Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA144895 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage [ChIP-Seq]
| PRJNA146041 | ENA
Project description:Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by stem cells (SCs). During the rest phase, the HF-SCs remain quiescent due to extrinsic inhibitory signals within the niche. As activating cues accumulate, HF-SCs become activated, proliferate, and grows downward to form transient-amplifying matrix progenitor cells. We used ChIP-seq to reveal the genome-wide maps of histone modifications underlying the states of hair follicle stem cells and their transient-amplifying progeny before differentiation. Quiescent hair follicle stem cells (qHF-SCs), activated hair follicle stem cells (aHF-SCs) and transient-amplifying matrix cells (HF-TACs) were FACS-purified for ChIP-sequcencing.
2011-09-02 | E-GEOD-31239 | biostudies-arrayexpress
Project description:Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by stem cells (SCs). During the rest phase, the HF-SCs remain quiescent due to extrinsic inhibitory signals within the niche. As activating cues accumulate, HF-SCs become activated, proliferate, and grows downward to form transient-amplifying matrix progenitor cells. We used ChIP-seq to reveal the genome-wide maps of histone modifications underlying the states of hair follicle stem cells and their transient-amplifying progeny before differentiation.
2011-09-02 | GSE31239 | GEO
Project description:Posttranslational protein modifications have emerged as a mechanism regulating progenitor cell state transitions during tissue formation. Herein, we exploit the stereotyped hair follicle development to delineate the function of PADI4; an enzyme converting peptidylarginine to citrulline. Single cell-sequencing places Padi4 in both progenitor and differentiated hair lineage cells and indicate that PADI4 acts to repress transcription during hair follicle development. We establish PADI4 as a negative regulator of proliferation, acting on LEF1-positive hair shaft committed progenitor cells. Mechanistically, PADI4 citrullinates proteins associated with mRNA-processing and ribosomal biogenesis, and lack of PADI4 promotes protein synthesis and rRNA transcription in vivo. Characterizing key translational effectors, we demonstrate that PADI4 citrullinates the translational repressor 4E-BP1 and reveal a crosstalk between PADI4 activity and 4E-BP1 phosphorylation. This work sheds new light on how posttranslational modifications impact progenitor cell states and tissue formation.
2025-07-28 | PXD064137 | Pride
Project description:Tissue formation requires a coordinated balance of progenitor cell proliferation and differentiation. Posttranslational protein modifications have emerged as a mechanism utilized to regulate progenitor cell state transitions. Herein, we exploit the well characterized and stereotyped hair follicle development to delineate the function of PADI4; an enzyme converting peptidylarginine to citrulline. Single cell-sequencing places Padi4 in both progenitor and differentiated hair lineage cells during hair follicle development. We show that the absence of PADI4 induces gene expression across hair follicle cell clusters, suggesting that PADI4 acts to negatively impact transcription. In addition, we establish PADI4 as a negative regulator of proliferation, acting of LEF1-positive hair shaft committed progenitor cells. Mechanistically, PADI4 citrullinates proteins associated with mRNA-processing and ribosomal biogenesis, and lack of PADI4 promotes protein synthesis and rRNA transcription in vivo, in both hair follicle progenitor and committed lineage cells. Characterizing key translational effectors, we demonstrate that PADI4 interacts with 4E-BP1 and reveal a crosstalk between PADI4 activity and 4E-BP1 phosphorylation. We report that PADI4 contributes to hair follicle development by repressing progenitor cell proliferation and translational activity. This work sheds new light on how posttranslational modifications impact progenitor cell states and tissue formation.
2025-07-28 | GSE288124 | GEO
Project description:Tissue homeostasis and regeneration require activation and subsequent lineage commitment of tissue-resident stem cells (SCs). These state changes are controlled by epigenetic barriers. Using hair follicle stem cells (HFSCs) as paradigm, we studied how aging impacts the chromatin landscape and function of mammalian SCs. Analyses of genome-wide chromatin accessibility revealed that aged HFSCs displayed widespread reduction of chromatin accessibility specifically at key SC self-renewal and differentiation genes that were characterized by bivalent promoters carrying both activating and repressive chromatin marks. Consistently, aged HFSCs showed reduced self-renewing capacity and attenuated ability to activate expression of these bivalent genes upon regeneration. These functional defects were niche-dependent as transplantation of aged HFSCs into young recipients or into ex vivo niches restored SC functions and transcription of poised genes. Mechanistically, aged HFSC niche displayed wide-spread alterations in extracellular matrix composition and mechanics, resulting in compressive forces on SCs and subsequent transcriptional repression, leading to loss of bivalent promoters. Tuning tissue mechanics both in vivo and in vitro recapitulated age-related SC changes, implicating niche mechanics as a central regulator of genome organization and function leading to age-dependent SC exhaustion.
2021-05-07 | PXD018352 | Pride
Project description:Mechanisms of plasticity to acquire different cell fates are critical for adult stem cell (SC) potential, yet are poorly understood. Reduced global histone methylation is an epigenetic state known to mediate plasticity in cultured embryonic SCs and T cell progenitors. We used mouse hair follicle stem cells (HFSCs) at two different hair cycle stages (early anagen and late catagen) to compare the genome-wide changes in the levels of histone modification marks H3K4me3, H3K9me3, and H3K27me3. Hair follicle stem cells from Early Anagen (EA-HFSCs) and Late Catagen (LC-HFSCs), and their non-HFSCs counterparts (nEA-HFSCs and nLC-HFSCs), were FACS-isolated for Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) analysis of H3K4me3, H3K9me3, and H3K27me3.
2016-04-13 | E-GEOD-78749 | biostudies-arrayexpress
Project description:Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs). We used ChIP-seq to unfold genome-wide chromatin landscapes of Nfatc1 and dissect the biological relevence of its upstream BMP signaling in HFSC aging. Telogen quiescent hair follicle stem cells (HFSCs) were FACS-purified for ChIP-sequcencing.
2013-11-14 | E-GEOD-52328 | biostudies-arrayexpress
Project description:Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs) and transit-amplifying cells (TACs). We used ChIP-seq to unfold genome-wide chromatin landscapes of H3K27ac and Med1 to identify super-enhancers and dissect their biological relevance in cell identity and plasticity of HFSCs in vivo and in vitro.
2015-03-19 | GSE61316 | GEO
Project description:Profiling combinations of histone modifications identifies gene regulatory elements in different states and discovers features controlling transcriptional and epigenetic programmes. However, efforts to map chromatin states in defined cell types are hindered by the lack of methods that can profile multiple histone modifications together with transcriptome in individual cells. Here we describe single-cell Multi-Targets and mRNA sequencing (scMTR-seq), which enables simultaneous profiling of six histone modifications and transcriptome in single cells. As a proof of concept, we apply scMTR-seq to uncover the dynamics of chromatin state change during human endoderm differentiation. We also use scMTR-seq to produce lineage-resolved chromatin maps and gene regulatory networks in mouse blastocysts, revealing striking epigenetic asymmetries at gene regulatory regions between the three embryo lineages. We identify the transcription factor Trps1 as a potential repressor in epiblast cells of trophectoderm-associated enhancer networks and their target genes. Together, scMTR-seq enables investigation of combinatorial epigenetic modalities in low-cell number and heterogeneous samples.
2025-08-07 | GSE277776 | GEO