GSE133435
lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture
Both three-dimensional chromatin architecture and long non-coding RNAs (lncRNAs) play essential roles in pluripotency maintenance.  However, whether lncRNAs are involved in organizing 3D chromatin structure remains largely unexplored.  Here, we identified 39 lncRNAs bound by Klf4, a pluripotency factor mediating long-range chromatin interactions.  Among these 39 Klf4-bound lncRNAs, we further investigated the function of 5430416N02Rik.  4C-seq and capture-C experiments revealed that the 5430416N02Rik promoter is a chromatin interaction hub, and 5430416N02Rik RNA functions to facilitate chromatin interactions with the 5430416N02Rik promoter.  Knockout of 5430416N02Rik reduces the proliferation rate of embryonic stem cells (ESCs).  Moreover, compared to deletion of the gene body alone, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and a more profound  impact on the transcriptome.  The reduced proliferation of 5430416N02Rik knockout ESCs is mainly due to the down-regulation of Mid1 transcription, the activation of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci.  In summary, our data demonstrated that lncRNA 5430416N02Rik maintains the proliferation of ESCs by activating the expression of Mid1 through its function of mediating chromatin interaction. Overall design: We performed RIP-seq (5 conditions * 3 replicates), 4C-seq (2 replicates), capture-C-seq (2 conditions * 2 replicates), and RNA-seq (8 conditions * 3 replicates) to investigate the role of lncRNA 5430416N02Rik in proliferation and pluripotency of mouse embryonic stem cells through inter-chromosome interaction.