Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (ATAC-Seq)

Here, we showed that a long non-coding RNA (lncRNA), ncRNA-a3 that is transcribed from TAL1 erythroid +51kb enhancer, is required for TAL1 activation during EPO-induced lineage commitment and formation of erythroblasts. ncRNA-a3 regulates long-range chromatin interactions between +51 enhancer, promoter and other regulatory elements in the TAL1 locus to maintain the erythroid interaction hub. By binding and recruiting p300/BRG1 to the TAL1 locus ncRNA-a3 facilitates chromatin accessibility in the TAL1 locus and activates TAL1 transcription program, including subsequent epigenetic and transcriptional activation of erythroid specific TAL1 target genes. We performed the RNA-seq, ATAC-seq, Cut&Run, NG Capture-C for WT and ncRNA-a3 KD in K562 cell lines and primary CD34+ cord blood hematopoietic cells to investigate ncRNA-a3 function during erythropoiesis

本研究证实，源自TAL1红细胞系+51kb增强子的长链非编码RNA（long non-coding RNA，lncRNA）ncRNA-a3，在促红细胞生成素（Erythropoietin，EPO）诱导的细胞谱系定向分化及成红细胞形成过程中，是TAL1基因激活所必需的。ncRNA-a3通过调控TAL1基因座上+51kb增强子、启动子与其他调控元件之间的远程染色质相互作用，维持红细胞系相互作用枢纽的稳定性。该长链非编码RNA可结合并招募p300/BRG1至TAL1基因座，增强该基因座的染色质开放性，进而激活TAL1转录程序，包括后续红细胞系特异性TAL1靶基因的表观遗传与转录激活。本研究在K562细胞系与原代CD34+脐带血造血细胞中分别设置野生型（wild type，WT）及ncRNA-a3敲低（knockdown，KD）组，通过RNA测序（RNA-seq）、转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing，ATAC-seq）、靶标切割与释放法（Cleavage Under Targets and Release Using Nuclease，Cut&Run）及下一代捕获-C测序（Next-Generation Capture-C，NG Capture-C）实验，探究ncRNA-a3在红细胞生成过程中的功能。