Doose Gero, Haake Andrea, Bernhart Stephan H, López Cristina, Duggimpudi Sujitha, Wojciech Franziska, Bergmann Anke K, Borkhardt Arndt, Burkhardt Birgit, Claviez Alexander, Dimitrova Lora, Haas Siegfried, Hoell Jessica I, Hummel Michael, Karsch Dennis, Klapper Wolfram, Kleo Karsten, Kretzmer Helene, Kreuz Markus, Küppers Ralf, Lawerenz Chris, Lenze Dido, Loeffler Markus, Mantovani-Löffler Luisa, Möller Peter, Ott German, Richter Julia, Rohde Marius, Rosenstiel Philip, Rosenwald Andreas, Schilhabel Markus, Schneider Markus, Scholz Ingrid, Stilgenbauer Stephan, Stunnenberg Hendrik G, Szczepanowski Monika, Trümper Lorenz, Weniger Marc A, Hoffmann Steve, Siebert Reiner, Iaccarino Ingram
Transcriptome Bioinformatics, Leipzig Research Center for Civilization Diseases, University of Leipzig, D-04107 Leipzig, Germany;
Institute of Human Genetics, University Hospital Schleswig-Holstein, Christian Albrechts University, D-24105 Kiel, Germany;
Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5261-70. doi: 10.1073/pnas.1505753112. Epub 2015 Sep 8.
Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long noncoding RNAs (lncRNAs), on MYC ability to influence the cellular transcriptome. Here, we have intersected RNA-sequencing data from two MYC-inducible cell lines and a cohort of 91 B-cell lymphomas with or without genetic variants resulting in MYC overexpression. We identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them, we focused on a lncRNA that we named MYC-induced long noncoding RNA (MINCR), showing a strong correlation with MYC expression in MYC-positive lymphomas. To understand its cellular role, we performed RNAi and found that MINCR knockdown is associated with an impairment in cell cycle progression. Differential gene expression analysis after RNAi showed a significant enrichment of cell cycle genes among the genes down-regulated after MINCR knockdown. Interestingly, these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of the MYC transcriptional program. Accordingly, MINCR knockdown was associated with a reduction in MYC binding to the promoters of selected cell cycle genes. Finally, we show that down-regulation of Aurora kinases A and B and chromatin licensing and DNA replication factor 1 may explain the reduction in cellular proliferation observed on MINCR knockdown. We, therefore, suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes.
尽管转录因子MYC在癌症中的作用已被确定,但对于一类新的转录调节因子——长链非编码RNA(lncRNA)对MYC影响细胞转录组能力的影响却知之甚少。在此,我们将来自两个MYC诱导细胞系以及91例有或无导致MYC过表达的基因变异的B细胞淋巴瘤队列的RNA测序数据进行了交叉分析。我们在IG-MYC阳性伯基特淋巴瘤中鉴定出13种差异表达的lncRNA,并且在模型细胞系中它们受MYC的调控方向相同。其中,我们重点研究了一种lncRNA,将其命名为MYC诱导的长链非编码RNA(MINCR),它在MYC阳性淋巴瘤中与MYC表达呈强相关。为了解其细胞作用,我们进行了RNA干扰实验,发现敲低MINCR与细胞周期进程受损有关。RNA干扰后的差异基因表达分析显示,在敲低MINCR后下调的基因中细胞周期基因显著富集。有趣的是,这些基因在其启动子中的MYC结合位点富集,这表明MINCR作为MYC转录程序的调节因子发挥作用。相应地,敲低MINCR与MYC与所选细胞周期基因启动子的结合减少有关。最后,我们表明极光激酶A和B以及染色质许可和DNA复制因子1的下调可能解释了敲低MINCR后观察到的细胞增殖减少。因此,我们认为MINCR是MYC转录网络中一个新发现的能够控制细胞周期基因表达的因子。