DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency

Area of Science:

• Epigenetics
• Stem Cell Biology
• Genomics

Background:

• Ground-state naive pluripotency in embryonic stem cells (ESCs) involves DNA hypomethylation.
• This hypomethylation is associated with the redistribution of Polycomb repressive complex 2 (PRC2) and its histone mark H3K27me3.
• Changes in 3D genome organization accompany these epigenetic modifications.

Purpose of the Study:

• To investigate the impact of DNA hypomethylation on 3D genome organization during the transition to the ESC ground state.
• To determine if restoring DNA methylation can reverse alterations in 3D genome structure and Polycomb distribution.
• To assess the functional consequences of maintaining normal 3D genome organization in ground-state ESCs.

Main Methods:

• Culturing ESCs in the presence of two small molecule inhibitors (2i) to induce the ground state.
• Manipulating DNA methylation levels during the transition to the ground state.
• Analyzing H3K27me3 distribution using ChIP-seq.
• Assessing 3D genome organization using techniques like Hi-C.
• Evaluating functional characteristics of ESCs.

Main Results:

• Culture in 2i leads to DNA hypomethylation, H3K27me3 redistribution away from target loci, and chromatin decompaction.
• Long-range Polycomb interactions are lost in 2i conditions.
• Preventing DNA hypomethylation in 2i-cultured ESCs restores H3K27me3 distribution and Polycomb-mediated 3D genome organization.
• These restored cells maintain functional ground-state ESC characteristics.

Conclusions:

• DNA methylation plays a critical role in shaping 3D genome organization in ESCs.
• The epigenetic landscape and 3D genome organization are not solely causal for gene regulation and function in ESCs.
• Dissecting the interplay between DNA methylation, Polycomb, and 3D genome structure is crucial for understanding ESC pluripotency.