Tümpel Stefan, Cambronero Francisco, Wiedemann Leanne M, Krumlauf Robb
Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5419-24. doi: 10.1073/pnas.0600993103. Epub 2006 Mar 28.
Sequence divergence in cis-regulatory elements is an important mechanism contributing to functional diversity of genes during evolution. Gene duplication and divergence provide an opportunity for selectively preserving initial functions and evolving new activities. Many vertebrates have 39 Hox genes organized into four clusters (Hoxa-Hoxd); however, some ray-finned fishes have extra Hox clusters. There is a single Hoxa2 gene in most vertebrates, whereas fugu (Takifugu rubripes) and medaka (Oryzias latipes) have two coparalogous genes [Hoxa2(a) and Hoxa2(b)]. In the hindbrain, both genes are expressed in rhombomere (r) 2, but only Hoxa2(b) is expressed in r3, r4, and r5. Multiple regulatory modules directing segmental expression of chicken and mouse Hoxa2 genes have been identified, and each module is composed of a series of discrete elements. We used these modules to investigate the basis of differential expression of duplicated Hoxa2 genes, as a model for understanding the divergence of cis-regulatory elements. Therefore, we cloned putative regulatory regions of the fugu and medaka Hoxa2(a) and -(b) genes and assayed their activity. We found that these modules direct reporter expression in a chicken assay, in a manner corresponding to their endogenous expression pattern in fugu. Although sequence comparisons reveal many differences between the two coparalogous genes, specific subtle changes in seven cis elements of the Hoxa2(a) gene restore segmental regulatory activity. Therefore, drift in subsets of the elements in the regulatory modules is responsible for the differential expression of the two coparalogous genes, thus providing insight into the evolution of cis elements.
顺式调控元件中的序列差异是进化过程中促成基因功能多样性的重要机制。基因复制和分化为选择性保留初始功能和进化新活性提供了机会。许多脊椎动物有39个Hox基因，分为四个簇（Hoxa - Hoxd）；然而，一些硬骨鱼有额外的Hox簇。大多数脊椎动物中有单个Hoxa2基因，而河豚（红鳍东方鲀）和青鳉（青鳉）有两个旁系同源基因[Hoxa2(a)和Hoxa2(b)]。在后脑，这两个基因都在菱脑节（r）2中表达，但只有Hoxa2(b)在r3、r4和r5中表达。已经鉴定出多个指导鸡和小鼠Hoxa2基因节段性表达的调控模块，每个模块由一系列离散元件组成。我们利用这些模块研究复制的Hoxa2基因差异表达的基础，作为理解顺式调控元件分化的模型。因此，我们克隆了河豚和青鳉Hoxa2(a)和-(b)基因的假定调控区域并检测了它们的活性。我们发现这些模块在鸡的检测中指导报告基因的表达，其方式与它们在河豚中的内源表达模式相对应。尽管序列比较揭示了这两个旁系同源基因之间的许多差异，但Hoxa2(a)基因七个顺式元件中的特定细微变化恢复了节段性调控活性。因此，调控模块中元件子集的漂移导致了这两个旁系同源基因的差异表达，从而为顺式元件的进化提供了见解。
