Context. The chemistry of protoplanetary disks is thought to be dominated by two major processes: photodissociation near the disk surface and depletion on dust grains in the disk midplane, resulting in a layered structure with molecules located in a warm layer above the disk midplane. Aims: We attempt here to confront this warm molecular layer model prediction with the distribution of two key molecules for dissociation processes: CN and HCN Methods: Using the IRAM Plateau de Bure interferometer, we obtained high spatial and spectral resolution images of the CN J = 2-1 and HCN J = 1-0 lines in the disks surrounding the two T Tauri DM Tau and LkCa 15 and the Herbig Ae MWC 480. We have derived disk properties by assuming power-law distributions. The hyperfine structure of the observed transitions allowed us to constrain the line opacities and excitation temperatures. We compare the observational results with predictions from existing chemical models, and used a simple PDR model (without freeze-out of molecules on grains and surface chemistry) to illustrate dependencies on UV field strength, grain size, and gas-to-dust ratio. We also evaluated the impact of Ly α radiation. Results: The temperature ordering follows the trend found from CO lines, with DM Tau the coldest object and MWC 480 the warmest. Although CN indicates somewhat higher excitation temperatures than HCN, the derived values in the T Tauri disks are very low (8-10 K). They agree with results obtained from C2H, and contradict thermal and chemical model predictions. These very low temperatures, as well as geometrical constraints, suggest that substantial amounts of CN and HCN remain in the gas phase close to the disk midplane and that this midplane is quite cold. The observed CN/HCN ratio ( ≃ 5 - 10) is in better agreement with the existence of large grains and possibly also with a substantial contribution of Ly α radiation. Based on observations carried out with the IRAM Plateau de Bure Interferometer. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).CID is an international collaboration dedicated to the study of Chemistry In proto-planetary Disks.Appendices A and B are available in electronic form at http://www.aanda.orgRead less <