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Genome-wide transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

ABSTRACT: We report the genome-wide RNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. RNA-seq was performed to identify all RNAs expressed in both ESCs and neuronal cells. In total, In total, 14,443 expressed genes were detected, of which 1,834 were up-regulated and 1,477 down-regulated (fold change (FC) > -/+2.0 and p-value < 0.035) during RA-induced neuronal differentiation. The top down-regulated genes included members of the pluripotency core transcriptional network, including Klf4, Sox2, Oct4, Nanog, Suz12, Esrrb, Stat3 and Tcfcp2l1. The top up-regulated genes are important for neuronal differentiation (e.g. Pax3, Irx3, Rest and Foxd3) and reside in the RA-pathway (e.g. various homeobox genes), the retinoic acid receptors and the RA-degradation enzyme Cyp26a1. Examination, identification and comparision of mRNA expression profliles in two cellular states.

ORGANISM(S): Mus musculus

SUBMITTER: Michal Stachowiak 

PROVIDER: E-GEOD-65697 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1).

Terranova Christopher C   Narla Sridhar T ST   Lee Yu-Wei YW   Bard Jonathan J   Parikh Abhirath A   Stachowiak Ewa K EK   Tzanakakis Emmanuel S ES   Buck Michael J MJ   Birkaya Barbara B   Stachowiak Michal K MK  

PloS one 20150429 4

Genetic studies have placed the Fgfr1 gene at the top of major ontogenic pathways that enable gastrulation, tissue development and organogenesis. Using genome-wide sequencing and loss and gain of function experiments the present investigation reveals a mechanism that underlies global and direct gene regulation by the nuclear form of FGFR1, ensuring that pluripotent Embryonic Stem Cells differentiate into Neuronal Cells in response to Retinoic Acid. Nuclear FGFR1, both alone and with its partner  ...[more]

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