Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
Nat Struct Mol Biol. 2011 Nov 6;18(12):1435-40. doi: 10.1038/nsmb.2143.
Transcriptome sequencing allows for analysis of mature RNAs at base pair resolution. Here we show that RNA-seq can also be used for studying nascent RNAs undergoing transcription. We sequenced total RNA from human brain and liver and found a large fraction of reads (up to 40%) within introns. Intronic RNAs were abundant in brain tissue, particularly for genes involved in axonal growth and synaptic transmission. Moreover, we detected significant differences in intronic RNA levels between fetal and adult brains. We show that the pattern of intronic sequence read coverage is explained by nascent transcription in combination with co-transcriptional splicing. Further analysis of co-transcriptional splicing indicates a correlation between slowly removed introns and alternative splicing. Our data show that sequencing of total RNA provides unique insight into the transcriptional processes in the cell, with particular importance for normal brain development.
转录组测序允许在碱基对分辨率下分析成熟的 RNA。在这里，我们表明 RNA-seq 也可用于研究正在转录的新生 RNA。我们对人脑和肝组织的总 RNA 进行了测序，发现多达 40%的读段位于内含子内。内含子 RNA 在脑组织中含量丰富，特别是对于涉及轴突生长和突触传递的基因。此外，我们还检测到胎儿和成人脑组织之间内含子 RNA 水平存在显著差异。我们表明，内含子序列读取覆盖率的模式是由新生转录与共转录剪接共同解释的。对共转录剪接的进一步分析表明，缓慢去除的内含子与选择性剪接之间存在相关性。我们的数据表明，总 RNA 的测序为细胞中的转录过程提供了独特的见解，对于正常的大脑发育尤其重要。
