Chung Nicky, Jonaid G M, Quinton Sophia, Ross Austin, Sexton Corinne E, Alberto Adrian, Clymer Cody, Churchill Daphnie, Navarro Leija Omar, Han Mira V
1School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA.
2Department of Computer Science, University of Nevada, Las Vegas, NV 89154 USA.
Mob DNA. 2019 Sep 3;10:39. doi: 10.1186/s13100-019-0180-5. eCollection 2019.
Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined.
Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated expression across broad classes of TEs. Despite this co-expression within tissues, there are individual TE loci that exhibit tissue-specific expression patterns, when compared across tissues. The core TE modules were negatively correlated with other gene modules that consisted of immune response genes in interferon signaling. KRAB Zinc Finger Proteins (KZFPs) were over-represented gene members of the TE modules, showing positive correlation across multiple tissues. But we did not find overlap between TE-KZFP pairs that are co-expressed and TE-KZFP pairs that are bound in published ChIP-seq studies.
We find unexpected variation in TE derived transcripts, within and across non-tumorous tissues. We describe a broad view of the RNA state for non-tumorous tissues exhibiting higher level of TE transcripts. Tissues with higher level of TE transcripts have a broad range of TEs co-expressed, with high expression of a large number of KZFPs, and lower RNA levels of immune genes.
尽管长期以来人们一直认为转座子通常仅在生殖系中表达，但最近的证据表明，在体细胞中经常发现转座元件（TE）序列的转录本。然而，不同组织和不同个体间TE转录水平的变化程度尚不清楚，并且尚未研究TE与宿主基因mRNA之间的共表达情况。
在此我们报告了在为癌症基因组图谱收集的非肿瘤组织中观察到的跨组织和个体间TE衍生转录水平的变化。我们发现主要由转座子组成的核心TE共表达模块，显示出在广泛的TE类别中存在相关表达。尽管在组织内存在这种共表达，但在跨组织比较时，有个别TE位点表现出组织特异性表达模式。核心TE模块与由干扰素信号通路中的免疫反应基因组成的其他基因模块呈负相关。KRAB锌指蛋白（KZFPs）是TE模块中过度表达的基因成员，在多个组织中呈正相关。但我们未在共表达的TE-KZFP对与已发表的ChIP-seq研究中结合的TE-KZFP对之间发现重叠。
我们在非肿瘤组织内部和之间发现了TE衍生转录本的意外变化。我们描述了非肿瘤组织中TE转录本水平较高时的RNA状态的广泛情况。TE转录本水平较高的组织有广泛的TE共表达，大量KZFPs高表达，免疫基因的RNA水平较低。
