a Department of Molecular Biology and Genetics , Aarhus University , Aarhus , Denmark.
b Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus , Denmark.
RNA Biol. 2018 Feb 1;15(2):280-291. doi: 10.1080/15476286.2017.1409931. Epub 2017 Dec 28.
The expression patterns of endogenous circular RNA (circRNA) molecules during epidermal stem cell (EpSC) differentiation have not previously been explored. Here, we show that circRNAs are abundantly expressed in EpSCs and that their expression change dramatically during differentiation in a coordinated manner. Overall, circRNAs are expressed at higher levels in the differentiated cells, and many upregulated circRNAs are derived from developmental genes, including four different circRNAs from DLG1. The observed changes in circRNA expression were largely independent of host gene expression, and circRNAs independently upregulated upon differentiation are more prone to AGO2 binding and have more predicted miRNA binding sites compared to stably expressed circRNAs. In particular, upregulated circRNAs from the HECTD1 and ZNF91 genes have exceptionally high numbers of AGO2 binding sites and predicted miRNA target sites, and circZNF91 contains 24 target sites for miR-23b-3p, which is known to play important roles in keratinocyte differentiation. We also observed that upregulated circRNAs are less likely to be flanked by homologues inverted Alu repeats compared to stably expressed circRNAs. This coincide with DHX9 being upregulated in the differentiated keratinocytes. Finally, none of the circRNAs upregulated upon differentiation were also upregulated upon DNMT3A or DNMT3B knockdown, making it unlikely that epigenetic mechanisms are governing the observed circRNA expression changes. Together, we provide a map of circRNA expression in EpSCs and their differentiated counterparts and shed light on potential function and regulation of differentially expressed circRNAs.
内源性环状 RNA（circRNA）分子在表皮干细胞（EpSC）分化过程中的表达模式尚未被探索。在这里，我们表明 circRNA 在 EpSCs 中大量表达，并且它们的表达在分化过程中以协调的方式发生显著变化。总体而言，分化细胞中 circRNA 的表达水平更高，许多上调的 circRNA 来自发育基因，包括 DLG1 基因的四个不同的 circRNA。circRNA 表达的观察到的变化在很大程度上独立于宿主基因表达，并且在分化时独立上调的 circRNA 更倾向于与 AGO2 结合，并且与稳定表达的 circRNA 相比，具有更多预测的 miRNA 结合位点。特别是，HECTD1 和 ZNF91 基因的上调 circRNA 具有异常高数量的 AGO2 结合位点和预测的 miRNA 靶位点，并且 circZNF91 包含 24 个 miR-23b-3p 的靶位点，miR-23b-3p 已知在角质形成细胞分化中发挥重要作用。我们还观察到，与稳定表达的 circRNA 相比，上调的 circRNA 不太可能被同源倒置 Alu 重复序列包围。这与分化的角质形成细胞中 DHX9 的上调一致。最后，分化过程中上调的 circRNA 没有一个也在 DNMT3A 或 DNMT3B 敲低时上调，这使得表观遗传机制不太可能控制观察到的 circRNA 表达变化。总之，我们提供了 EpSCs 及其分化对应物中 circRNA 表达的图谱，并揭示了差异表达 circRNA 的潜在功能和调节。
