BioProject

The analysis of several mammalian genomes has revealed between 20,000 to 30,000 genes in each genome, a number that may seem hard to reconcile with the large number of cell types and complex functions of these organisms. More...

The analysis of several mammalian genomes has revealed between 20,000 to 30,000 genes in each genome, a number that may seem hard to reconcile with the large number of cell types and complex functions of these organisms. The solution to this paradox partly lies in the large array of transcripts that each gene can potentially generate through usage of alternative promoters and the variable levels of transcripts that each gene produces in different tissues and cell types. Thus, in order to understand the mechanisms that control diverse patterns of gene expression in mammals, it is necessary to accurately define the active promoters and monitor their cell or tissue-dependent activity. Previous high throughput strategies for assaying tissue-specific gene expression have primarily relied on measurements of steady-state transcript levels by microarrays or tag sequencing. Here, we employ a new experimental strategy to identify and characterize tissue specific promoters by integrating genome-wide maps of RNA polymerase II (Pol II) binding, chromatin modifications and gene expression profiles. We applied this strategy to mouse embryonic stem cells (mES), and adult brain, heart, kidney, and liver. Our results delineated 24,363 Pol II binding sites throughout the genome, 91% of which correspond to 5’ end annotation based on known transcripts and cap-analysis of gene expression (CAGE) and can be regarded as promoters. A majority of these experimentally defined promoters are active in all tissues, while only 4,396 can be characterized as tissue-specific using a quantitative measure of Pol II occupancy. In general, Pol II occupancy at these tissue specific promoters is correlated with the presence of active histone modification marks. However, a set of mES- specific promoters display persistent levels of H3K4me3 in non-ES tissues despite undetectable Pol II binding and transcript. Broadly, our results expand the knowledge of tissue-specific mammalian genes and provide a resource for understanding the transcriptional programs in mammalian development and differentiation. Keywords: ChIP-chip, expression, mouse, brain, heart, kidney, liver, ES Overall design: To map promoters in the mouse genome, we performed 5 genomewide (37 array set) ChIP-chip of Pol II binding in R1 ES cells and brain, heart, kidney, and liver from 10-12 week-old female BL6 mouse. To validate genome-wide Pol II enriched regions across tissues, we filtered the genome-wide microarray set to a 4-array set which covers Pol II regions bound in any tissue. We repeated Pol II ChIP-chip across tissues using this 4-array set. We also performed (without replicates) ChIP-chip across tissues for H3ac and H3K4me3 using this condensed array set. To complement our promoter mapping efforts with transcript levels, we performed expression profiling (no replicates) across tissues using Affymetrix 430 v2.0 arrays. Less...