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The transition from quiescent to activated states in human hematopoietic stem cells is governed by dynamic 3D genome reorganization [ATAC-Seq]

ABSTRACT: We profiled chromatin accessibility in sorted hematopoietic populations. We used this to identify signatures of chromatin accessibility which discriminated LT-HSC from other hematopoietic stem and progenitor cell populations, discriminated by CTCF binding sites. We further validated this with RNA-Seq on sorted cord blood populations following shCTCF, and Hi-C and CTCF ChIP-Seq on the OCIAML-2 cell line.

ORGANISM(S): Homo sapiens

PROVIDER: GSE125060 | GEO | 2020/11/23

REPOSITORIES: GEO

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The transition from quiescent to activated states in human hematopoietic stem cells is governed by dynamic 3D genome reorganization [Hi-C]

Project description:We profiled chromatin accessibility in sorted hematopoietic populations. We used this to identify signatures of chromatin accessibility which discriminated LT-HSC from other hematopoietic stem and progenitor cell populations, discriminated by CTCF binding sites. We further validated this with RNA-Seq on sorted cord blood populations following shCTCF, and Hi-C and CTCF ChIP-Seq on the OCIAML-2 cell line.

2020-11-23 | GSE125062 | GEO

The transition from quiescent to activated states in human hematopoietic stem cells is governed by dynamic 3D genome reorganization [ChIP-Seq]

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The transition from quiescent to activated states in human hematopoietic stem cells is governed by dynamic 3D genome reorganization [RNA-Seq]

2020-11-23 | GSE125063 | GEO

The transition from quiescent to activated states in human hematopoietic stem cells is governed by dynamic 3D genome reorganization [Low-C]

Project description:Life-long blood production requires long-term hematopoietic stem cells (LT-HSC) - marked by stemness states involving quiescence and self-renewal - to transition into activated short-term HSC (ST-HSC) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk ATAC-seq on human HSC and stem/progenitor subsets (HSPC) to uncover chromatin accessibility signatures, one including LT-HSC (LT/HSPC signature) and another excluding LT-HSC (Act/HSPC signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CTCF binding sites mediating 351 chromatin interactions, engaged in ST-HSC but not LT-HSC, enclosing multiple stemness pathway genes active in LT-HSC and repressed in ST-HSC. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSC from transitioning to activated ST-HSC. Hence, 3D chromatin interactions centrally mediated by CTCF, endow a gatekeeper function that governs the earliest fate transitions HSC make by coordinating disparate stemness pathways linked to quiescence and self-renewal.

2020-11-23 | GSE159287 | GEO

ea9af326-25e0-42af-a639-732a3bafd94b - samples

Project description:To elucidate the epigenetic changes which occur when human long-term hematopoietic stem cells (LT-HSC) become activated we performed Bulk ATAC-Seq on 13 sorted bulk hematopoietic populations from cord bloodas well as single-cell ATAC-Seq upon CD34+CD38-CD45RA- cells enriched for HSC as well as CD34+/CD38+ progenitor cells both from cord blood. These studies revealed gains of chromatin accessibility around CTCF binding sites during HSPC activation, as such we additionally performed Low-C to directly profile the 3D conformation of human cord-blood derived LT-HSC and Short-term hematopoietic stem cells (ST-HSC), as well as Hi-C , ATAC-Seq and CTCF ChIP-Seq upon the OCIAML-2 cell line in which CTCF sites gained during LT-HSC activation are enriched. Finally we transduced human cord-blood LT-HSC with an shCTCF vector; in-vitro cultured LT-HSC cells harbouring shCTCF were used to perform RNA-Seq, and scATAC-Seq was performed on CD34+/CD38- human CB cells transduced with shCTCF, four weeks post xeno-transplantation into mice. Collectively these studies have helped us demonstrate the role of 3D chromatin conformation changes during human LT-HSC activation.

| EGAD00001006447 | EGA

Gene expression profile at sorted microglia and border-associated macrophage with Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp bone marrow transplantation

Project description:After irradiation and bone-marrow transplantation, most of microglia and boarder-associated macrophages in the central nervous system is replaced by engranft cells. Taking advantages of Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp mice, we discriminated cells from monocyte precursors and hematopoietic stem cells with colors at 32 weeks following irradiation and bone-marrow transplantation. We sorted HSC-derived, monocyte-derived, and endogenouse microglia and leptomeningeal macrophages, and analyzed gene expression level between different cell populations using a bulk RNAseq method.

2024-12-02 | GSE282221 | GEO

Development of gene expression signatures of CTCF-expressing vs CTCF-depleted hepatocellular carcinoma cells

Project description:To understand the functional role of CTCF in the oncogenesis of HCC, we constructed lentiviruses expressing control shRNA (shCont) or shRNA agains CTCF (shCTCF) and transduced them into PLC5 cells respectively. After 24 hours, cells were cultered in puromycin containing medium (5 ug) for another 24 hours. Cells were returned to normal medium for another 48 hours before total mRNAs were corrected for whole genome gene expression array analysis. Expression of FoxM1 gene from this signature was quantified in an independent set of RNA samples by real-time PCR, confirming differntial expression of this gene in shCTCF expressing cells.

2017-09-30 | GSE100533 | GEO

mRNA-seq in human 293T HEK cells in the presence (shScr) or absence of HSF1 (shHSF1) or CTCF (shCTCF).

Project description:Profiling the mRNA content in 293T human embryonic kidney (HEK) cells in the presence and absence of HSF1 or CTCF. The mRNA was enriched from total cellular RNA using using polyadenyltion-selection. HSF1 (shHSF1) or CTCF (shCTCF) was downregulated using shRNA for 48hours. Scrambled RNA (shScr) was used as a negative control.

2020-11-17 | GSE155541 | GEO

Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for proper CTCF function

Project description:Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. While this reduces distances to the adjacent nucleosomes it only modestly impacts CTCF binding itself. In absence of accessibility, the insulator function of CTCF is nevertheless impaired resulting in lower occupancy of cohesin and cohesin-loading factors, and reduced insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. Our comprehensive analysis reveals a specific role for NURF in mediating Snf2h localization and chromatin opening at bound CTCF sites showing that local accessibility is critical for cohesin binding and insulator function.

2024-03-13 | PXD042945 | Pride

Spatial reorganization of telomeres in long-lived quiescent cells.

Project description:The spatiotemporal behavior of chromatin is an important control mechanism of genomic function. Studies in Saccharomyces cerevisiae have broadly contributed to demonstrate the functional importance of nuclear organization. Although in the wild yeast survival depends on their ability to withstand adverse conditions, most of these studies were conducted on cells undergoing exponential growth. In these conditions, as in most eukaryotic cells, silent chromatin that is mainly found at the 32 telomeres accumulates at the nuclear envelope, forming three to five foci.Here, combining live microscopy, DNA FISH and chromosome conformation capture (HiC) techniques, we report that chromosomes adopt distinct organizations according to the metabolic status of the cell. In particular, following carbon source exhaustion the genome of long-lived quiescent cells undergoes a major spatial re-organization driven by the grouping of telomeres into a unique focus or hypercluster localized in the center of the nucleus. This change in genome conformation is specific to quiescent cells able to sustain long-term viability. We further show that reactive oxygen species produced by mitochondrial activity during respiration commit the cell to form a hypercluster upon starvation. Importantly, deleting the gene encoding telomere associated silencing factor SIR3 abolishes telomere grouping and decreases longevity, a defect that is rescued by expressing a silencing defective SIR3 allele competent for hypercluster formation.Our data show that mitochondrial activity primes cells to group their telomeres into a hypercluster upon starvation, reshaping the genome architecture into a conformation that may contribute to maintain longevity of quiescent cells.

| S-EPMC4581094 | biostudies-literature

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