Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Elife. 2024 Apr 3;12:RP87811. doi: 10.7554/eLife.87811.
Aging and senescence are characterized by pervasive transcriptional dysfunction, including increased expression of transposons and introns. Our aim was to elucidate mechanisms behind this increased expression. Most transposons are found within genes and introns, with a large minority being close to genes. This raises the possibility that transcriptional readthrough and intron retention are responsible for age-related changes in transposon expression rather than expression of autonomous transposons. To test this, we compiled public RNA-seq datasets from aged human fibroblasts, replicative and drug-induced senescence in human cells, and RNA-seq from aging mice and senescent mouse cells. Indeed, our reanalysis revealed a correlation between transposons expression, intron retention, and transcriptional readthrough across samples and within samples. Both intron retention and readthrough increased with aging or cellular senescence and these transcriptional defects were more pronounced in human samples as compared to those of mice. In support of a causal connection between readthrough and transposon expression, analysis of models showing induced transcriptional readthrough confirmed that they also show elevated transposon expression. Taken together, our data suggest that elevated transposon reads during aging seen in various RNA-seq dataset are concomitant with multiple transcriptional defects. Intron retention and transcriptional readthrough are the most likely explanation for the expression of transposable elements that lack a functional promoter.
衰老是一个普遍存在的转录功能障碍的过程,包括转座子和内含子的表达增加。我们的目的是阐明这种表达增加的机制。大多数转座子位于基因和内含子内,只有一小部分靠近基因。这就提出了一个可能性,即转录通读和内含子保留可能是导致转座子表达随年龄变化的原因,而不是自主转座子的表达。为了验证这一点,我们编译了来自衰老的人类成纤维细胞、人类细胞的复制性和药物诱导性衰老以及衰老小鼠和衰老小鼠细胞的 RNA-seq 的公共 RNA-seq 数据集。实际上,我们的重新分析揭示了跨样本和样本内转座子表达、内含子保留和转录通读之间的相关性。内含子保留和通读都随着衰老或细胞衰老而增加,并且与小鼠相比,这些转录缺陷在人类样本中更为明显。为了支持通读和转座子表达之间存在因果关系,对显示诱导转录通读的模型的分析证实,它们也显示出转座子表达的升高。总之,我们的数据表明,在各种 RNA-seq 数据集中观察到的衰老过程中,转座子的转录本升高伴随着多种转录缺陷。内含子保留和转录通读是缺乏功能性启动子的可移动元件表达的最可能解释。