What is the question asked or the overall problem?

Hox genes express themselves in the same time order as their physical order in their cluster. The mechanism for this is unclear. Early studies involving examination of the genomes of various cell lines during Hox gene expression revealed specific genomic profiles during different phases. The first genes to be expressed are on the telomeric end of the cluster and the last genes to be expressed are at the centromeric end. This paper determines whether the genes need to be in a single cluster on the genome, as well as a mechanism critical for transcription that also can independently be responsible for transcription.

What is the experimental system/techniques?

The last Hox genes are expressed in mouse tail buds during late somitogenesis. Mouse tail buds were isolated at E8.5, E9 and E9.5 and gene expression of Hox and nearby genes was determined using tiling arrays; this procedure was repeated using embryonic stem cells, which ought have no expression of Hox genes. Chromatin immunoprecipitation combined with the tiling array hybridization was used to map sites occupied by RNAP II.

To determine whether there is a mechanism whereby the HoxD cluster chomatin decondensation propagates from the telomeric end to the centromeric end, mice were engineered with a HoxD cluster containing a 3Mb inversion that separated Hoxd1-10 from Hoxd11-13. Studying Hox gene expression with this construct reveals whether an internal gene cluster is required for progressive gene expression. The same techniques were used as in the wild-type.

What are the results and conclusions?

Chromatin decondensation correlated directly to areas of RNAP II binding and active transcription. This collinear chromatin dynamic suggests a mechanism whereby modifications spread from the telomeric extremity of the cluster to the centromeric extremity. In the mutant construct, Hoxd1-9 were expressed normally but Hoxd10 was expressed early. This suggests a telomeric activator of expression of these genes. Hoxd 13 was expressed early, likely due to activity of a spurious enhancer. Hoxd 11 and Hoxd12 had very low levels of expression. However, Hoxd11-13 were decondensed. This indicates the requirement of a telomeric enhancer element to activate Hoxd11 and Hoxd12 expression, and the change in Hoxd13′s location resulting in susceptibility to some third-party enhancer element. The fact that decondensation still occurred revealed that an internal gene cluster may be necessary for proper expression but is not necessary for decondensation.

Note: Received a 27/30.