Neural differentiation of human embryonic stem cells

Human embryonic stem cells (hESCs) are pluripotent stem cells derived from the blastocyst stage of early mammalian embryos [Wikipedia]. They can be distinguished by their ability to differentiate into any embryonic cell type [Wikipedia]. During this differentiation process they undergo a variety of chromatin changes that influence gene expression patterns as well as the activity of associated signaling pathways. Here we study the differentiation of human H1 embryonic stem cells (H1-hESC) into neural progenitor cells (NPC).

Analysis

We downloaded ChIP-Seq experiments for H1 cells (ENCSR938GXK) and NPCs (ENCSR539JGB) from the ENCODE portal. In particular, we downloaded BED files containing narrow peaks for the following histone modifications: H3K4me3, H3K9me3, H3K27ac, H3K27me3, H3K36me3. We then used the epigenomics workflow to study which biological pathways are affected by genes whose chromatin state switches from poised in H1-hESCs to active in NPCs.

Data set

The input for the epigenomics workflow is an archive of BED files.

The archive of all BED files used for the analysis can be found here.

Technical Background

Some research projects may have blacklist regions, i.e. regions that are excluded from the analysis. If a data set from a project with blacklisted regions is uploaded, the blacklisted regions should be uploaded as well. Otherwise these regions may cause artifacts in the results, since they appear to have no ChIP-Seq peaks in their vicinity.

Parameter

File upload and genome annotation

  • Used genome assembly: GRCh38 (hg38)
  • Annotation project: GENCODE
  • Include sex chromosomes: yes
  • Include enhancers: yes
  • Gene blacklist: none

Over-representation analysis (ORA)

  • P-value strategy: Upper tailed
  • P-value adjustment method: Benjamini-Hochberg
  • Significance level: 0.05

Step-by-step slideshow

The following slideshow depicts the different analysis steps of the GeneTrail3 workflow.

Results

In the following a few results of our conducted analysis are shown. In particular, we look at biological processes that are affected by genes whose chromatin state is switched from poised in H1-hESCs to active in NPCs. Since this transition should affect genes involved in neural development, we expect to see active biological processes that are in accordance with this process.

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Neuron development

We indeed find many processes that are directly related to neuron development.

Neurogenesis

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Neuron differentiation

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Nervous system development

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Neuron projection

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Neurotrophin activated signaling

Additionally, we see an increased activity of Neurotrophin signaling pathway, which is known to involved in differentiation and survival of neural cells (KEGG). "Neurotrophins exert their functions through engagement of Trk tyrosine kinase receptors or p75 neurotrophin receptor (p75NTR). Neurotrophin/Trk signaling is regulated by connecting a variety of intracellular signaling cascades, which include MAPK pathway, PI-3 kinase pathway, and PLC pathway, transmitting positive signals like enhanced survival and growth (KEGG)." Accordingly, we also see an enrichment of many categories that belong to the MAPK signaling pathway, PI3K signaling pathway, Phospholipase signaling pathway, phosphorilation, cell growth, and proliferation.

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MAPK signaling pathway

GO - Biological Processes

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KEGG

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WikiPathways

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PI3K signaling pathway

KEGG

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WikiPathways

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Phospholipase signaling pathway and phosphorilation

KEGG

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GO - Biological Process

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Cell growth and proliferation

GO - Biological Process

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