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An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F

ABSTRACT: An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F

PROVIDER: PRJNA427162 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6410464.fastq.gz	Fastqsanger.gz
	SRR6410465.fastq.gz	Fastqsanger.gz

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Similar Datasets

An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F (Affymetrix data set)

Project description:The role of Gata2 in regulating the expression of HLA in human decidual stromal cells

2018-01-02 | GSE108407 | GEO

An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F (ChIP-Seq data set)

Project description:The role of Gata2 in regulating the expression of HLA in huamn decidual stromal cells

2018-01-02 | GSE108408 | GEO

An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F (Affymetrix data set)

Project description:An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F (Affymetrix data set)

| PRJNA427169 | ENA

An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F (ChIP-Seq data set)

Project description:An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F (ChIP-Seq data set)

| PRJNA427171 | ENA

An Ancient Fecundability-Associated Polymorphism Creates a GATA2 Binding Site in a Distal Enhancer of HLA-F.

Project description:Variation in female reproductive traits, such as fertility, fecundity, and fecundability, are heritable in humans, but identifying and functionally characterizing genetic variants associated with these traits have been challenging. Here, we explore the functional significance and evolutionary history of a G/A polymorphism at SNP rs2523393, which is an eQTL for HLA-F and is significantly associated with fecundability (the probability of being pregnant within a single menstrual cycle). We replicated the association between the rs2523393 genotype and HLA-F expression by using GTEx data and demonstrate that HLA-F is upregulated in the endometrium during the window of implantation and by progesterone in decidual stromal cells. Next, we show that the rs2523393 A allele creates a GATA2 binding site in a progesterone-responsive distal enhancer that loops to the HLA-F promoter. Remarkably, we found that the A allele is derived in the human lineage and that the G/A polymorphism arose before the divergence of modern and archaic humans and segregates at intermediate to high frequencies across human populations. Remarkably, the derived A allele is has also been identified in a GWAS as a risk allele for multiple sclerosis. These data suggest that the polymorphism is maintained by antagonistic pleiotropy and a reproduction-health tradeoff in human evolution.

| S-EPMC6174278 | biostudies-literature

An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F

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

2018-01-02 | GSE108409 | GEO

Pre-fractionation extends, but creates a bias in the detectable HLA class Ι ligandome

Project description:HLA class Ι molecules on the cell surface enable CD8+ T lymphocytes to recognize cellular alterations in the form of antigens, including mutations, protein copy number alterations, aberrant post-translational modifications or pathogen proteins. At any given moment, tens of thousands of different self and foreign HLA class Ι peptide ligands may be presented on the cell surface by MHC class Ι complexes. Analysis of the HLA ligandome thrusts therefore unique challenges due to their enormous biochemical diversity and inherently wide range of abundances. Despite advances in enrichment, separation, MS instrumentation and fragmentation, it is still not achievable to cover the HLA class Ι ligandome in sufficient depth to support routine identification of e.g. viral pathogens or immuno-therapeutically important tumor neo-antigens. In this study, we evaluate two pre-fractionation techniques, high pH reversed phase and strong cation exchange for complementary analysis of HLA class Ι peptide ligands, benchmarking them against analyses circumventing pre-fractionation. We observe that pre-fractionation substantially extends the detectable HLA class Ι ligandome, but also creates an identification bias. We advocate a rational choice between no-fractionation, high pH reversed phase or strong cation exchange pre-fractionation for deeper HLA class Ι ligandome analysis depending on the targeted HLA locus, allele or peptide ligand modification

2019-02-25 | PXD011257 | Pride

GATA2 Deficiency

Project description:GATA2 Deficiency

| PRJNA684645 | ENA

GATA2 Deficiency

Project description:GATA2 Deficiency

| PRJNA684644 | ENA

A novel GATA2 enhancer single nucleotide mutation results in the MonoMAC syndrome phenotype in two second cousins

Project description:Inherited or sporadic mutations in the transcription factor GATA2 have been shown to be responsible for MonoMAC syndrome, a GATA2 deficiency disease characterized by a constellation of findings including disseminated non-tuberculous mycobacterial infections, severe deficiencies of monocytes, natural killer cells, and B-lymphocytes, and myelodysplastic syndrome. Mutations in the GATA2 gene are found in ~90% of patients with a GATA2 deficiency phenotype and are largely missense mutations in the conserved second zinc-finger domain or truncation mutations elsewhere in the coding sequence. Mutations in an intron 5 regulatory enhancer element are also well described in GATA2 deficiency. Here we present a large multigeneration kindred with the clinical features of GATA2 deficiency but lacking an apparent GATA2 mutation. Whole Genome Sequencing revealed a unique Adenine-to-Thymine variant in the GATA2 -110 enhancer 116,855bp upstream of the GATA2 gene. The mutation creates a new E-box consensus in position with an existing GATA-box to generate a new hematopoietic regulatory composite element. The mutation segregates with the disease pattern in five generations of the family pedigree. Cell-type specific allelic imbalance of GATA2 expression is observed in a patient’s bone marrow with higher expression from the mutant-linked allele. Allele-specific overexpression of GATA2 is observed in CRISPR/Cas9-modified HL60 cultured cells and in luciferase assays with the enhancer mutation. This study demonstrates overexpression of GATA2 resulting from a single nucleotide change in an upstream regulatory enhancer element in patients with MonoMAC syndrome.

2023-10-31 | GSE227436 | GEO

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