Ontology highlight
ABSTRACT:
PROVIDER: PRJNA703755 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13762100_1.fastq.gz | Fastqsanger.gz | |||
| SRR13762100_2.fastq.gz | Fastqsanger.gz | |||
| SRR13762101_1.fastq.gz | Fastqsanger.gz | |||
| SRR13762101_2.fastq.gz | Fastqsanger.gz | |||
| SRR13762102_1.fastq.gz | Fastqsanger.gz |
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Project description:Delta-Beta thalassemia is an unusual variant of thalassemia caused by large deletions in the β globin gene cluster involving δ- and β-globin genes. The mutations are characterized by high fetal hemoglobin with significant phenotypic diversity. Routinely used diagnostic tests targeting point mutations and small insertions, deletions of the β-globin gene are not suitable for detection of large deletion mutations. This is overcome by either direct globin chain synthesis analysis or beta-cluster gene analysis using different methods. In the current study, we use direct globin chain analysis to diagnose a family with δβ-thalassemia using high resolution mass spectrometry.
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Project description:In genomes of modern fish and amphibia α- and β- globin genes are grouped at a single locus that may resemble the ancestral one and is syntenic to α-globin locus of modern warm-blooded vertebrates. In Danio rerio, the major locus of α/β globin genes comprises two subclusters, one of them harboring genes expressed in adult and the other – genes expressed in embryonic and larval erythrocytes. The results of our previous study suggested that the adult subcluster of this locus has evolved into α-globin gene domain of vertebrate animals. Here we studied how adult and embryo-larval genes of Danio rerio major globin gene locus are repressed in fibroblasts. The results obtained suggest that that at least some of the globin genes present within the adult subcluster are repressed by Polycomb similarly to human α-globin genes. Furthermore, within two α/β gene pairs repression of α-type and β-type genes appears to be mediated by different mechanisms as increasing the level of histone acetylation can activate transcription of only β-type genes.
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Project description:Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and find that globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detect distinct folding patterns at the developmentally controlled b-globin locus. Specifically, new fetal stage-specific contacts are uncovered between a region separating the fetal (g-) and adult (b-) globin genes (encompassing the HBBP1 and BGLT3 non-coding genes) and two distal chromosomal sites (HS5 and 3'HS1) that flank the locus. In contrast, in adult cells the HBBP1-BGLT3 region contacts the embryonic e-globin gene, physically separating the fetal globin genes from the enhancer (LCR). Removal of the HBBP1 gene strongly reactivates g-globin expression, accompanied by increased LCR-g-globin and decreased BGLT3-e-globin interactions, mimicking the effects of deleting the fetal globin repressor BCL11A. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements.
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Project description:The alpha and beta-globin loci harbour genes that are expressed during development and silenced throughout post-natal life. Learning to reactivate these genes may offer new therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address the mechanisms underlying the regulation of the gene encoding zeta-globin, the embryonically expressed alpha-like globin.
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Project description:Haemoglobin, the oxygen-carrying molecule of red blood cells, at all stages of development comprises a tetramer of two α-like and two β-like globin chains. In humans and mice the highly conserved α- and β-globin loci contain genes encoding globin chains specifically expressed only during the first trimester of gestation (termed embryonic globins) in addition to the genes encoding globin chains expressed throughout adult life. In humans the β-globin locus also encodes a β-like chain that is expressed throughout the second and third trimesters of development; this is termed γ-globin and complexes with α-globin to form fetal haemoglobin (HbF). The sequential activation and repression of the genes at each of these loci throughout development to maturity is termed haemoglobin switching and is a poorly understood process. α-thalassemia, which results from insufficient production of α-globin, is a major global health problem with several hundred thousand sufferers world-wide. The embryonically expressed ζ-globin, encoded by the gene HBZ (Hba-x in mice), can functionally substitute for α-globin in adult erythroid cells. Reactivation of this gene is consequently likely to ameliorate the symptoms of α-thalassemia in individuals with a severe phenotype. Little is currently known about the regulation of ζ-globin expression in terms of both the trans- and cis-acting regulatory elements responsible for high-levels of expression of this gene during embryonic erythropoiesis and its maintenance in a transcriptionally inactive state throughout adult life. Using ATACseq and NG Capture C and mutant mouse lines this work aims to identify and define the cis-acting regulatory network underlying zeta-globin expression, and define the contribution of each regulatory element.
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Project description:Haemoglobin, the oxygen-carrying molecule of red blood cells, at all stages of development comprises a tetramer of two α-like and two β-like globin chains. In humans and mice the highly conserved α- and β-globin loci contain genes encoding globin chains specifically expressed only during the first trimester of gestation (termed embryonic globins) in addition to the genes encoding globin chains expressed throughout adult life. In humans the β-globin locus also encodes a β-like chain that is expressed throughout the second and third trimesters of development; this is termed γ-globin and complexes with α-globin to form fetal haemoglobin (HbF). The sequential activation and repression of the genes at each of these loci throughout development to maturity is termed haemoglobin switching and is a poorly understood process. α-thalassemia, which results from insufficient production of α-globin, is a major global health problem with several hundred thousand sufferers world-wide. The embryonically expressed ζ-globin, encoded by the gene HBZ (Hba-x in mice), can functionally substitute for α-globin in adult erythroid cells. Reactivation of this gene is consequently likely to ameliorate the symptoms of α-thalassemia in individuals with a severe phenotype. Little is currently known about the regulation of ζ-globin expression in terms of both the trans- and cis-acting regulatory elements responsible for high-levels of expression of this gene during embryonic erythropoiesis and its maintenance in a transcriptionally inactive state throughout adult life. Using ATACseq, ChIP-seq and NG Capture C and mutant mouse lines this work aims to identify and define the cis-acting regulatory network underlying zeta-globin expression, and define the contribution of each regulatory element.
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