Nuclear retention of mRNA in mammalian tissues. Mus musculus

Messenger RNA is thought to predominantly reside in the cytoplasm, where it is translated and eventually degraded. Although nuclear retention of mRNA has a regulatory potential it is considered extremely rare in mammals. Here to explore the extent of mRNA retention in metabolic tissues we combine deep sequencing of nuclear and cytoplasmic RNA fractions with single molecule transcript imaging in mouse beta cells, liver and gut. We identify a wide range of protein coding genes for which the levels of spliced polyadenylated mRNA are higher in the nucleus than in the cytoplasm. These include genes such as the transcription factor ChREBP, Nlrp6, Glucokinase and Glucagon receptor. We demonstrate that nuclear retention of mRNA can efficiently buffer cytoplasmic transcript levels from noise that emanates from transcriptional bursts. Our study challenges the view that transcripts predominantly reside in the cytoplasm and reveals a role of the nucleus in dampening gene expression noise. Overall design: we have total of 8 samples all are mice. liver nuclear RNA (2 replicates), liver cytoplasmic RNA (2 replicates), MIN6 (cell line) nuclear RNA (2 replicates), MIN6 (cell line) cytoplasmic RNA (2 replicates)

学界普遍认为，信使RNA（Messenger RNA，mRNA）主要定位于细胞质，并在其中完成翻译过程，最终发生降解。尽管mRNA的核滞留具备调控潜力，但在哺乳动物中该现象被认为极为罕见。为探究代谢组织中mRNA核滞留的普遍程度，本研究结合核质RNA组分深度测序与单分子转录本成像技术，在小鼠β细胞、肝脏及肠道中开展相关实验。本研究鉴定出大量蛋白编码基因，其剪接后多聚腺苷酸化mRNA在细胞核中的表达水平显著高于细胞质。此类基因包括转录因子ChREBP、Nlrp6、葡萄糖激酶（Glucokinase）以及胰高血糖素受体（Glucagon receptor）。研究证实，mRNA的核滞留可有效缓冲由转录爆发产生的噪声对细胞质转录本水平的影响。本研究挑战了"转录本主要定位于细胞质"的传统观点，并揭示了细胞核在抑制基因表达噪声方面的新功能。实验整体设计：本研究共包含8个小鼠来源样本，分别为肝脏细胞核RNA（2个生物学重复）、肝脏细胞质RNA（2个生物学重复）、MIN6细胞系细胞核RNA（2个生物学重复）以及MIN6细胞系细胞质RNA（2个生物学重复）。