Eng Diana, Vogel Walter K, Flann Nicholas S, Gross Michael K, Kioussi Chrissa
Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA.
Department of Computer Science, Utah State University, United States, Institute for Systems Biology, Seattle, United States.
Open Access Bioinformatics. 2014 Sep 10;6(2014):1-11. doi: 10.2147/OAB.S59043.
Cell types are defined at the molecular level during embryogenesis by a process called pattern formation and created by the selective utilization of combinations of sequence specific transcription factors. Developmental programs define the sets of genes that are available to each particular cell type, and real-time biochemical signaling interactions define the extent to which these sets are used at any given time and place. Gene expression is regulated through the integrated action of many -regulatory elements, including core promoters, enhancers, silencers, and insulators. The chromatin state in developing body parts provides a code to cellular populations that direct their cell fates. Chromatin profiling has been a method of choice for mapping regulatory sequences in cells that go through developmental transitions.
We used antibodies against histone H3 lysine 4 trimethylations (H3K4me3) a modification associated with promoters and open/active chromatin, histone H3 lysine 27 trimethylations (H3K27me3) associated with Polycomb-repressed regions and RNA polymerase II (Pol2) associated with transcriptional initiation to identify the chromatin state signature of the mouse forelimb during mid-gestation, at embryonic day 12 (E12). The families of genes marked included those related to transcriptional regulation and embryogenesis. One third of the marked genes were transcriptionally active while only a small fraction were bivalent marked. Sequence specific transcription factors that were activated were involved in cell specification including bone and muscle formation.
Our results demonstrate that embryonic limb cells do not exhibit the plasticity of the ES cells but are rather programmed for a finer tuning for cell lineage specification.
细胞类型在胚胎发育过程中通过一种称为模式形成的过程在分子水平上得以确定，该过程由对序列特异性转录因子组合的选择性利用所产生。发育程序定义了每种特定细胞类型可利用的基因集，而实时生化信号相互作用则决定了这些基因集在任何给定时间和地点的使用程度。基因表达通过许多调控元件的综合作用来调节，这些调控元件包括核心启动子、增强子、沉默子和绝缘子。发育中身体部位的染色质状态为指导细胞命运的细胞群体提供了一种编码。染色质分析一直是绘制经历发育转变的细胞中调控序列的首选方法。
我们使用了针对组蛋白H3赖氨酸4三甲基化（H3K4me3，一种与启动子及开放/活性染色质相关的修饰）、组蛋白H3赖氨酸27三甲基化（H3K27me3，与多梳蛋白抑制区域相关）以及与转录起始相关的RNA聚合酶II（Pol2）的抗体，来鉴定妊娠中期（胚胎第12天，E12）小鼠前肢的染色质状态特征。被标记的基因家族包括那些与转录调控和胚胎发生相关的基因。三分之一的被标记基因具有转录活性，而只有一小部分具有双价标记。被激活的序列特异性转录因子参与了细胞特化，包括骨骼和肌肉的形成。
我们的结果表明，胚胎肢体细胞不表现出胚胎干细胞的可塑性，而是为细胞谱系特化进行了更精细的编程。
