Functional Analysis of Human Chromosome 21 Proteins

( Hans-Jörg Warnatz )

Studying the proteome encoded by human chromosome 21 (HSA21) is of high medical interest, in particular for the molecular analysis of the effects of trisomy 21, which results in Down syndrome (DS). The gene catalog of HSA21 contains ca. 240 protein-coding genes. Only about half of these have a gene ontology (GO) annotation. Assigning functions to uncharacterized proteins is a critical step to elucidate their biological role and contributes to understand the gene dosage effects in the pathogenesis of DS.

The identification of protein-protein interactions can greatly help functional annotation. Large-scale Y2H screens yielded relatively few interactions involving HSA21 proteins (Rual et al. 2005; Stelzl et al. 2005). We set out to systematically identify HSA21 protein interactions using an automated yeast two-hybrid mating-array setup. First, we cloned HSA21 open reading frames (ORFs) using a recombinatorial cloning strategy. To date, we obtained 167 complete ORFs. From these, a bait set of 62 HSA21 proteins yielded 57 new PPIs for 23 different proteins, a subset of which was validated by co-immunoprecipitation and cellular co-localization assays.

In parallel, we used a combination of manual and automatic retrieval of interaction data leading to a list of 634 known HSA21 PPIs. We generated a HSA21 interactome network by computationally integrating all 691 interactions for 108 HSA21 proteins into a meshwork composed of a total of 14,949 PPIs between 5,655 different proteins retrieved from the databases BIND and HPRD as well as the two large Y2H studies. This is the first interactome for HSA21. Our interaction network allows us to generate new hypotheses for a number of HSA21 protein functions, e.g. PCP4, MCM3AP, C21orf91 and C21orf127.

In addition, we report the results of a computational search for regulatory networks that are prone to perturbation by gene-dosage dependent changes in the expression level of HSA21 proteins. Our list of potentially affected cellular pathways comprises known cases, such as interferon, VEGF and p38 signaling, and new candidates, for example the YY1-/p300 pathway, growth factor-dependent signal transduction and the p73 pathway. Our HSA21 interactome contributes to the unravelling of novel gene functions and to the understanding of the metabolic and regulatory pathways involved in the pathologies involving HSA21 genes.