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Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (tiling)

ABSTRACT: Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with expression tiling arrays to characterize the early dynamics of expression of coding and non-coding RNAs in and around the Hox clusters.

ORGANISM(S): Mus musculus

PROVIDER: GSE61585 | GEO | 2015/04/27

SECONDARY ACCESSION(S): PRJNA261544

REPOSITORIES: GEO

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Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (tiling)

Project description:Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with expression tiling arrays to characterize the early dynamics of expression of coding and non-coding RNAs in and around the Hox clusters. Gene expression is examined at various timepoints (0-72 hrs) after retinoic acid induced neuronal differentiation

2015-04-27 | E-GEOD-61585 | biostudies-arrayexpress

Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters.

Project description:Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with expression tiling arrays and RNA-seq to characterize the early dynamics of expression of coding and non-coding RNAs in and around the Hox clusters. Gene expression is examined at various timepoints (0-72 hrs) after retinoic acid induced neuronal differentiation

2015-04-27 | E-GEOD-67610 | biostudies-arrayexpress

Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters.

Project description:Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with expression tiling arrays and RNA-seq to characterize the early dynamics of expression of coding and non-coding RNAs in and around the Hox clusters.

2015-04-27 | GSE67610 | GEO

Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (ChIP-chip)

Project description:Physiologically relevant concentrations of retinoic acid are added to Mouse ES cells and a time course (0-72 hours) is examined with tiling array ChIP-chip and RNA-seq to characterize the early dynamics of expression of coding and non-coding RNAs and epigenetics in and around the Hox clusters. Expression, epigenetics, and RARs are examined at various timepoints (0-24hrs) after retinoic acid induced neuronal differentiation

2015-04-27 | E-GEOD-61584 | biostudies-arrayexpress

Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (ChIP-chip)

2015-04-27 | GSE61584 | GEO

Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters

Project description:Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters

| PRJNA261542 | ENA

Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters

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

2015-04-27 | GSE61590 | GEO

The Dynamic Architecture of Hox Gene Clusters

Project description:The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the collinear activation of these compact gene clusters.

2011-10-13 | GSE31570 | GEO

The Dynamic Architecture of Hox Gene Clusters

2011-10-12 | E-GEOD-31570 | biostudies-arrayexpress

Rapid clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation: ChIP-chip

Project description:[original Title] Rapid and synchronous clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation. Hox genes are expressed in patterns that are spatially and temporally collinear with their chromosomal organization. This feature is an evolutionarily conserved hallmark of embryonic development, and in vertebrates it is critical, among others, for the specification of motor neuron subtypes and the wiring of sensory-motor circuits. We show here that the differentiation of motor neurons from stem cells is accompanied by a synchronous, domain-wide clearance of M-bM-^@M-^\repressiveM-bM-^@M-^] Polycomb (PcG)-dependent histone methylation from Hox gene chromatin domains. These findings argue against the idea, advanced recently, that the collinear dynamics of Hox gene expression invariably reflects the progressive clearance of repressive chromatin modifications. The rapid establishment of stable chromatin domains in response to a transient patterning signal likely serves as a molecular correlate of enduring rostro-caudal neural identity, which underlies the specification of postmitotic motor neuron subtype diversity and neuronal circuit assembly. The differentiation of ventral motor neurons is induced by treating embryonic stem cell cultures with retinoic acid and hedgehog agonist. Here, ChIP-chip using a custom Agilent array is used to profile the occupancy of H3K27me3, H3K4me3, and H3K79me2 at various defined stages during the differentiation process.

2013-07-04 | E-GEOD-19447 | biostudies-arrayexpress

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