The Genom of Homo sapiens.pdf

DOWN SYNDROME AND HUMAN CHROMOSOME 21 427The extensive and systematic functional and evolutionarystudy of CNGs will enhance our understanding ofthese important genomic elements. Further studies willaddress the contribution of CNGs to health and disease,both Mendelian and complex phenotypes; in addition,they may reveal their potential involvement in the differentphenotypes of trisomy 21.Number of genesEXPRESSION ATLAS OF MOUSE ORTHOLOGSOF Hsa21 GENESThe completion of the human genome, and the continuedeffort to identify all the human genes, present now theformidable task of the elucidation of the function of allthese genes. The next logical level of gene annotation isto determine the expression pattern of each individualgene in terms of tissue, cellular, and temporal specificity.High-resolution methods, such as RNA in situ hybridization(ISH) provide an accurate description of the spatiotemporaldistribution of transcripts as well as a threedimensional“in vivo” gene expression overview.We set out to analyze systematically the expressionpattern of genes from the entire Hsa21. We chose to developthis gene expression atlas using the mouse orthologsof the Hsa21 genes; these genes map in the syntenicregion of the mouse genome; i.e., segments ofMmu16, Mmu17, and Mmu10. A total of 161 murinegenes out of the 178 confirmed human genes were studied.The expression atlas, which was a collaborative effortwith the laboratories of A. Ballabio, TIGEM, Naples,and G. Eichele, Max Planck Institute, Hannover, consistsof (1) whole-mount ISH of mouse embryos at E9.5 andE10.5; (2) ISH on serial sagittal sections of E14.5; and(3)RT-PCR in four developmental stages (E8.5, E9.5,E12.5, and E19) and 12 adult tissues (brain, heart, kidney,thymus, liver, stomach, muscle, lung, testis, ovary, skin,and eyes). All the data (gene list, original ISH images, annotationtables, details on probes and oligonucleotideprimers) are publicly available through Web siteshttp://www.tigem.it/ch21exp/ or http://www.nature.com/nature (Reymond et al. 2002).By whole-mount ISH at E10.5, patterned (regional)gene expression was observed in 28%, and ubiquitous expressionin 24%, of genes; furthermore, weak ubiquitousand strong regional expression was observed in 47% ofgenes. The ISH in tissue sections at E14.5 revealed patterned(regional) gene expression in 42%, ubiquitous expressionin 13%, and combined weak ubiquitous andstrong regional expression in 9% of genes. The highestnumbers of genes with a restricted expression patternwere observed in the brain, the eye, and the gut at allstages (Fig. 4a). The RT-PCR analysis resulted in an averageof eight adult tissues per gene (Fig. 4b). The transcriptomesof the brain and kidney showed the highestcomplexity, each tissue expressing 85% of the 161 genesexamined. Muscle, as expected, had the lowest transcriptomecomplexity, since only 21% of genes examinedwere expressed there.Figure 4. (a) Number of the Hsa21 mouse orthologous genesanalyzed by RT-PCR expressed in 0, 1, 2–3, 4–5, 6–7, 8–9, and10–12 adult tissues. (b) Percentage of the Hsa21 mouse orthologousgenes analyzed by RT-PCR identified in each murine adulttissue. (c) Schematic representation of a cluster of Hsa21 orthologousgenes (Pdxk to Hrmtl1) mapping to Mmu10 that show asignificant absence of expression in muscle (p = 0.02). Mb distanceswere published in Hattori et al. (2000). Genes are representedby gray arrows. (Adapted from Reymond et al. 2002.)Unexpectedly, we found genomic regions containingclusters of genes with similar expression patterns. Regionscontaining either co-silenced or co-expressed geneswere observed. For example, RT-PCR analysis identifieda 3.9-Mb (from genes B3galt5 to Hsf2bp) and a 4.3-Mbregion (from genes Pdxk to Hrmtl1, Fig. 4c) in which allgenes were not expressed in heart (p