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Transcriptomic and epigenomic analysis during conversion from mouse microglia into induced-neuronal (iN) cells

ABSTRACT: Purpose: The goals of this study are to investigate the mechanisms underlying NeuroD1 (ND1)-mediated reprogramming.

ORGANISM(S): Mus musculus

PROVIDER: GSE104435 | GEO | 2018/12/21

REPOSITORIES: GEO

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Transcriptional changes and microRNA expression profiles during NeuroD1-mediated astrocyte-to-neuron conversion

Project description:To reveal the molecular mechanisms underlying astrocyte-to-neuron reprogramming, we performed RNA-seq analysis on human astrocyte cultures (HA1800) during NeuroD1(ND1)-mediated neuronal reprogramming.

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INDUCTION OF PANCREATIC ISLET CELL DIFFERENTIATION BY THE NEUROGENIN-NEUROD CASCADE

Project description:Neurog3 and NeuroD1 share the ability to induce endocrine differentiation when expressed ectopically in vivo (Apelqvist et al., 1999; Schwitzgebel et al., 2000; Grapin-Botton et al., 2001) and in vitro (Heremans et al., 2002; Gasa et al., 2004), suggesting that they target a common set of genes. To test this hypothesis, we directly compared in the same cells the effects of Neurog3 and NeuroD1 on global gene expression patterns. Normalized M and A values [limmaGUI output] for the neurogenin3 (Ngn3) and neuroD1 (Nd1) experiments (individual or combined) have been linked below as Supplementary files. Note that M=log2(test/ref), eg, log2(Nd1/Bgal); A=[log2(test*ref)]/2, eg, [log2(Nd1*Bgal)]/2. Additional measures of reliability/probability are also included within the supplementary files. Mouse pancreatic ductal cells (mPAC cells) were infected with equal titers of recombinant adenoviruses encoding human Neurogenin3 (AdCMV-NEUROG3) or mouse NeuroD1 (AdCMV-NeuroD1), and 48 hrs later their transcriptomes were compared with that of control cells infected with an adenovirus encoding betagalactosidase (beta-gal; AdCMV-Bgal) using cDNA microarrays. Differences in the activation patterns of the two transcription factors were then determined by comparing the fold-change (FC) values of the pair-wise hybridizations Neurog3/Bgal and NeuroD1/beta-gal.

2007-08-29 | E-GEOD-7884 | biostudies-arrayexpress

INDUCTION OF PANCREATIC ISLET CELL DIFFERENTIATION BY THE NEUROGENIN-NEUROD CASCADE

2007-08-29 | GSE7884 | GEO

Single cell RNA-sequencing analysis of astrocyte-to-neuron conversion in 5xFAD mouse hippocampus

Project description:Collectively, our findings demonstrate that NeuroD1 significantly alters the transcriptomic landscape of astrocytes, suggesting a role for NeuroD1 in neuronal fate reprogramming.

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Project description:Cell fate specification relies on the action of critical transcription factors that become available at distinct stages of embryonic development. One such factor is NeuroD1, which is essential for eliciting the neuronal development program and possesses the ability to reprogram other cell types into neurons. Given this capacity, it is important to understand its targets and the mechanism underlying neuronal specification. Here, we show that NeuroD1 directly binds regulatory elements of neuronal genes that are developmentally silenced by epigenetic mechanisms. This targeting is sufficient to initiate events that confer transcriptional competence, including reprogramming of transcription factor landscape, conversion of heterochromatin to euchromatin and increased chromatin accessibility, indicating potential pioneer factor ability of NeuroD1. The transcriptional induction of neuronal fate genes is maintained via epigenetic memory despite a transient NeuroD1 induction during neurogenesis. Our study not only reveals the NeuroD1-dependent gene regulatory program driving neurogenesis but also increases our understanding of how cell-fate specification during development involves a concerted action of transcription factors and epigenetic mechanisms. 1. Ectopic NeuroD1 was induced for 48 hours (+Dox) in ES cells for checking initiation of neuronal transcriptional program in comparison to uninduced condition (-Dox) 2. ChIP-seq was performed after 24 hours of NeuroD1 induction in ES cells.

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NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

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Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues.

Project description: Not available

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Project description:Transcriptomic and epigenomic analysis during conversion from mouse microglia into induced-neuronal (iN) cells

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