In the gene regulation networks the links are interpreted as putative regulation where TFs physically regulate genes through binding to DNA.
Moreover, pre-synaptic D2 receptors strongly contribute to physically regulate density and activity of the dopamine transporter (DAT) [22] [29].
The cohesin complex has been shown to physically regulate expression via looping at the IGF2-H19 impregion region [ 22].
The BRCA2 and RAD51 C. elegans orthologs (named BRC-2 and RAD-51, respectively) interact physically and regulate homologous recombination, so that brc-2 mutants fail to locate RAD-51 to sites of double-strand breaks present in meiosis or induced by DNA damage agents [ 61].
Some promoters can be regulated both physically and chemically.
A number of mechanisms have been proposed to explain the existence of these co-expression clusters including the presence of duplicate genes that are in close physical proximity, shared regulatory regions, chromatin-level regulation, and common pathway or tissue regulated expression of physically clustered genes [ 1, 8, 21].
Since tyrosine phosphorylation of vertebrate DCC is required for attractive responses, axon outgrowth and orientation of the axon (e.g. [68] [74]), it will be important to systematically assess how Fra and Abl physically interact to regulate each other's activity during midline guidance.
One of such gene candidates could be KANK1 since it is highly expressed in the mouse embryonic genital tract (http://www.genepaint.org) and is able to physically interact and regulate the subcellular localization of beta catenin whose activation in normal XY mice has been shown to disrupt the male program and result in male-to-female sex-reversal [28], [29].
In this case, we hypothesized that in the absence of lamin A/C, which physically interacts and regulates MAN-1 activity in the nucleus [15], Runx2 changes its localization and availability therefore affecting its capacity to interact and to form the Runx2 nuclear binding complex, decreasing OCN and OPN transcription and thus affecting osteoblastogenesis.
