Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA.
Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, California 90095, USA.
Genome Res. 2021 Jun;31(6):1106-1119. doi: 10.1101/gr.273904.120. Epub 2021 Apr 8.
Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular locations in mouse embryonic stem cells, neuronal progenitor cells, and postmitotic neurons. We find disparate patterns of RNA enrichment between the cytoplasmic, nucleoplasmic, and chromatin fractions, with some genes maintaining more polyadenylated RNA in chromatin than in the cytoplasm. We bioinformatically defined four regulatory groups for intron retention, including complete cotranscriptional splicing, complete intron retention in the cytoplasmic RNA, and two intron groups present in nuclear and chromatin transcripts but fully excised in cytoplasm. We found that introns switch their regulatory group between cell types, including neuronally excised introns repressed by polypyrimidine track binding protein 1 (PTBP1). Transcripts for the neuronal gamma-aminobutyric acid (GABA) B receptor, 1 () are highly expressed in mESCs but are absent from the cytoplasm. Instead, incompletely spliced RNA remains sequestered on chromatin, where it is bound by PTBP1, similar to certain long noncoding RNAs. Upon neuronal differentiation, RNA becomes fully processed and exported for translation. Thus, splicing repression and chromatin anchoring of RNA combine to allow posttranscriptional regulation of over development. For this and other genes, polyadenylated RNA abundance does not indicate functional gene expression. Our data sets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
mRNA 成熟的步骤是发生在不同细胞位置的重要基因调控事件。然而，转录组分析通常会丢失加工和未加工转录本的亚细胞分布信息。我们生成了广泛的 RNA-seq 数据集，以追踪小鼠胚胎干细胞、神经祖细胞和有丝分裂后神经元中跨亚细胞位置的 mRNA 成熟情况。我们发现细胞质、核质和染色质部分之间的 RNA 富集模式存在明显差异，有些基因在染色质中保持比细胞质更多的多聚腺苷酸化 RNA。我们通过生物信息学方法定义了内含子保留的四个调控组，包括完全共转录剪接、细胞质 RNA 中的完全内含子保留，以及在核和染色质转录本中存在但在细胞质中完全切除的两个内含子组。我们发现，内含子在细胞类型之间切换其调控组，包括被多嘧啶 tract 结合蛋白 1 (PTBP1) 抑制的神经元剪接内含子。神经元 γ-氨基丁酸 (GABA) B 受体的转录本 1 () 在 mESCs 中高度表达，但不存在于细胞质中。相反，不完全剪接的 RNA 仍然被束缚在染色质上，被 PTBP1 结合，类似于某些长非编码 RNA。在神经元分化过程中，RNA 完全剪接并输出进行翻译。因此，RNA 的剪接抑制和染色质锚定结合起来，允许在发育过程中对 进行转录后调控。对于这个和其他基因，多聚腺苷酸化 RNA 的丰度并不表示功能基因表达。我们的数据集为分析亚细胞位置和发育过程中许多其他方面的 mRNA 成熟提供了丰富的资源。
