Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis.
Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis.
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DOI：
10.1534/g3.115.019166
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发表时间：
2015-05-20
期刊：
影响因子：
--
通讯作者：
Arnosti DN
中科院分区：
文献类型：
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作者：
Wei Y;Mondal SS;Mouawad R;Wilczyński B;Henry RW;Arnosti DN
RBf2 是果蝇中最近进化的视网膜母细胞瘤家族成员，与 RBf1 不同，尤其是在 C 末端。为了研究 RBf2 的独特特征是否有助于基因调控中的不同作用，我们对胚胎中的 RBf2 和 RBf1 进行了染色质免疫沉淀测序。先前的 RB−E2F 相互作用模型表明 RBf1 结合 dE2F1 或 dE2F2，而 RBf2 仅限于结合 dE2F2；然而，我们发现 RBf2 靶向的基因数量大约是 RBf1 的两倍。 RBf2 靶标中高度富集的是核糖体蛋白基因。我们通过评估核糖体蛋白启动子和内源基因的 RBf 活性来测试这一发现的功能意义。 RBf1 和 RBf2 显着抑制一些核糖体蛋白基因的表达，尽管并非所有结合基因都显示转录效应。有趣的是，许多核糖体蛋白基因在人类细胞中也有类似的靶点，表明这些相互作用可能与核糖体生物合成和生长的控制有关。我们进行了生物信息学分析，以研究这两种蛋白差异靶向的基础，发现 RBf2 特异性启动子具有不同的序列基序，表明独特的靶向机制。 RBf2 与这些启动子的关联似乎独立于 dE2F2/dDP，尽管 RBf1 和 RBf2 结合的启动子需要 dE2F2/dDP。独特的 RBf2 靶标的存在表明，这种辅阻遏物的进化出现代表了 RB 家族在基因调控中潜在的新角色的获得。
RBf2 is a recently evolved retinoblastoma family member in Drosophila that differs from RBf1, especially in the C-terminus. To investigate whether the unique features of RBf2 contribute to diverse roles in gene regulation, we performed chromatin immunoprecipitation sequencing for both RBf2 and RBf1 in embryos. A previous model for RB−E2F interactions suggested that RBf1 binds dE2F1 or dE2F2, whereas RBf2 is restricted to binding to dE2F2; however, we found that RBf2 targets approximately twice as many genes as RBf1. Highly enriched among the RBf2 targets were ribosomal protein genes. We tested the functional significance of this finding by assessing RBf activity on ribosomal protein promoters and the endogenous genes. RBf1 and RBf2 significantly repressed expression of some ribosomal protein genes, although not all bound genes showed transcriptional effects. Interestingly, many ribosomal protein genes are similarly targeted in human cells, indicating that these interactions may be relevant for control of ribosome biosynthesis and growth. We carried out bioinformatic analysis to investigate the basis for differential targeting by these two proteins and found that RBf2-specific promoters have distinct sequence motifs, suggesting unique targeting mechanisms. Association of RBf2 with these promoters appears to be independent of dE2F2/dDP, although promoters bound by both RBf1 and RBf2 require dE2F2/dDP. The presence of unique RBf2 targets suggest that evolutionary appearance of this corepressor represents the acquisition of potentially novel roles in gene regulation for the RB family.