Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation.
Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation.
复制标题
DOI：
10.1038/s41598-021-97909-w
复制
发表时间：
2021-09-23
影响因子：
4.6
通讯作者：
Sætrom P
中科院分区：
文献类型：
--
作者：
Hegre SA;Samdal H;Klima A;Stovner EB;Nørsett KG;Liabakk NB;Olsen LC;Chawla K;Aas PA;Sætrom P
细胞周期的适当调节是所有生物体正常生长和发育所必需的。相反，改变的细胞周期调节通常是增殖性疾病如癌症的基础。长链非编码RNA（lncRNA）被认为是基因表达的重要调节因子，并且经常在疾病（包括癌症）中发现失调。然而，鉴定具有细胞周期功能的lncRNA是具有挑战性的，因为它们通常低表达且具有细胞类型特异性。我们提出了一种非常有效的方法，分析启动子活性，转录和RNA水平的变化，以确定富集细胞周期功能的基因。具体而言，通过将RNA测序与ChIP测序相结合，通过同步化的人角质形成细胞的细胞周期，我们确定了1009个具有细胞周期依赖性表达的基因，并通过组蛋白3赖氨酸4三甲基化（H3 K4 me 3）测定了RNA聚合酶II占用率或启动子活性的相关变化。这些基因高度富集具有已知细胞周期功能的基因，包括57个lncRNA。我们选择了这些lncRNA中的四种-SNHG 26、EMSLR、ZFAS 1和EPB 41 L4 A-AS 1-用于进一步的实验验证，并发现敲低四种lncRNA中的每一种都会影响细胞周期时相分布并减少多个细胞系中的增殖。这些结果表明，许多具有细胞周期功能的基因在启动子活性、转录和RNA水平方面具有伴随的细胞周期依赖性变化，并支持我们的多组学方法非常适合于鉴定参与细胞周期的lncRNA。
Proper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 57 lncRNAs. We selected four of these lncRNAs—SNHG26, EMSLR, ZFAS1, and EPB41L4A-AS1—for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.