Both 3D 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. We identified 39 lncRNAs bound by Klf4, among which we further revealed the 5430416N02Rik promoter is a chromatin interaction hub. Knockout of the 5430416N02Rik locus reduces the proliferation rate of embryonic stem cells (ESCs). Moreover, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and has a more profound impact on the transcriptome than deleting the gene body alone. The reduced proliferation of the 5430416N02Rik locus knockout ESCs is mainly due to the downregulation of Mid1, the expression of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci. In summary, our data demonstrated that the lncRNA 5430416N02Rik gene locus maintains the fast proliferation of ESCs by activating the expression of Mid1 through chromatin interaction.

3D染色质体系结构和长非编码RNA（lncRNA）都在多能性维持中起着至关重要的作用。但是，lncRNAs是否参与组织3D染色质结构尚不清楚。我们鉴定了39个与Klf4结合的lncRNA，其中我们进一步揭示了5430416N02Rik启动子是染色质相互作用的中心。所述的敲除5430416N02Rik轨迹降低的胚胎干细胞（ESC）的增殖速率。而且，与单独删除基因体相比，删除5430416N02Rik的启动子和基因体均会导致更严重的增殖缺陷，并对转录组产生更深远的影响。5430416N02Rik的增殖减少基因敲除ESCs主要是由于Mid1的下调，其表达需要Mid1与5430416N02Rik基因座之间的染色体间相互作用。总之，我们的数据表明，lncRNA 5430416N02Rik基因位点通过染色质相互作用激活Mid1的表达，从而维持ESC的快速增殖。