Comparison of REST cistromes across human cell types reveals common and context-specific functions.
Comparison of REST cistromes across human cell types reveals common and context-specific functions.
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DOI：
10.1371/journal.pcbi.1003671
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发表时间：
2014-06
影响因子：
4.3
通讯作者：
Zheng D
中科院分区：
文献类型：
--
作者：
Rockowitz S;Lien WH;Pedrosa E;Wei G;Lin M;Zhao K;Lachman HM;Fuchs E;Zheng D
最近的研究表明，REST的转录功能比在非神经元系统中抑制神经元基因要广泛得多。REST是否在不同的细胞类型中占据相似的染色质区域，以及它如何与其他转录调节因子相互作用，以上下文依赖的方式执行其功能，尚未得到充分的研究。我们应用ChIP-seq分析来鉴定人CD 4 + T细胞中的REST顺式组，并将其与来自其他15种细胞类型的已发表数据进行比较。我们发现，REST顺反在细胞类型之间是不同的，REST与癌细胞中特异性的几种肿瘤抑制因子结合，而非神经元细胞中7%的REST峰普遍存在，并且在≥5种细胞类型中鉴定出<25%。然而，使用直接比较原始ChIP-seq信号的定量指标，我们发现大多数（约80%）由≥2种细胞类型共享。与RNA-seq数据的整合显示，REST结合通常与低基因表达相关。仔细检查发现，多种情况与REST靶点的表达减少相关，例如，同源RE 1基序的存在和REST结合的细胞特异性。这些情况下，发挥了作用，在差异辅阻遏招聘。此外，转录结果受到REST辅因子的高度影响，例如，SIN 3和EZH 2共占据分别标志着REST靶标的较高和较低表达。出乎意料的是，分化的神经元中的REST顺反子组表现出在非神经元细胞中未观察到的独特特征，例如，缺乏RE 1基序和与活性基因表达的关联。最后，我们的分析表明，REST如何差异调节由miRNA，REST复合物和神经元因子组成的转录网络。总的来说，我们的研究结果的背景下发挥关键作用的REST占用和监管结果提供了深入了解REST的不同功能的分子相互作用，并指出新的作用REST在分化的神经元。RE-1沉默转录因子（REST）与DNA结合，并已被证明在非神经元系统中抑制神经元基因，但最近的研究已将其功能扩展到远远超出此范围。在分子水平上，REST与其他蛋白质协同作用以执行其转录调控作用。REST结合和辅因子募集的动力学及其与潜在DNA序列的关联仍不清楚。在这里，我们应用染色质免疫沉淀和深度测序来鉴定REST在16种不同细胞类型（包括神经元）中的结合。我们的研究结果表明，REST结合事件是动态的，在细胞之间是非常不同的，REST结合通常与低基因表达相关。更仔细的检查发现，REST结合位点处的DNA序列的背景与REST相关靶标的较低表达相关，并且不同的背景与不同的辅因子募集相关。这些反过来又对REST目标的表达产生影响。然而，人类神经元中的REST靶点与其他细胞类型中的靶点截然不同。这些发现提供了对基因组和细胞环境对REST的不同功能的影响的见解，并指出了REST在神经元中的独特和新颖的作用。
Recent studies have shown that the transcriptional functions of REST are much broader than repressing neuronal genes in non-neuronal systems. Whether REST occupies similar chromatin regions in different cell types and how it interacts with other transcriptional regulators to execute its functions in a context-dependent manner has not been adequately investigated. We have applied ChIP-seq analysis to identify the REST cistrome in human CD4+ T cells and compared it with published data from 15 other cell types. We found that REST cistromes were distinct among cell types, with REST binding to several tumor suppressors specifically in cancer cells, whereas 7% of the REST peaks in non-neuronal cells were ubiquitously called and <25% were identified for ≥5 cell types. Nevertheless, using a quantitative metric directly comparing raw ChIP-seq signals, we found the majority (∼80%) was shared by ≥2 cell types. Integration with RNA-seq data showed that REST binding was generally correlated with low gene expression. Close examination revealed that multiple contexts were correlated with reduced expression of REST targets, e.g., the presence of a cognate RE1 motif and cellular specificity of REST binding. These contexts were shown to play a role in differential corepressor recruitment. Furthermore, transcriptional outcome was highly influenced by REST cofactors, e.g., SIN3 and EZH2 co-occupancy marked higher and lower expression of REST targets, respectively. Unexpectedly, the REST cistrome in differentiated neurons exhibited unique features not observed in non-neuronal cells, e.g., the lack of RE1 motifs and an association with active gene expression. Finally, our analysis demonstrated how REST could differentially regulate a transcription network constituted of miRNAs, REST complex and neuronal factors. Overall, our findings of contexts playing critical roles in REST occupancy and regulatory outcome provide insights into the molecular interactions underlying REST's diverse functions, and point to novel roles of REST in differentiated neurons. The RE-1 silencing transcription factor (REST) binds to DNA and has been shown to repress neuronal genes in non-neuronal systems, but more recent studies have expanded its functions much beyond this. At the molecular level, REST acts cooperatively with other proteins to execute its transcriptional regulatory roles. The dynamics of REST binding and cofactor recruitment and its association with the underlying DNA sequence remain unclear. Here, we have applied chromatin immunoprecipitation and deep sequencing to identify REST binding across 16 different cell types, including neurons. Our results demonstrate that REST binding events are dynamic and quite distinct among cells and that REST binding is generally associated with low gene expression. Closer examination finds that the context of the DNA sequence at REST bound sites is associated with the lower expression of REST-associated targets and that different contexts correlate with different cofactor recruitment. These in turn have an effect on the expression of REST targets. REST targets in human neurons, however, are drastically different from those in other cell types. These findings provide insights into the effect of genomic and cellular contexts on REST's diverse functions and point to distinct and novel roles for REST in neurons.
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影响因子：
7
作者：
Arnold P;Schöler A;Pachkov M;Balwierz PJ;Jørgensen H;Stadler MB;van Nimwegen E;Schübeler D
通讯作者：
Schübeler D
影响因子：
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作者：
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作者：
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影响因子：
4.6
作者：
Covey, Matthew V.;Streb, Jeffrey W.;Ballas, Nurit
通讯作者：
Ballas, Nurit
影响因子：
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作者：
Ballas, N;Grunseich, C;Mandel, G
通讯作者：
Mandel, G