Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart
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DOI：
10.1073/pnas.1016959108
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发表时间：
2011-04-05
影响因子：
11.1
通讯作者：
Pu, William T.
中科院分区：
文献类型：
--
作者：
He, Aibin;Kong, Sek Won;Pu, William T.
鉴定控制组织特异性基因表达的基因组区域目前是有问题的。增强子相关蛋白（如p300）的ChIP和高通量测序（ChIP-seq）可以识别一些但不是所有在组织中活跃的增强子。在这里，我们展示了多个转录因子（TFs）在染色质区域的共占用识别出一组不同的增强子。gata结合蛋白4 （GATA4）、NK2转录因子相关、基因座5 （NKX2-5）、T-box 5 （TBX5）、血清反应因子（SRF）和肌细胞增强因子2A (MEF2A)，在这里被称为“心脏tf”，已经被假设协同指导心脏基因表达。使用改进的ChIP-seq程序，我们定义了这些tf和p300基因组范围内的染色质占用，并为这一假设提供了无偏倚的支持。我们使用这一原理来证明多个tf在染色质区域的共占用可以用来识别心脏增强因子。在瞬时转基因胚胎中测试的13个这样的区域中，有7个（54%）驱动心脏基因的表达。在这些区域中有Gata4、Srf和swItch/蔗糖不可发酵相关的、基质相关的、依赖于动作蛋白的染色质调控子，亚家族d，成员3 (Smarcd3)，一个心脏基因表达的表观遗传调控因子。多个心脏tf和p300结合区域与心脏富集基因和与心脏发育相关的功能注释相关。重要的是，绝大多数（1375 / 1715）由多个心脏tf结合的位点不重叠p300结合的位点。我们的数据确定了数千个潜在的心脏调节序列，并表明一个基因组区域的多个TF共占用确定了与p300相关的增强子在很大程度上不同的发育相关增强子。
Identification of genomic regions that control tissue-specific gene expression is currently problematic. ChIP and high-throughput sequencing (ChIP-seq) of enhancer-associated proteins such as p300 identifies some but not all enhancers active in a tissue. Here we show that co-occupancy of a chromatin region by multiple transcription factors (TFs) identifies a distinct set of enhancers. GATA-binding protein 4 (GATA4), NK2 transcription factor-related, locus 5 (NKX2-5), T-box 5 (TBX5), serum response factor (SRF), and myocyte-enhancer factor 2A (MEF2A), here referred to as "cardiac TFs," have been hypothesized to collaborate to direct cardiac gene expression. Using a modified ChIP-seq procedure, we defined chromatin occupancy by these TFs and p300 genome wide and provided unbiased support for this hypothesis. We used this principle to show that co-occupancy of a chromatin region by multiple TFs can be used to identify cardiac enhancers. Of 13 such regions tested in transient transgenic embryos, seven (54%) drove cardiac gene expression. Among these regions were three cardiac-specific enhancers of Gata4, Srf, and swItch/sucrose nonfermentable-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d,member 3 (Smarcd3), an epigenetic regulator of cardiac gene expression. Multiple cardiac TFs and p300-bound regions were associated with cardiac-enriched genes and with functional annotations related to heart development. Importantly, the large majority (1,375/1,715) of loci bound by multiple cardiac TFs did not overlap loci bound by p300. Our data identify thousands of prospective cardiac regulatory sequences and indicate that multiple TF co-occupancy of a genomic region identifies developmentally relevant enhancers that are largely distinct from p300-associated enhancers.