The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4–CHD4, NKX2-5–CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11. We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.

中文翻译：

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CHD4 被 GATA4 和 NKX2-5 招募来抑制发育中的心脏中的非心脏基因程序


核小体重塑和脱乙酰酶（NuRD）复合物是介导基因抑制的中央染色质重塑复合物之一。 NuRD 对于许多发育事件至关重要，包括心脏发育。临床和遗传学研究为染色质结构域解旋酶 DNA 结合蛋白 4 (CHD4)（NuRD 的催化成分）在先天性心脏病 (CHD)（包括房间隔缺损）中的作用提供了直接证据。此外，已经证明CHD4对于哺乳动物心肌细胞的形成和功能至关重要。一个尚未解决的关键问题是 CHD4/NuRD 如何定位于特定的心脏靶基因，因为 CHD4 和 NuRD 都不能直接结合 DNA。在这里，我们将基于生物信息学的方法与质谱分析相结合，证明 CHD4 在胚胎心脏发育过程中与核心心脏转录因子 GATA4、NKX2-5 和 TBX5 相互作用。利用转录组学和全基因组占用数据，我们描述了 GATA4、NKX2-5 和 TBX5 抑制的基因组图谱，并定义了 GATA4-CHD4、NKX2-5-CHD4 和 TBX5-CHD4 复合物的直接心脏基因靶标。这些数据用于鉴定由这些复合物控制的假定的顺式调节元件。我们在体内对其中两个沉默子进行了基因检测： Acta1和Myh11 。我们发现，删除这些沉默子会分别导致胚胎心脏中骨骼和平滑肌基因的不适当表达。这些结果描述了 CHD4/NuRD 如何定位于特定的心脏位点，并阐明了广泛表达的 CHD4 蛋白的突变如何导致心脏特异性疾病状态。