Nucleosome dynamics of human iPSC during neural differentiation

Abstract

Nucleosome positioning is important for neurodevelopment, and genes mediating chromatin remodelling are strongly associated with human neurodevelopmental disorders. To investigate changes in nucleosome positioning during neural differentiation, we generate genome‐wide nucleosome maps from an undifferentiated human‐induced pluripotent stem cell (hi PSC ) line and after its differentiation to the neural progenitor cell ( NPC ) stage. We find that nearly 3% of nucleosomes are highly positioned in NPC , but significantly, there are eightfold fewer positioned nucleosomes in pluripotent cells, indicating increased positioning during cell differentiation. Positioned nucleosomes do not strongly correlate with active chromatin marks or gene transcription. Unexpectedly, we find a small population of nucleosomes that occupy similar positions in pluripotent and neural progenitor cells and are found at binding sites of the key gene regulators NRSF / REST and CTCF . Remarkably, the presence of these nucleosomes appears to be independent of the associated regulatory complexes. Together, these results present a scenario in human cells, where positioned nucleosomes are sparse and dynamic, but may act to alter gene expression at a distance via the structural conformation at sites of chromatin regulation.

Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv

“…The only exceptions are CTCF, RAD21, and REST. These factors are commonly associated with strongly phased nucleosomes (Fu et al, 2008;Harwood et al, 2019;Sadeh and Allis, 2011;Wiechens et al, 2016); we speculate that this may render regions bound by them less sensitive to variability in Tn5 concentration. Overall, these results show that technical variation in ATAC-seq data is associated with selectively biased profiling of functional genomic regions.…”

Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

“…If not, we advise to employ N = 250,000, a value we consider to be reliable enough for all different conditions in human, and also in other mammalian genomes like mouse. The only exception to this rule are embryonic stem cell lines, in which nucleosome occupancy has been shown to be significantly lower (Celona et al, 2011;Harwood et al, 2019), with an average number of genomic loci available for binding almost doubled. Thus, for these the suggested value is N = 500,000.…”

Epigenetic regulation in adult neural stem cells

“…There was correlation between nucleosome occupancy and histone modifications in the genome, and there was also an increase in average length of the nucleosomes in the differentiated neuronal cells derived from mouse ESCs ( Teif et al, 2012 ). Nucleosome positioning may be also important for neural differentiation from human iPSCs, with an increase in the number of positioned nucleosomes as well as repositioning of nucleosomes upon differentiation of human iPSCs ( Harwood et al, 2019 ). CTCF is an important regulator in enhancer-promoter interactions and 3D genome organization necessary for proper gene expression ( Ghirlando and Felsenfeld, 2016 ; Chen and Long, 2023 ).…”