The NuRD complex regulates chromatin dynamics driving exit from naïve pluripotency

Abstract

The Nucleosome Remodelling and Deacetylase (NuRD) complex is essential for exit from naive pluripotency both in mammalian embryonic stem cell (ESC) culture and in vivo. However, the specific mechanisms of chromatin modulation by NuRD in this process have not been fully characterised. This study used rapid, auxin-inducible removal of NuRD components in mouse ESCs to dissect its role in the regulation of transcription factor (TF) binding dynamics, chromatin accessibility, genome organisation and ultimately gene expression in naive pluripotency through to lineage specification. Single-molecule tracking of pluripotency-associated TFs in live mouse ESCs revealed that remodelling by NuRD acts to actively promote the dissociation of these TFs from chromatin, limiting their residence times. The regulation of TF occupancy through modulation of dissociation rates was also discovered to play a role in the early ERK response, a major pathway driving lineage specification. In vitro neuroectodermal specification combined with the removal of NuRD at different timepoints showed that NuRD was required for sufficient upregulation of the formative pluripotency gene regulatory network, ensuring proper passage through intermediate formative pluripotency before lineage specification. High-resolution imaging uncovered a large-scale reorganisation of highly accessible chromatin during pluripotency progression, which is dependent on NuRD. Notably, NuRD was found to regulate a global loss in chromatin accessibility from naive to formative pluripotency. NuRD specifically facilitates silencing of a set of ‘permissive’ enhancers that, if left accessible, allow for aberrant expression of genes specifying non-neuroectodermal germ layers. This work demonstrates that NuRD can act in a complex and context-dependent manner to regulate TF binding dynamics, chromatin accessibility, genome organisation and ultimately transcription to coordinate cell fate decisions.