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Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [HsMmMicroarray]

ABSTRACT: Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [HsMmMicroarray]

OTHER RELATED OMICS DATASETS IN: GSE107295GSE107297

PROVIDER: PRJNA419647 | ENA |

REPOSITORIES: ENA

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Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

Project description:Genome-wide association studies (GWASs) have been instrumental in understanding complex phenotypic traits. However, they have rarely been used to understand lineage-specific pathways and functions that contribute to the trait. In this study, by integrating publicly available lineage-specific enhancers from mesenchymal and myeloid compartments with bone mineral density loci, we were able to segregate osteoblast- and osteoclast (OC)-specific functions. Specifically, in OCs, a PU.1-dependent transcription factor (TF) network was revealed. Further we conducted functional genomic analysis PU.1 and MITF genome wide binding with corresponding gene expression analysis which revealed a TF network essential for OC differentiation. Several of these TFs were regulated by cooperative binding of PU.1 with BRD4 to form superenhancers. Further, PU.1 is essential for conformational changes in the superenhancer region of Nfatc1. In summary, our study demonstrates that utilizing GWASs with genome-wide binding studies as a filter helps to decipher lineage-specific pathways contributing to complex disease states.

2018-04-10 | GSE107294 | GEO

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

Project description:Eavluation of temporal expression kinetics during mouse osteoclast differentiation evaluated by microarray. We overlayed gene expression data with correspoding DNA binding data from MITF and PU.1 ChIP-seq to evaluate gene regulatory networks in osteoclasts.

2018-04-10 | GSE107296 | GEO

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

| PRJNA419645 | ENA

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

| PRJNA419648 | ENA

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

| PRJNA419649 | ENA

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-04-10 | GSE107297 | GEO

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [HsMmMicroarray]

Project description:Similar temporal expression kinetics of transcription factors in human and mouse osteoclast differentiation evaluated by microarray We used the identical differentiation conditions to evaluate gene expression kinetics of mouse and human osteoclast differentiation by microarray

2018-04-10 | GSE107295 | GEO

Pu-miR172d negatively regulates stomatal differentiation response to drought stress in poplar

Project description:We characterized Pu-miR172d, a miRNA that negatively regulates stomatal differentiation in Populus ussuriensis. Overexpression of Pu-miR172d significantly decreased stomatal density in P. ussuriensis. Molecular analysis indicated that PuGTL1 as a major target of Pu-miR172d by cleavage. Moreover, chimeric dominant repressor version of PuGTL1 (PuGTL1-SRDX) lines resembled the Pu-miR172d overexpression (Pu-miR172d-OE) lines, resulting in reduced stomatal density, net photosynthetic rate, stomatal conductance, transpiration and enhanced instantaneous water use efficiency, and thus improving tolerance to drought stress. QRT-PCR analysis showed that PuSDD1 transcript abundance in young leaves of PuGTL1-SRDX and Pu-miR172d-OE plants compared to WT plants, suggesting that Pu-miR172d positively regulates PuSDD1 expression through repression of PuGTL1. RNA-seq analysis showed Pu-miR172d overexpression significantly reduced the expression of many genes related to photosynthesis under drought stress. Overall, the present results demonstrate that Pu-miR172d/PuGTL1/PuSDD1 module plays an important role in stomatal differentiation and regulate WUE, illustrating its capacity for engineering drought tolerance improvement in poplar under future drier environments.

2022-06-13 | GSE133658 | GEO

A novel method to efficiently differentiate human osteoclasts from blood-derived monocytes

Project description:Osteoclasts are the tissue-specific macrophage population of the bone and unique in their bone-resorbing activity. Hence, they are fundamental for bone physiology in health and disease. However, efficient protocols for the isolation and study of primary human osteoclasts are scarce. In this study, we aimed to establish a protocol, which enables the efficient differentiation of functional human osteoclasts from monocytes. To this end, human monocytes were isolated through a double-density gradient from healthy donor blood. The differentiation to macrophages was performed either in cell culture dishes or in Teflon-coated bags. The impact of these two distinct differentiation protocols on the gene expression profile of macrophages was assessed via RNA-Sequencing. The macrophages were then further differentiated to terminal osteoclasts through the addition of Receptor Activator of NF-κB Ligand (RANKL). The yield and function of multinuclear osteoclasts was significantly increased upon initial differentiation of monocytes to macrophages in Teflon-coated bags. Our study has established a novel protocol for the isolation of primary human osteoclasts that improves osteoclastogenesis in comparison to the conventionally used cultivation approach.

2023-12-04 | GSE248902 | GEO

Murine Osteoclasts: Stat5 flox vs. Stat5 cKO

Project description:Transcriptional profiling of mouse osteoclasts comparing control osteoclasts from Stat5 flox mice with osteoclasts from Stat5 cKO mice. Two-condition experiment, Stat5 flox cells vs. Stat5 cKO cells

2013-12-09 | E-GEOD-51283 | biostudies-arrayexpress

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