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Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE54761 | GEO | 2015/02/04

SECONDARY ACCESSION(S): PRJNA237563

REPOSITORIES: GEO

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Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-02-04 | E-GEOD-54761 | biostudies-arrayexpress

Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [RNA-seq]

Project description:We knocked down TR4 expression by 2 lentiviral mediated vectors at day 11 of erythroid differentiation in order to identify TR4 downstream targets. Two lentiviruses and one empty control were used to knockdown TR4 expression. The cells were harvested at day 11 during erythroid differentiation.

2015-02-04 | E-GEOD-54760 | biostudies-arrayexpress

Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [ChIP-seq]

Project description:In this study, we resolved the genome-wide binding of TR4 in differentiating human erythroid cells by performing chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). We found that TR4 preferentially binds to DR1 elements in the promoters of its target genes, and that the majority of these genes encode proteins that participate in fundamental biological functions such as mRNA processing, translation, RNA splicing and primary metabolic process. Interestingly, we also found an increased occurrence of other repeat element motifs (such as DR4, IR1 and ER6) at TR4-bound distal sites that are located more than 10 Kbp away from the nearest gene. This raises the tantalizing possibility that TR4 may heterodimerize with unique partners, including other nuclear receptors such as RXR, thus allowing TR4 to elicit unique transcriptional responses when acting at proximal (promoter) and distal (enhancer and silencer) regulatory sites during human erythropoiesis. Examination of TR4 genome wild binding in human erythroid cells, which are harvested at day 8, 11 and 14 during in vitro differentiation. Two replicates were included for each differentiation stage.

2015-02-04 | E-GEOD-54759 | biostudies-arrayexpress

Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [ChIP-seq]

2015-02-04 | GSE54759 | GEO

Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [RNA-seq]

Project description:We knocked down TR4 expression by 2 lentiviral mediated vectors at day 11 of erythroid differentiation in order to identify TR4 downstream targets.

2015-02-04 | GSE54760 | GEO