Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

Area of Science:

• Epigenetics and Chromatin Biology
• Developmental Biology
• Stem Cell Biology

Background:

• Chromatin structure, specifically nucleosome occupancy, dictates DNA accessibility.
• Understanding changes in chromatin during cell state transitions is crucial for developmental and reprogramming studies.

Purpose of the Study:

• To compare nucleosome occupancy across different cell types, including embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cells.
• To develop a bioinformatic method to identify significant differences in nucleosome occupancy between cell states.

Main Methods:

• Micrococcal nuclease digestion followed by sequencing (MNase-seq) to assess nucleosome occupancy.
• Development of a bioinformatic approach to identify "regions of difference" (RoD) in nucleosome occupancy.
• Analysis of RoDs in relation to genes, regulatory elements, and transcription factor binding sites.

Main Results:

• Most chromatin structure remains stable; rearrangements often involve single nucleosomes.
• Regions of difference (RoD) are enriched at genes and regulatory elements, particularly enhancers linked to pluripotency and differentiation.
• Nucleosomal landscapes in ESC enhancers show significantly lower occupancy in pluripotent cells compared to somatic cells.
• RoDs co-localize with binding sites of key developmental regulators like Klf4, Oct4/Sox2, and c-Myc.

Conclusions:

• Changes in nucleosome occupancy are a fundamental characteristic of cell differentiation and reprogramming.
• Identified regions of difference likely represent critical regulatory elements controlling these cellular transitions.
• Most observed nucleosomal changes are reversed during the reprogramming of somatic cells to pluripotency.