A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
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全基因组长非编码 RNA CRISPRi 筛选将 PRANCR 鉴定为表皮稳态的新型调节剂
DOI：
10.1101/gr.251561.119
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发表时间：
2020-01-01
期刊：
影响因子：
7
通讯作者：
Sun, Bryan K.
中科院分区：
文献类型：
--
作者：
Cai, Pengfei;Otten, Auke B. C.;Sun, Bryan K.
全基因组关联研究表明，许多疾病易感区域位于基因组的非蛋白质编码区。长链非编码RNA（lncRNA）是非编码基因组的主要组成部分，但其生物学影响尚未完全了解。在这里，我们对2263种表皮表达的lncRNA进行了CRISPR干扰（CRISPRi）筛选，并鉴定了9种调节角质形成细胞增殖的新型候选lncRNA。我们使用RNA干扰介导的敲低和器官型人类组织中的表型分析，进一步表征了来自筛选的顶部命中，祖细胞更新相关非编码RNA（PRANCR）。PRANCR调节角质形成细胞增殖、细胞周期进程和克隆形成。PRANCR缺陷的表皮表现出分层受损，分化基因表达减少，这些基因在人类皮肤病中改变，包括角蛋白1和10、聚丝蛋白和兜甲蛋白。转录组分析表明，PRANCR控制1136个基因的表达，具有较强的富集细胞周期晚期基因，含有一个启动子元件。此外，PRANCR耗竭导致总CDKN1A和细胞核CDKN1A（也称为p21）水平增加，已知其控制角质形成细胞增殖和分化。总的来说，这些数据表明，PRANCR是一种新的lncRNA调节表皮稳态，并确定其他lncRNA候选人，可能在这一过程中的作用。
Genome-wide association studies indicate that many disease susceptibility regions reside in non-protein-coding regions of the genome. Long noncoding RNAs (lncRNAs) are a major component of the noncoding genome, but their biological impacts are not fully understood. Here, we performed a CRISPR interference (CRISPRi) screen on 2263 epidermis-expressed lncRNAs and identified nine novel candidate lncRNAs regulating keratinocyte proliferation. We further characterized a top hit from the screen, progenitor renewal associated non-coding RNA (PRANCR), using RNA interference–mediated knockdown and phenotypic analysis in organotypic human tissue. PRANCR regulates keratinocyte proliferation, cell cycle progression, and clonogenicity. PRANCR-deficient epidermis displayed impaired stratification with reduced expression of differentiation genes that are altered in human skin diseases, including keratins 1 and 10, filaggrin, and loricrin. Transcriptome analysis showed that PRANCR controls the expression of 1136 genes, with strong enrichment for late cell cycle genes containing a CHR promoter element. In addition, PRANCR depletion led to increased levels of both total and nuclear CDKN1A (also known as p21), which is known to govern both keratinocyte proliferation and differentiation. Collectively, these data show that PRANCR is a novel lncRNA regulating epidermal homeostasis and identify other lncRNA candidates that may have roles in this process as well.