Suppression of Progenitor Differentiation Requires the Long Non-Coding RNA ANCR [lincRNA 391k Tiling Array V2]

Long non-coding RNAs (lncRNAs) regulate diverse processes, yet a potential role for lncRNAs in maintaining the undifferentiated state in somatic tissue progenitor cells remains uncharacterized. We used transcriptome sequencing and tiling arrays to compare lncRNA expression in epidermal progenitor populations versus differentiating cells. We identified ANCR (anti differentiation ncRNA) as an 855 bp lncRNA down-regulated during differentiation. Depleting ANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis. Custom tiling arrays designed to assay the intergenic space corresponding to regions of H3K4me3-H3K36me3 domains (Khalil et al., 2009) were used to assay changes in RNA expression of putative lncRNAs. RNA from progenitor populations and terminally differentiated populations of human keratinocytes, adipocytes, and osteoblasts were hybridized to these arrays and differential expression was assessed.

长链非编码RNA（long non-coding RNAs，lncRNAs）参与调控多种生物学过程，但lncRNAs在维持体细胞组织祖细胞未分化状态中的潜在作用仍未被阐明。本研究通过转录组测序与瓦片阵列（tiling arrays）技术，对比了表皮祖细胞群体与分化细胞中的lncRNA表达谱，鉴定出ANCR（抗分化非编码RNA，anti-differentiation ncRNA）是一条在分化过程中表达下调的855 bp长链非编码RNA。在仅含祖细胞的群体中敲低ANCR且无需其他外界刺激，即可快速诱导分化相关基因的表达。在表皮组织中，ANCR的缺失会破坏正常情况下祖细胞所在区域对分化过程的排斥作用，由此可见，ANCR长链非编码RNA对于维持表皮组织内细胞的未分化状态是必需的。本研究使用针对H3K4me3-H3K36me3结构域对应基因间区域设计的定制化瓦片阵列（Khalil等，2009），检测预测性lncRNA的RNA表达变化；将人类角质形成细胞、脂肪细胞和成骨细胞的祖细胞群体及终末分化细胞群体的RNA与上述阵列进行杂交，并评估其差异表达情况。