Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming

Abstract

Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both gene-proximal promoter regions and distally located regulatory elements. In the three-dimensional space of the nucleus, distal elements are localized in close physical proximity to the gene-proximal regulatory sequences through the formation of chromatin loops. These looping features in the genome are highly dynamic as embryonic stem cells differentiate and commit to specific lineages, and throughout reprogramming as differentiated cells reacquire pluripotency. Identifying these functional distal regulatory regions in the genome provides insight into the regulatory processes governing early mammalian development and guidance for improving the protocols that generate induced pluripotent cells.

Keywords: chromatin; chromatin looping; differentiation; embryonic stem cell; epigenetics; gene expression; induced pluripotent stem cell; reprogramming; transcription factor.

Figure 1

Changes in chromatin accessibility and modification drive the processes of differentiation and reprogramming. Pluripotent cells possess less compact chromatin compared to differentiated cells (light and medium intensity blue, respectively) and lack the compact chromocentres (dark blue) present in differentiated cells (top). The more open chromatin configuration in ES and iPS cells creates less nucleosome compaction (bottom left); as a result, nucleosomes are found in smaller clutches in ES and iPS cells as indicated by two clutches of four and seven nucleosomes, respectively. On the right the more compact chromatin of differentiated cells displays a greater overall density of nucleosomes and larger clutches of nucleosomes. Despite this chromatin compaction in differentiated cells, the reprogramming factors, OSKM, can access enhancer regions in condensed chromatin (blue bar), initiate chromatin remodeling at the enhancer, lead to chromatin remodeling at the gene (black bar) TSS, and eventually activate target genes as cells acquire the iPS state. This process converts the heterochromatic regions in fibroblasts marked by H4K27me3 to euchromatic regions in the iPS cells marked by H3K27ac and H3K4me1 or H3K4me3 at the enhancer and promoter respectively. CTCF and cohesin are found at both tissue-specific and constitutive chromatin loops. The coactivators (p300 and the mediator complex) are found at tissue-specific enhancer-promoter chromatin loops and are thought to bridge transcription factors at distal enhancers to the RNA polymerase II complex at the gene TSS.