Promoters and enhancers are cis-regulatory DNA sequences that control specificity and quantity of transcription. Both are rich on clusters of cis-acting sites that interact with sequence-specific DNA-binding transcription factors (TFs). At the level of chromatin, these regions display increased nuclease sensitivity, reduced nucleosome density, including nucleosome-free regions, and specific combinations of posttranslational modifications of core histone proteins. Together, “open” and “closed” chromatins represent transcriptionally active and repressed states of individual genes, respectively. Cellular differentiation is marked by changes in local chromatin structure. Lens morphogenesis, regulated by TF Pax6, includes differentiation of epithelial precursor cells into lens fibers in parallel with differentiation of epithelial precursors into the mature lens epithelium. Using ATAC-seq, we investigated dynamics of chromatin changes during mouse lens fibers and epithelium differentiation. Tissue-specific features of these processes are demonstrated via comparative studies of embryonic stem cells, forebrain, and liver chromatins. Unbiased analysis reveals cis-regulatory logic of lens differentiation through known (e.g., AP-1, Ets, Hsf4, Maf, and Pax6 sites) and novel (e.g., CTCF, Tead, and NF1) motifs. Twenty-six DNA-binding TFs, recognizing these cis-motifs, are markedly up-regulated in differentiating lens fibers. As specific examples, our ATAC-seq data uncovered both the regulatory regions and TF binding motifs in Foxe3, Prox1, and Mip loci that are consistent with previous, though incomplete, experimental data. A cross-examination of Pax6 binding with ATAC-seq data demonstrated that Pax6 bound to both open (H3K27ac and P300-enriched) and closed chromatin domains in lens and forebrain. Our study has generated the first lens chromatin accessibility maps that support a general model of stage-specific chromatin changes associated with transcriptional activities of batteries of genes required for lens fiber cell formation. Analysis of active (or open) promoters and enhancers reveals important cis-DNA motifs that establish the molecular foundation for temporally and spatially regulated gene expression in lens. Together, our data and models open new avenues for the field to conduct mechanistic studies of transcriptional control regions, reconstruction of gene regulatory networks that govern lens morphogenesis, and identification of cataract-causing mutations in noncoding sequences.

中文翻译：

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染色质可及性分析和控制两种晶状体分化途径的一般顺式调节机制的识别。

启动子和增强子是控制转录特异性和数量的顺式调控 DNA 序列。两者都富含与序列特异性 DNA 结合转录因子 (TF) 相互作用的顺式作用位点簇。在染色质水平上，这些区域表现出核酸酶敏感性增加、核小体密度降低（包括无核小体区域）以及核心组蛋白翻译后修饰的特定组合。“开放”和“封闭”染色质一起分别代表单个基因的转录活性和抑制状态。细胞分化的标志是局部染色质结构的变化。晶状体形态发生由 TF Pax6 调节，包括上皮前体细胞分化为晶状体纤维，同时上皮前体细胞分化为成熟的晶状体上皮。使用 ATAC-seq，我们研究了小鼠晶状体纤维和上皮分化过程中染色质变化的动态。这些过程的组织特异性特征通过胚胎干细胞、前脑和肝脏染色质的比较研究得到证明。无偏分析通过已知（例如，AP-1、Ets、Hsf4、Maf 和 Pax6 位点）和新颖（例如，CTCF、Tead 和 NF1）基序揭示了晶状体分化的顺式调控逻辑。识别这些顺式基序的 26 个 DNA 结合 TF 在分化晶状体纤维中显着上调。作为具体示例，我们的 ATAC-seq 数据揭示了 Foxe3、Prox1 和 Mip 位点中的调控区和 TF 结合基序，这与之前（尽管不完整）的实验数据一致。Pax6 与 ATAC-seq 数据结合的交叉检查表明，Pax6 与晶状体和前脑中的开放（H3K27ac 和 P300 富集）和闭合染色质结构域结合。我们的研究生成了第一个晶状体染色质可及性图，该图支持与晶状体纤维细胞形成所需基因组的转录活性相关的特定阶段染色质变化的一般模型。对活性（或开放）启动子和增强子的分析揭示了重要的顺式 DNA 基序，为晶状体中时间和空间调节基因表达奠定了分子基础。总之，我们的数据和模型为该领域开辟了新的途径，以进行转录控制区域的机制研究、重建控制晶状体形态发生的基因调控网络以及识别非编码序列中引起白内障的突变。