Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comprehensive, high resolution analysis of cis-acting regulatory networks at the alpha globin locus (array)

ABSTRACT: We have combined the 4C chromosome conformation capture protocol with high throughput, genome-wide sequence analysis to characterise in full a cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000kb), the 4C approach provides a comprehensive, high resolution analysis of a specific locus with the aim of defining, in detail, all cis- regulatory elements controlling a single gene or gene cluster. Using the human M-NM-1-globin locus as a model we detected all known local and long-range interactions with this gene cluster. In addition we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the M-NM-1-globin cluster. Using paired-end sequencing it was possible for the first time to identify interactions between specific subsets of cis-regulatory elements in populations of cells and within individual cells. Two biological replicates of 4C amplification from the promoters of the human HBA and HBB genes and B-Cell controls. Quality of B-cell material was confirmed using amplification from a CTCF bound region associated with Human Axin Gene.

ORGANISM(S): Homo sapiens

SUBMITTER: Richard Gibbons

PROVIDER: E-GEOD-42383 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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High-resolution analysis of cis-acting regulatory networks at the α-globin locus.

Hughes Jim R JR Lower Karen M KM Dunham Ian I Taylor Stephen S De Gobbi Marco M Sloane-Stanley Jacqueline A JA McGowan Simon S Ragoussis Jiannis J Vernimmen Douglas D Gibbons Richard J RJ Higgs Douglas R DR

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20130506 1620

We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a ...[more]

PMID: 23650635

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Project description:Thyroid hormone receptors (TRs) represent important regulators of development, homeostasis, cell proliferation and differentiation. Here we investigated the impact of thyroid hormone (T3) on growth and differentiation of human red blood cells. T3 was found to effectively accelerate differentiation of SCF/Epo dependent red cell progenitors in vitro concomitantly with inducing growth arrest. This T3 activity was further enhanced by 9-cis retinoic acid (9cRA) that activates retinoid X receptor (RXR), the obligate heterodimeric partner of TR. To identify molecular targets for T3 activity in red cells, we employed a genome wide approach with DNA microarrays. We demonstrate that T3 and 9cRA induces specific gene expression patterns of up-or down-regulated genes, including ALAD and GATA-2, respectively. This study also revealed gene clusters, indicating accelerated differentiation in response to treatment. Mining for T3 induced genes identified BTEB1 (KLF9) and GAR22 as TR target genes. BTEB1/ KLF9 (basic transcription element binding protein 1/ KrÃ¼ppel-like factor 9) is a known TR target gene. GAR22 (growth arrest specific 2 (GAS2)-related gene on chromosome 22), initially found as a putative tumor suppressor gene, was induced by T3 also in the presence of cycloheximide, identifying it as a direct target of TR. Thus, our study uncovers novel targets of TR action with a potential function in T3 induced differentiation and growth arrest of red cell progenitors. Experiment Overall Design: 13 hybridizations in two individual experiments. Experiment Overall Design: Experiment 1: Experiment Overall Design: 1_SCF/Epo, 1_Epo/insulin(8h), 1_Epo/insulin(24h), 1_Epo/insulin(48h) Experiment Overall Design: Experiment 2: Experiment Overall Design: 2_SCF/Epo, 2_Epo/insulin(8h), 2_Epo/insulin(24h), 2_Epo/insulin(48h) Experiment Overall Design: 2_Epo/insulin+T3(8h), 2_Epo/insulin+9cRA(8h) Experiment Overall Design: 2_Epo/insulin+T3+9cRA(8h), , 2_Epo/insulin+T3+9cRA(24h), 2_Epo/insulin+T3+9cRA(48h)

Dataset Information

Comprehensive, high resolution analysis of cis-acting regulatory networks at the alpha globin locus (array)

Publications

High-resolution analysis of cis-acting regulatory networks at the α-globin locus.

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