RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.
RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.
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RBPJ 与定相核小体内的共有元件和甲基化顺式元件结合，并与 SRF 配合控制人主动脉平滑肌细胞中的基因表达。
DOI：
10.1093/nar/gky617
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发表时间：
2018
影响因子：
14.9
通讯作者：
Mack,ChristopherP
中科院分区：
文献类型：
--
作者：
Rozenberg,JulianM;Taylor,JoanM;Mack,ChristopherP
鉴于我们之前证明 RBPJ 结合甲基化阻遏元件并调节平滑肌细胞 (SMC) 特异性基因表达，我们使用全基因组方法来识别人主动脉 SMC 中的 RBPJ 结合区域，并评估 RBPJ 对染色质结构和基因表达的影响。 RBPJ 与共有顺式元件结合，但也与 Alu 重复内的 TCmGGGA 序列结合，根据 DNAse 超敏性、H3K9 乙酰化以及 Notch3 和 RNA Pol II 结合评估，这些序列的转录活性较低。有趣的是，RBPJ 结合经常在开放染色质的边缘检测到，并且 RBPJ 耗竭诱导或抑制的大部分基因与这组 RBPJ 结合位点相关。 RBPJ 结合与血清反应因子 (SRF) 显着共定位，在 RBPJ 和 SRF 耗尽的 SMC 中进行的 RNA seq 实验表明，这些因子在功能上相互作用，调节收缩和炎症基因程序，从而帮助定义 SMC 表型。最后，我们发现 RBPJ 优先与定相核小体结合，独立于位于核小体二联体开始和中间的活性染色质标记和顺顺元件。这些新发现为了解 RBPJ 在 SMC 染色质结构和基因表达中的作用提供了重要的见解。
Given our previous demonstration that RBPJ binds a methylated repressor element and regulates smooth muscle cell (SMC)-specific gene expression, we used genome-wide approaches to identify RBPJ binding regions in human aortic SMC and to assess RBPJ’s effects on chromatin structure and gene expression. RBPJ bound to consensus cis elements, but also to TCmGGGA sequences within Alu repeats that were less transcriptionally active as assessed by DNAse hypersensitivity, H3K9 acetylation, and Notch3 and RNA Pol II binding. Interestingly, RBPJ binding was frequently detected at the borders of open chromatin, and a large fraction of genes induced or repressed by RBPJ depletion were associated with this cluster of RBPJ binding sites. RBPJ binding dramatically co-localized with serum response factor (SRF) and RNA seq experiments in RBPJ- and SRF-depleted SMC demonstrated that these factors interact functionally to regulate the contraction and inflammatory gene programs that help define SMC phenotype. Finally, we showed that RBPJ bound preferentially to phased nucleosomes independent of active chromatin marks and tociselements positioned at the beginning and middle of the nucleosome dyad. These novel findings add important insight into RBPJ’s role in chromatin structure and gene expression in SMC.