In a recent Nature article, the FANTOM (Functional Annotation of the Mammalian Genome) project announced the release of data from a large effort to produce an "atlas" of promotors across cell types in human and mouse. The group performed cap analysis of gene expression (CAGE) via single molecule sequencing across 573 normal human and 128 normal mouse cell samples, as well as human cancer cell lines, human post-mortem cells, and mouse cell types at various developmental stages. This sequencing approach results in sequences of full cDNAs for transcribed mRNAs within cells, including the 5' transcription start site, allowing for the comparison of transcription start sites (TSS) across cell types. The study strongly indicates that gene expression and promotor function is highly cell-type specific, with only 6% of identified genes' expression patterns characterized as "housekeeping," defined as expressed within a 10-fold range in >50% of cell types. This ubiquitously- and uniformly-expressed gene set was enriched for genes involved in RNA processing. Comparison with mouse TSS suggests differing evolutionary patterns for cell-specific v. broadly functioning TSS, with more restricted TSS showing more evolutionary change.
A companion paper published in the same issue looks at enhancer activity across cell types. Data from the project is available online.