Assessment of the total number of human transcription units

Variation in the estimates of the number of genes encoded by the human geno me (28,000-120,000) attests to the difficulty of systematically identifying human genes. Sequencing of human chromosome 22 (Chr22) provided the first comprehensive, unbiased view of an entire human chromosome, and intensive a nalysis of this sequence identified 545 genes and 134 pseudogenes that had similarity or identity to known proteins and/or ESTs and which were listed in the gene annotation (http://www.sanger.ac.uk/HGP/Chr22). This analysis y ielded an estimate of approximately 36,000 functional expressed genes in th e human genome (and 9000 pseudogenes). However, a key uncertainty in this e stimate was that hundreds of additional genes beyond those annotated in the Chr22 sequence are predicted by the gene prediction program Genscan, an un known number of which might represent additional expressed genes. To determ ine what fraction of these "predicted novel genes" (PNGs) represents expres sed human genes, we used a sensitive RT-PCR assay to detect predicted trans cripts in 17 tissues and one cell line. Our results indicate that at least 5000-9000 additional human genes which lack similarity to known genes or pr oteins exist in the human genome, increasing baseline gene estimates to sim ilar to 41,000-45,000.