The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [2]

Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes. Proliferating and retinoic acid (RA-) differentiated N2A cells stably transfected with a non-targeting (scrambled) control vector were compared to proliferating and RA-differentiated N2A cells stably transfected with a Dali knockdown construct. Three biological replicates of each cell type and condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

诸多基因间长链非编码RNA（intergenic long noncoding RNA，lncRNA）基因座可调控邻近蛋白编码基因的表达。目前尚不明确基因间lncRNA是否普遍通过调控基因组远端位点的染色质状态来调控转录。本研究报道了保守表达于中枢神经系统的基因间lncRNA Dali的基因组局部与远端RNA依赖性功能：Dali转录于转录因子基因Pou3f3的下游，敲低Dali会破坏神经母细胞瘤细胞的分化过程。在局部层面，Dali转录本可调控Pou3f3基因座的转录；在远端层面，其优先靶向活性启动子并调控神经分化基因的表达，部分机制依赖于与POU3F3蛋白的物理相互作用。Dali在小鼠与人类细胞中均可与DNA甲基转移酶1（DNA methyltransferase 1，DNMT1）结合，并反式调控CpG岛相关启动子的DNA甲基化状态。本研究首次证实，单条基因间lncRNA可通过调控基因组远端调控元件的活性与甲基化状态，进而调控大规模转录程序。实验中，将稳定转染非靶向（乱序）对照载体的增殖型与经视黄酸（retinoic acid，RA）诱导分化的N2A细胞，与稳定转染Dali敲低载体的同类型细胞进行对照比较；每组细胞类型与培养条件均设置3次生物学重复，并通过Affymetrix GeneChip Mouse Gene 1.0 ST基因芯片完成表达谱分析。