Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province, China; Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, China.
Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.
Genomics. 2022 Jul;114(4):110421. doi: 10.1016/j.ygeno.2022.110421. Epub 2022 Jun 30.
Estrogen drives key transcriptional changes in breast cancer and stimulates breast cancer cells' growth with multiple mechanisms to coordinate transcription and translation. In addition to protein-coding transcripts, estrogen can regulate long non-coding RNA (lncRNA) transcripts, plus diverse non-coding RNAs including antisense, enhancer, and intergenic. LncRNA genes comprise the majority of human genes. The accidental, or regulated, translation of their short open reading frames by ribosomes remains a controversial topic. Here we report for the first time an integrated analysis of RNA abundance and ribosome occupancy level, using Ribo-seq combined with RNA-Seq, in the estrogen-responsive, estrogen receptor α positive, human breast cancer cell model MCF7, before and after hormone treatment. Translational profiling can determine, in an unbiased manner, which fraction of the genome is actually translated into proteins, as well as resolving whether transcription and translation respond concurrently, or differentially, to estrogen treatment. Our data showed specific transcripts more robustly detected in RNA-Seq than in the ribosome-profiling data, and vice versa, suggesting distinct gene-specific estrogen responses at the transcriptional and the translational level, respectively. Here, we showed that estrogen stimulation affects the expression levels of numerous lncRNAs, but not their association with ribosomes, and that most lncRNAs are not ribosome-bound. For the first time, we also demonstrated the transcriptional and translational response of expressed pseudogenes to estrogen, pointing to new perspectives for drug-target development in breast cancer in the future.
雌激素驱动乳腺癌中的关键转录变化，并通过多种机制刺激乳腺癌细胞的生长，以协调转录和翻译。除了蛋白质编码转录本外，雌激素还可以调节长非编码 RNA（lncRNA）转录本，以及多种非编码 RNA，包括反义、增强子和基因间。lncRNA 基因构成了人类基因的大部分。核糖体偶然或受调控地翻译它们的短开放阅读框仍然是一个有争议的话题。在这里，我们首次报道了使用 Ribo-seq 与 RNA-Seq 相结合，在激素治疗前后，对雌激素反应性、雌激素受体 α 阳性的人类乳腺癌细胞模型 MCF7 中的 RNA 丰度和核糖体占据水平进行综合分析。翻译谱分析可以以无偏倚的方式确定基因组的哪一部分实际上被翻译成蛋白质，以及确定转录和翻译是否对雌激素处理同时或不同步地做出反应。我们的数据显示，在 RNA-Seq 中比在核糖体分析数据中更能强烈检测到特定的转录本，反之亦然，这表明在转录和翻译水平上分别存在特定基因的雌激素反应。在这里，我们表明雌激素刺激会影响众多 lncRNA 的表达水平，但不会影响它们与核糖体的结合，并且大多数 lncRNA 与核糖体不结合。我们首次证明了表达假基因对雌激素的转录和翻译反应，为未来乳腺癌的药物靶点开发提供了新的视角。
