The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification.
The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification.
复制标题
使用转录模型对新型远端CEBPA增强子和消音器的分析揭示了造血谱系规范的复杂调节逻辑。
DOI：
10.1016/j.ydbio.2016.02.030
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发表时间：
2016-05-01
影响因子：
2.7
通讯作者：
Manu
中科院分区：
文献类型：
--
作者：
Bertolino E;Reinitz J;Manu
C/EBPα在巨噬细胞-中性粒细胞的命运决定中起指导作用，其表达是中性粒细胞发育所必需的。Cebpa本身如何在髓系中调节尚不清楚。我们使用实验-计算相结合的方法解码了Cebpa和其他两个髓系转录因子Egr 1和Egr 2的顺式调控逻辑。报告设计能够检测远端增强子和沉默子，我们分析了46个假定的顺式调节模块（CRM）的细胞代表髓系祖细胞，衍生早期巨噬细胞或中性粒细胞。除了新型增强剂之外，这项分析还发现了数量惊人的沉默剂。我们通过测试32，768个基于序列的替代转录模型来确定15个潜在转录调控因子的调控作用。这种全面的分析使我们能够推断出大多数CRM的顺式调节逻辑。发现沉默子介导的Cebpa抑制主要受非髓系中表达的TF的影响，突出了长距离沉默对造血谱系分辨率的先前未被认识到的贡献。Cebpa的镇压由多种因素表达的替代血统表明，造血基因组织成紧密相连的抑制网络，而不是层次结构的相互抑制对关键TF。更一般地说，我们的研究结果表明，从头顺式调控解剖是可行的，在大规模的转录建模的帮助下。
C/EBPα plays an instructive role in the macrophage-neutrophil cell-fate decision and its expression is necessary for neutrophil development. How Cebpa itself is regulated in the myeloid lineage is not known. We decoded the cis-regulatory logic of Cebpa, and two other myeloid transcription factors, Egr1 and Egr2, using a combined experimental-computational approach. With a reporter design capable of detecting both distal enhancers and silencers, we analyzed 46 putative cis-regulatory modules (CRMs) in cells representing myeloid progenitors, and derived early macrophages or neutrophils. In addition to novel enhancers, this analysis revealed a surprisingly large number of silencers. We determined the regulatory roles of 15 potential transcriptional regulators by testing 32,768 alternative sequence-based transcriptional models against CRM activity data. This comprehensive analysis allowed us to infer the cis-regulatory logic for most of the CRMs. Silencer-mediated repression of Cebpa was found to be effected mainly by TFs expressed in non-myeloid lineages, highlighting a previously unappreciated contribution of long-distance silencing to hematopoietic lineage resolution. The repression of Cebpa by multiple factors expressed in alternative lineages suggests that hematopoietic genes are organized into densely interconnected repressive networks instead of hierarchies of mutually repressive pairs of pivotal TFs. More generally, our results demonstrate that de novo cis-regulatory dissection is feasible on a large scale with the aid of transcriptional modeling.