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Characterisation of DNA methylomic signatures of induced pluripotent stem cells during neuronal differentiation

ABSTRACT: Characterisation of DNA methylomic signatures of induced pluripotent stem cells during neuronal differentiation

PROVIDER: PRJNA663913 | ENA |

REPOSITORIES: ENA

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Characterisation of DNA methylomic signatures of induced pluripotent stem cells during neuronal differentiation

Project description:In development, inducing pluripotency and differentiation into different cell types results in global epigenetic changes, although the extent this occurs in induced pluripotent stem cell (iPSC)-based neuronal models has not been extensively characterized. We have differentiated iPSCs (33Qn1 cell line) into cortical neurons and assessed their DNA methylation profile at different time points during differentiation and maturation to identify DNA methylomic trajectories of neuronal aging. Samples were collected at four different time points, these were at the iPSC, neuronal precursor (NPC) and two different terminally differentiated neuronal time points (day 37 and day 58). We have identified loci undergoing significant DNA methylation changes throughout differentiation, have created an epigenetic trajectory signature associated with differentiation/maturation and identified highly connected and influential loci using gene-gene interaction analysis.

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Characterization of DNA Methylomic Signatures in Induced Pluripotent Stem Cells During Neuronal Differentiation.

Project description:In development, differentiation from a pluripotent state results in global epigenetic changes, although the extent to which this occurs in induced pluripotent stem cell-based neuronal models has not been extensively characterized. In the present study, induced pluripotent stem cell colonies (33Qn1 line) were differentiated and collected at four time-points, with DNA methylation assessed using the Illumina Infinium Human Methylation EPIC BeadChip array. Dynamic changes in DNA methylation occurring during differentiation were investigated using a data-driven trajectory inference method. We identified a large number of Bonferroni-significant loci that showed progressive alterations in DNA methylation during neuronal differentiation. A gene-gene interaction network analysis identified 60 densely connected genes that were influential in the differentiation of neurons, with STAT3 being the gene with the highest connectivity.

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Project description:The production of alternative RNA variants contributes to the tissue-specific regulation of gene expression. In the animal nervous system, a shift towards more distal 3’ processing sites generates hundreds of substantially extended messenger RNAs. These neuronal transcript signatures are crucial for nervous system development and function. However, no clear understanding of the mechanism of systematic 3’ extension in neurons has yet been achieved. Here, we report that the highly conserved RNA-binding protein ELAV globally regulates all events of neuronal 3’ end processing by directly binding to the proximal 3’ end of its target RNAs. We uncover an endogenous strategy of functional gene rescue, by which neuronal RNA signatures are safeguarded in a loss-of-function context. When not directly repressed by ELAV, the transcript encoding the ELAV paralogue FNE acquires a mini‑exon, which equips the new FNE protein with the ability to translocate to the nucleus and rescue neuronal 3’ end processing. We propose that exon-activated functional rescue is a widespread mechanism that ensures robustness of processes that are regulated by a hierarchy, rather than by redundancy, of effectors.

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