary cell populations and SOX10 ChIP-seq on PY230 tumors

2018-06-29 | GSE116384 | GEO

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

Project description:We performed ATAC-seq on normal mammary cell populations and mouse mammary tumor cell populations

2018-06-29 | GSE116383 | GEO

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

ChIP-seq analysis of chromatin state plasticity in primary human adult erythroid progenitor cells

Project description:We report a computational approach for investigation of chromatin state plasticity. We applied this approach to investigate an ENCODE ChIP-seq dataset profiling the genome-wide distribution of H3K27me3 in 19 human cell lines. We found that high plasticity regions (HPRs) can be divided into two functionally and mechanistically distinct groups, consisting of CpG island proximal and distal regions. We identified cell-type specific regulators correlating with H3K27me3 patterns at distal HPRs in ENCODE cell lines. Furthermore, we applied this approach to investigate mechanisms for poised enhancer establishment in primary human erythroid precursors. We predicted and validated a previously unrecognized role of TAL1 in modulating H3K27me3 patterns through interaction with additional cofactors, such as GFI1B. Our integrative approach provides mechanistic insights into chromatin state plasticity and is broadly applicable to other epigenetic marks. Analysis of genomic occupancy of H3K27me3, H3K27ac, GATA1, TAL1/SCL and GFI1B in primary adult human proerythroblasts by ChIP-seq.

2014-01-01 | E-GEOD-52924 | biostudies-arrayexpress

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