Similar Datasets
Project description:Each TMT6 sample contains one replicate with the sub-samples representing subsequent time points. Detailed culture and processing methods are described in Panariello et al, Nat Comm, under revision.
2022-12-22 | MSV000090954 | MassIVE
Project description:After characterizing super-enhancer-associated chromatin dynamics accompanied by malignant progression of skin stem cells, we show that ETS family members auto-regulate themselves and a cohort of cancer-associated super-enhancer transcription factors which together are essential for tumor maintenance. Mouse skin squamouse cell carcinoma (SCC) tumor-initiating stem cells (SCC-SC), hair follicle stem cells (HF-SC) and epidermal stem cells (Epi-SC) were FACS-prufied for RNA-sequencing.
2015-11-22 | E-GEOD-72146 | biostudies-arrayexpress
Project description:Reprogramming to iPSCs resets the epigenome of somatic cells including the reversal of X chromosome-inactivation. We sought to gain insight into the steps underlying the reprogramming process by examining the means by which reprogramming leads to X chromosome-reactivation (XCR). Analyzing single cells in situ, we found that hallmarks of the inactive X (Xi) change sequentially, providing a direct readout of reprogramming progression. Several epigenetic changes on the Xi occur in the inverse order of developmental X-inactivation, while others are uncoupled from this sequence. Among the latter, DNA methylation has an extraordinary long persistence on the Xi during reprogramming, and, like Xist expression, is erased only after pluripotency genes are activated. Mechanistically, XCR requires both DNA demethylation and Xist silencing, ensuring that only cells undergoing faithful reprogramming initiate XCR. Our study defines the epigenetic state of multiple sequential reprogramming intermediates and establishes a paradigm for studying cell fate transitions during reprogramming. RRBS profiles were generated from female and male ES cells, female iPS cells, SSEA1+ and SSEA1- reprogramming intermediates, and male and female MEFs, for a total of 18 samples.
2014-12-18 | E-GEOD-58109 | biostudies-arrayexpress
Project description:Gene regulation in mammals involves a complex interplay between promoter and distal regulatory elements that function in concert to drive precise spatio-temporal gene expression programs. However, the dynamics of distal gene regulatory elements and its function in transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here we use a combinatorial analysis of genomewide datasets for chromatin accessibility (FAIRE-Seq) and enhancer mark H3K27ac to reveal a highly dynamic nature of chromatin accessibility during neurogenesis that gets restricted to certain genomic regions as neurons acquire a post-mitotic, terminally differentiated state. We further reveal that the distal open regions serve as target sites of distinct transcription factors that function in a stage-specific manner to contribute to the transcriptional program underlying neuronal commitment and maturation. A prolonged NMDA-driven neural activity results in epigenetic reprogramming at a large number of distal regulatory elements as well as dramatic reorganization of super-enhancers that in turn mediate critical transcriptional responses. Taken together, these findings reveal dynamics of distal regulatory landscape during neurogenesis and uncover novel regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate transcriptome underlying neuronal development and function. FAIRE-Seq and H3K27ac profiles for three stages on neuronal differentation viz. neuronal progenitors, day 1 neurons and day 10 neurons, were generated to understand the dynamics of accessible and ehancer chromatin landscape. Along with this we also generated RNASeq and H3K27ac profiles for day 10 neurons upon control and NMDA treatment.
2015-07-08 | E-GEOD-65713 | biostudies-arrayexpress
Project description:Lima1 is an extensively studied prognostic marker of malignancy and is also considered to be a tumour suppressor, but its role in a developmental context of non-transformed cells is poorly understood. Here, we characterised the expression pattern and examined the function of Lima1 in mouse embryos and pluripotent stem cell lines. We found that Lima1 expression is controlled by the naïve pluripotency circuit and is required for the suppression of membrane blebbing. Moreover, Lima1 is essential for proper mitochondrial energetics, which is crucial for the growth of solid tumours. Forcing Lima1 expression enabled human pluripotent stem cells to be incorporated into murine pre-implantation embryos, trespassing the interspecies engraftment barrier. Thus, Lima1 is a key effector molecule that mediates the pluripotency control of membrane dynamics and cellular metabolism.
2021-12-16 | PXD025293 | Pride
Project description:My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology.
The four major questions I will address are:
1. How do age and aging affect normal human HSC dynamics in vivo?
2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics?
3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood?
4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?
| EGAS00001003397 | EGA
Project description:Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially of the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a finely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
2023-09-06 | GSE242423 | GEO
Project description:Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially of the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a finely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
2023-09-06 | GSE242421 | GEO
Project description:Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially of the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a finely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
2023-09-06 | GSE242419 | GEO
Project description:Advanced prostate cancer is a leading cause of cancer-related deaths in men, in large part due to our poor understanding of advanced castration-resistant prostate cancer (CRPC). This form of prostate cancer is uniformly lethal. Currently, the main treatments against this disease are anti-androgenic therapies; however, CRPC always develops resistance to these therapeutic modalities. Of particular interest is CRPC lacking androgen receptor (AR) activity, or AR-low CRPC. This subtype has dramatically increased in incidence in the past decade. While many studies have identified a complex architecture in the prostate, we still lack a unified view of the cellular interactions and phenotypes that facilitate advanced prostate cancer maintenance and survival, particularly without AR signaling.To better understand the cellular changes that drive CRPC, we harvested prostates from a mouse model of prostate cancer under multiple conditions and performed single-cell RNA sequencing (scRNASeq). Our findings reveal a subset of the epithelial compartment that is primed for AR-low survival during tumorigenesis, as well as a complex basal-driven mechanism to facilitate expansion of this subtype. Androgen deprivation via castration of the mouse modulates this process by increasing proliferation rates in epithelia. In addition, we observe a dramatic increase in immune cell population upon tumorigenesis. We identify this immune influx as pro-tumor and pinpoint unique signaling phenotypes from individual epithelial subtypes, demonstrating a multifaceted process of recruitment and remodeling by the tumor to build a favorable environment. Androgen signaling is also crucial for maintaining these immune populations, and castration dramatically remodels the tumor environment. Finally, we uncover the importance of protein synthesis regulation in maintaining these complex dynamics; inhibiting the eIF4F translation initiation complex leads to decreased epithelial proliferation and immune recruitment. These findings shed new light on the cellular dynamics of advanced prostate cancer and highlight the importance of employing high-throughput technologies to provide a complete picture of the tumor and its microenvironment. Better understanding of the epithelial subtypes involved in tumor growth, as well as their influence on immune populations in the prostate, can lead to new avenues of treatment.
2022-12-06 | GSE171336 | GEO