Ho Ho Ho.....Hox.

Hox Genes in Development: The Hox Code

By: PZ Myers, Ph.D. (University of Minnesota, Morris) © 2008 Nature Education
http://scienceblogs.com/pharyngula/2007/09/the_hox_code.php

What is Hox genes?

• Hox genes, a family of transcription factors, are major regulators of animal development. Unlike most genes, however, the order of Hox genes in the genome actually holds meaning.  These are genes that specify segment identity; the expression pattern is translated into the many different forms that animals (metazoans) exhibit.
• Discovery of Hox: Drosophila study
  果蠅有8個 hox genes (the top array of genes in figure 1) / 1 個 hox cluster。實驗發現這些基因異常時會造成體節構造異常：例如，Antp ==> Antennapedia。

Genomic organization of the Hox gene cluster (Figure 1 on the source article).  ** 這個圖的方向要把左邊看成3'，基因的排列方向（sense strand/ translation）等於要從右向左。zen, bcd, ftz  是 非 hox 的 homeobox containing genes. 

• 比較果蠅和小鼠的hox 構造，有幾個明顯的不同：
• number of hox casettes: 4 vs 1
• 5' 與腹部發育有關的基因，小鼠多好幾個 （hox9-13 vs Abd-B)
• 這個基因與cluster 數量的差距，顯然可以讓我們聯想到［產生比較多樣的組合來控制基因］===> 構造多樣化，"hox code" ?
• 果蠅：某個 segment 表現某一種 hox (不會有兩個 hox 都表現）
• 小鼠：某個 segment 表現一個以上 (同位的）hox ( hox4 可達四個）==> 魚可以有八個？
• multiple copies of hox 或許也是有功能上的 rescue 好處，例如 HoxA3 (表現在頸椎與頭相接的部位）ko 並沒有明顯表型/功能缺失，推測為 HoxD3 的補償作用。只做 D3 mutant 時，第一節頸椎出現嚴重的構造缺失，但還是有頸椎。double mutant A3, D3 則變成這節與頭部癒合==> 顯示 HoxA3 果然還是決定第一節頸椎構造的關鍵；構成這節骨頭的中胚層起始組織可受到相當程度的重新限定分化，而癒合到顱骨的構造去。（ 原文：HoxA3 is important after all; without it, the first neck vertebra doesn't form. In fact, in this instance, it is thought that the initial mesodermal tissue for the bone is so thoroughly respecified that it fuses completely with the skull instead, becoming part of the base of the skull）. 
• 要產生正確脊椎構造，需要適當的hox 基因表現組合，在小鼠的基因剔除分析的實驗結果分析變得相當複雜，即使是很重要的基因，只剔除一個基因可能顯現不出什麼表型缺陷，而必須把整群 "paralogous" 基因都剔除。這也是為什麼脊椎動物的 homeotic mutation 不像果蠅那麼容易被觀察到。
• In flies, one gene can be mutated, resulting in an altere (平衡桿，退化的第二對翅膀）being transformed into a wing, or an antenna turning into a leg; in the mouse, two to four genes must be simultaneously removed to get a similar complete transformation.)

Paralogous Knockouts in Mice

技術上的演進－小鼠發育生物學家發表了一些把整個 paralogous hox 拿掉的實驗結果: (figure 2, dorsal view and concludings in figure 3)

• delete all Hox5 genes: make C7 and T1 stay like C2 (cervical vertebrae with no dorsal neural arch) and T1 with an incomplete develop ribs.
• delete all Hox6: no ribs at T1; (almost) a complete homeotic transformation of T1 to C7.
• delete Hox9: extra ribs at L1: anterior shift in the midtrunk (extend the segment or shorter tail?)
• delete Hox10: extra ribs at L1~S1
• delete Hox11: no fused sacral wings at S1    

Changes in specific vertebral elements for the Hox5, Hox6, Hox9, Hox10, and Hox11 paralogous mutants  (figure 2 in the source).

Schematic representation of regions of reported phenotypes in Hox paralogous mutants. (figure 3 in the source).

Schematic of overlaps in and differences between the somite-derived primaxial phenotypes and the lateral plate-derived, abaxial（離軸） phenotypes of Hox paralogous mutants.

（remarks: from p261, ch16, "Bones and Cartilage: Developmental and Evolutionary Skeletal Biology" by Brian K. Hall. DOI: http://dx.doi.org/10.1016/B978-0-12-416678-3.00016-1）

• primaxial : structures that differentiate entirely within the somitic environment- the vertebral column, vertebral ribs, periaxial and intercostal uscles and associated connective tissue - and that are generated entirely from somitic cells
• abaxial: all structures that differentiate within the lateral plate environment, including the migrating somite-derived myoblasts that migrate into and differentiate within lateral-plate mesoderm, namely limb and abdominal muscles, sternal muscle and sternum.）

每一個 Hox paralog 控制某特定型態，不僅是由 paralog 內的組合，也包含paralog 間的組合。比如說，在薦椎段（sacral segment）有 Hox10 與 Hox11表現。其他的實驗顯示這裡的分化基礎型態為"胸椎"，推測 hox10 hox11 的作用為抑制肋骨形成。

所以，脊椎動物的中軸骨骼形成上，看起來彷彿有 ”數位化” 混合 Hox 控制的機制。

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Another material for easy-understanding Hox:

http://learn.genetics.utah.edu/content/variation/hoxgenes/

1. Scientists discovered homeotic genes by studying strange transformations in fruit flies. Scientists called these modifications "homeotic transformations," because one body part seemed to have been replaced by another. 

Top: (Left) Normal fruitfly; (Right) Fruitfly with mutation in antennapedia gene Bottom: (Left) Normal fruitfly; (Right) Fruitfly with a homeotic mutation that gives it two thoraxes. Bottom images courtesy of the Archives, California Institute of Technology and the whole sources are from learn.genetics http://learn.genetics.utah.edu/content/variation/hoxgenes/

It is awsome to view the body domain swayed by hox genes in arthopods: