Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells
Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells
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DOI：
10.1182/blood-2009-06-227017
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发表时间：
2010-02-04
期刊：
影响因子：
20.3
通讯作者：
Dalla-Favera, Riccardo
中科院分区：
文献类型：
--
作者：
Basso, Katia;Saito, Masumichi;Dalla-Favera, Riccardo
BCL 6是成熟B细胞生发中心（GC）形成所需的转录抑制因子，与淋巴瘤发生有关。BCL 6的生理功能仅部分已知，因为尚未鉴定其在GC B细胞中的完整靶点。为了解决这个问题，我们使用了一个集成的生物化学计算功能的方法来确定BCL 6的直接目标在正常的GC B细胞。该方法包括（1）通过全基因组染色质免疫沉淀鉴定BCL 6结合的启动子，（2）通过使用调控网络反向工程方法（ARACNe）推断转录关系，和（3）验证在GC B细胞中下调的候选靶标的生理相关性。我们的方法证明了大量的启动子（> 4000）被BCL 6物理结合，但在GC B细胞中只有一部分被抑制。这组1207个靶标鉴定了GC发育期间由BCL 6直接控制的几种细胞功能，包括活化、存活、DNA损伤反应、细胞周期阻滞、细胞因子信号传导、Toll样受体信号传导和分化。这些结果确定了BCL 6在阻止中心母细胞在完成增殖扩增和抗体亲和力成熟阶段之前对导致从GC退出的信号作出反应中的广泛作用。（血。2010;115：975-984）
BCL6 is a transcriptional repressor required for mature B-cell germinal center (GC) formation and implicated in lymphomagenesis. BCL6's physiologic function is only partially known because the complete set of its targets in GC B cells has not been identified. To address this issue, we used an integrated biochemical-computational-functional approach to identify BCL6 direct targets in normal GC B cells. This approach includes (1) identification of BCL6-bound promoters by genome-wide chromatin immunoprecipitation, (2) inference of transcriptional relationships by the use of a regulatory network reverse engineering approach (ARACNe), and (3) validation of physiologic relevance of the candidate targets down-regulated in GC B cells. Our approach demonstrated that a large set of promoters (> 4000) is physically bound by BCL6 but that only a fraction of them is repressed in GC B cells. This set of 1207 targets identifies several cellular functions directly controlled by BCL6 during GC development, including activation, survival, DNA-damage response, cell cycle arrest, cytokine signaling, Toll-like receptor signaling, and differentiation. These results define a broad role of BCL6 in preventing centroblasts from responding to signals leading to exit from the GC before they complete the phase of proliferative expansion and of antibody affinity maturaton. (Blood. 2010;115:975-984)