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Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST

ABSTRACT: Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST

PROVIDER: PRJNA1119975 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29275546_1.fastq.gz	Fastqsanger.gz
	SRR29275546_2.fastq.gz	Fastqsanger.gz
	SRR29275547_1.fastq.gz	Fastqsanger.gz
	SRR29275547_2.fastq.gz	Fastqsanger.gz
	SRR29275548_1.fastq.gz	Fastqsanger.gz

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Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST

Project description:A haplotype block at the sclerostin (SOST) gene correlates with bone mineral density (BMD) and increased periodontitis risk in smokers. Investigating the putative causal variants within this block, our study aimed to elucidate the impact of linked enhancer elements on gene expression and to evaluate their role on transcription factor (TF) binding. Using CRISPR/dCas9 activation (CRISPRa) screening in SaOS-2 cells, we quantified disease-related enhancer activities regulating SOST expression. Additionally, in SaOs2-cells, we investigated the influence of the candidate TFs CCAAT/enhancer-binding protein beta (CEBPB) on gene expression by antisense (GapmeR) knockdown, followed by RNA sequencing. The periodontitis-linked SNP rs9783823 displayed a significant cis-activating effect (25-fold change in SOST expression), with the C-allele containing a CEBPB binding motif (position weight matrix (PWM) = 0.98, Pcorrected = 7.7 x 10-7). CEBPB knockdown induced genome-wide upregulation but decreased epithelial-mesenchymal transition genes (P= 0.71, AUC = 2.2 x 10-11). This study identifies a robust SOST cis-activating element linked to BMD and periodontitis, carrying CEBPB binding sites and highlights CEBPB's impact on epithelial-mesenchymal transition.

2024-06-27 | GSE269019 | GEO

Gene expression study of blood monocytes in pre- and postmenopausal females with low or high bone mineral density (HG-U133A)

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Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoclast_0_3days]

Project description:The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. This gene pool comprised 141 genes that were previously not known to have a function in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 BMD genes also caused skeletal abnormalities. Further, evidence suggested a direct role for several of the identified BMD genes in osteoclasts and osteoblasts, and candidate genes for further investigation were prioritized. Overall, the results add novel pathophysiological and molecular insight into bone health and disease

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Project description:Comparison of circulating monocytes from pre- and postmanopausal females with low or high bone mineral density (BMD). Circulating monocytes are progenitors of osteoclasts, and produce factors important to bone metabolism. Results provide insight into the role of monocytes in osteoporosis. We identify osteoporosis genes by microarray analyses of monocytes in high vs. low hip BMD (bone mineral density) subjects. Microarray analyses of monocytes were performed using Affymetrix HG-133A arrays in 80 Caucasian females, including 40 high (20 pre- and 20 postmanopausal) and 40 low hip BMD (20 pre- and 20 postmanopausal) subjects

2016-06-01 | E-GEOD-56815 | biostudies-arrayexpress

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2024-03-04 | GSE256109 | GEO

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