Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
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DOI：
10.1261/rna.1441510
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发表时间：
2010-02-01
期刊：
影响因子：
4.5
通讯作者：
Lipovich, Leonard
中科院分区：
文献类型：
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作者：
Mohamed, Jameelah Sheik;Gaughwin, Philip Michael;Lipovich, Leonard
控制干细胞身份的遗传网络是人们强烈兴趣的焦点，因为它们具有明显的治疗潜力以及与早期发育模型的特殊相关性。小鼠胚胎干细胞（mESC）转录网络的全基因组定位揭示了许多内源性非编码RNA分子，包括长链非编码RNA（lncRNA），可能在控制多能状态中发挥作用。我们进行了全基因组筛选，将全长mESC转录组基因组作图数据与关键mESC转录因子Oct4和Nanog的染色质免疫沉淀基因组定位图相结合。此后，我们确定了四个mESC表达的，保守的lncRNA编码基因的近端的活性基因组结合位点的Oct4和Nanog。因此，这四个基因在多能性中具有潜在的作用。我们发现其中两种lncRNA，AK028326（Oct4激活）和AK141205（Nanog抑制）是Oct4和Nanog的直接靶点。最重要的是，我们证明了这些lncRNA不仅受mESC转录因子的控制，而且它们本身也调节发育状态：这些转录物的敲低和过表达导致Oct4和Nanog mRNA水平的强烈变化，以及细胞谱系特异性基因表达和mESC多能性的改变。我们进一步将AK028326表征为调节反馈回路中Oct4的共激活剂。这些结果首次暗示lncRNA参与mESC多能性的调节，并将已建立的mESC调控网络模型扩展到包括由关键mESC转录因子直接控制的功能性lncRNA。
The genetic networks controlling stem cell identity are the focus of intense interest, due to their obvious therapeutic potential as well as exceptional relevance to models of early development. Genome-wide mapping of transcriptional networks in mouse embryonic stem cells (mESCs) reveals that many endogenous noncoding RNA molecules, including long noncoding RNAs (lncRNAs), may play a role in controlling the pluripotent state. We performed a genome-wide screen that combined full-length mESC transcriptome genomic mapping data with chromatin immunoprecipitation genomic location maps of the key mESC transcription factors Oct4 and Nanog. We henceforth identified four mESC-expressed, conserved lncRNA-encoding genes residing proximally to active genomic binding sites of Oct4 and Nanog. Accordingly, these four genes have potential roles in pluripotency. We show that two of these lncRNAs, AK028326 (Oct4-activated) and AK141205 (Nanog-repressed), are direct targets of Oct4 and Nanog. Most importantly, we demonstrate that these lncRNAs are not merely controlled by mESC transcription factors, but that they themselves regulate developmental state: knockdown and overexpression of these transcripts lead to robust changes in Oct4 and Nanog mRNA levels, in addition to alterations in cellular lineage-specific gene expression and in the pluripotency of mESCs. We further characterize AK028326 as a co-activator of Oct4 in a regulatory feedback loop. These results for the first time implicate lncRNAs in the modulation of mESC pluripotency and expand the established mESC regulatory network model to include functional lncRNAs directly controlled by key mESC transcription factors.