lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs

Abstract

The open chromatin of embryonic stem cells (ESCs) condenses into repressive heterochromatin as cells exit the pluripotent state. How the 3D genome organization is orchestrated and implicated in pluripotency and lineage specification is not understood. Here, we find that maturation of the long noncoding RNA (lncRNA) pRNA is required for establishment of heterochromatin at ribosomal RNA genes, the genetic component of nucleoli, and this process is inactivated in pluripotent ESCs. By using mature pRNA to tether heterochromatin at nucleoli of ESCs, we find that localized heterochromatin condensation of ribosomal RNA genes initiates establishment of highly condensed chromatin structures outside of the nucleolus. Moreover, we reveal that formation of such highly condensed, transcriptionally repressed heterochromatin promotes transcriptional activation of differentiation genes and loss of pluripotency. Our findings unravel the nucleolus as an active regulator of chromatin plasticity and pluripotency and challenge current views on heterochromatin regulation and function in ESCs.

Role of the small subunit processome in the maintenance of pluripotent stem cells

“…First, in accordance with enhanced protein synthesis, our results and previous transcriptome/proteome data show that SSUP genes are up-regulated in undifferentiated cells compared with their differentiated counterparts. Consistently, the rDNA promoter is unmethylated and kept in an open state in mESCs, producing a high level of pre-rRNA (Savic et al 2014). Second, as pluripotent stem cells divide rapidly, they have a high demand for protein synthesis to support their unusually accelerated proliferation.…”

Helicase CHD4 is an epigenetic coregulator of PAX3-FOXO1 in alveolar rhabdomyosarcoma

“…ChIP has been recently described (73). For each ChIP assay, 30 μg of cross-linked and sonicated chromatin was incubated with 4 μg of antibody.…”

Long noncoding RNAs as Organizers of Nuclear Architecture

“…A recent report has revealed that the maturation of pRNA, originated from the processing of an IGS lncRNA, is required for the establishment of heterochromatin at ribosomal RNA genes during ES cell differentiation (Savic et al, 2014). These data suggested that lncRNA regulates the structure and function of the nucleolus under environmental stimuli and during development.…”