Activation of HOX genes during differentiation

Hox genes encode proteins that contain the DNA-binding homeobox motif and control early patterning of segments in the embryo as well as later events in development (reviewed in Rezsohazy et al. 2015). Mammals have 39 Hox genes arrayed in 4 linear clusters, with each cluster containing 9 to 11 genes. Based on homologies, the genes have been assigned to 13 paralogous groups. The nomenclature of Hox genes uses a letter to indicate the cluster and a number to indicate the paralog group. For example, HOXA4 is the gene in cluster A that is most similar with genes of paralog group 4 from other clusters. <br>One of the most striking aspects of mammalian Hox gene function is the mechanism of their activation during embryogenesis: the order of genes in a cluster correlates with the timing and location of their activation such that genes at the 3' end of a cluster are activated first and genes at the 5' end of a cluster are activated last. (5' and 3' refer to the transcriptional orientation of the genes in the cluster.) Because development of segments of the embryo proceeds from anterior to posterior this means that the anterior boundaries of expression of 3' genes are more anterior (rostral) and the anterior boundaries of expression of 5' genes are more posterior (caudal).
Expression of HOX genes initiates in the posterior primitive streak at the beginning of gastrulation at approximately E7.5 in mouse. As gastrulation proceeds, further 5' genes are sequentially activated and they too undergo the same chromatin changes and migration. After formation of the axis of the embryo, similar waves of activation of HOXA and HOXD clusters occur in developing limbs beginning at about E9. Retinoids, especially all trans retinoic acid (atRA), participate in initiating the process via retinoid receptors. Other factors such as FGFs and Wnt, also regulate Hox expression. After activation, Hox genes participate in maintaining their own expression (autoregulation), activating later, 5' Hox genes, and repressing prior, 3' Hox genes (crossregulation). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process in vitro (reviewed in Gudas et al. 2013). <br>Activation of Hox genes is accompanied by a change from bivalent chromatin to euchromatin (reviewed in Soshnikova and Duboule 2009). Bivalent chromatin has extensive methylation of lysine-9 on histone H3 (H3K9me3), a repressive mark, with interspersed punctate regions of methylation of lysine-4 on histone H3 (H3K4me2, H3K4me3), an activating mark. Euchromatization initiates at the 3' ends of clusters and proceeds towards the 5' ends, with the euchromatin migrating to an active region of the nucleus (reviewed in Montavon and Duboule 2013). This change in chromatin reflects a loss of H3K27me3 and a gain of H3K4me2,3. Polycomb repressive complexes bind H3K27me3 and are responsible for maintenance of repression, KDM6A and KDM6B histone demethylases remove H3K27me3, and members of the trithorax family of histone methylases (KMT2A, KMT2C, KMT2D) methylate H3K4.

Hox基因编码含有DNA结合的Homeobox结构域的蛋白质，并调控胚胎早期节段的模式形成以及发育过程中的后续事件（参见Rezsohazy等，2015年综述）。哺乳动物拥有39个Hox基因，排列成4个线性簇，每个簇包含9至11个基因。基于同源性，这些基因被划分为13个并行基因群。Hox基因的命名采用字母表示簇，数字表示并行基因群。例如，HOXA4是簇A中与来自其他簇的并行基因群4最相似的基因。哺乳动物Hox基因功能最引人注目的方面之一是它们在胚胎发生过程中的激活机制：簇中基因的顺序与其激活的时间和位置相关，簇的3'端基因首先激活，而5'端基因最后激活。（5'和3'分别指簇中基因的转录方向。）由于胚胎节段的发育从前向后进行，这意味着3'基因的表达边界更靠前（吻端），而5'基因的表达边界更靠后（尾端）。
Hox基因的表达始于胃胚形成初期，大约在E7.5的小鼠中，后原始条纹处的胚胎后部。随着胃胚的形成，进一步的5'基因依次被激活，它们也经历了相同的染色质变化和迁移。在胚胎轴形成后，大约在E9左右，HOXA和HOXD簇在发育肢体中发生类似的激活波。视黄醇，尤其是全反式视黄酸（atRA），通过视黄醇受体参与启动过程。其他因素，如FGFs和Wnt，也调节Hox的表达。激活后，Hox基因参与维持自身的表达（自调节），激活后续的5' Hox基因，并抑制先前的3' Hox基因（交叉调节）。在体外，通过视黄酸对胚胎癌细胞和胚胎干细胞的分化建模来模拟这一过程（参见Gudas等，2013年综述）。
Hox基因的激活伴随着从二价染色质到常染色质的转变（参见Soshnikova和Duboule，2009年综述）。二价染色质在组蛋白H3的赖氨酸-9（H3K9me3）上广泛甲基化，这是一种抑制性标记，而赖氨酸-4（H3K4me2、H3K4me3）的甲基化点状区域则是激活性标记。常染色质化始于簇的3'端，并向5'端推进，常染色质迁移到细胞核的活性区域（参见Montavon和Duboule，2013年综述）。这种染色质的变化反映了H3K27me3的丢失和H3K4me2、3的获得。多梳抑制复合物结合H3K27me3，负责维持抑制状态，KDM6A和KDM6B组蛋白去甲基化酶去除H3K27me3，而三梳家族组蛋白甲基化酶（KMT2A、KMT2C、KMT2D）甲基化H3。