Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de 
Lange Syndrome (CdLS), the most common "cohesinopathy". It has been proposed 
that the effects of Nipbl-haploinsufficiency result from disruption of 
long-range communication between DNA elements. Here we use zebrafish and mouse 
models of CdLS to examine how transcriptional changes caused by Nipbl deficiency 
give rise to limb defects, a common condition in individuals with CdLS. In the 
zebrafish pectoral fin (forelimb), knockdown of Nipbl expression led to size 
reductions and patterning defects that were preceded by dysregulated expression 
of key early limb development genes, including fgfs, shha, hand2 and multiple 
hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis 
revealed many similar gene expression changes, as well as altered expression of 
additional classes of genes that play roles in limb development. In both 
species, the pattern of dysregulation of hox-gene expression depended on genomic 
location within the Hox clusters. In view of studies suggesting that Nipbl 
colocalizes with the mediator complex, which facilitates enhancer-promoter 
communication, we also examined zebrafish deficient for the Med12 Mediator 
subunit, and found they resembled Nipbl-deficient fish in both morphology and 
gene expression. Moreover, combined partial reduction of both Nipbl and Med12 
had a strongly synergistic effect, consistent with both molecules acting in a 
common pathway. In addition, three-dimensional fluorescent in situ hybridization 
revealed that Nipbl and Med12 are required to bring regions containing 
long-range enhancers into close proximity with the zebrafish hoxda cluster. 
These data demonstrate a crucial role for Nipbl in limb development, and support 
the view that its actions on multiple gene pathways result from its influence, 
together with Mediator, on regulation of long-range chromosomal interactions.