Abstract
The application of deep sequencing to map 5′ capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: “focused” promoters with transcription start sites (TSSs) that occur in a narrowly defined genomic span and “dispersed” promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z) and marks (H3K4 methylation), as well as insulator binding (such as CTCF), independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5′ capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization.
Highlights
The development of high-throughput sequencing strategies, which generate millions of 59 sequence tags from capped RNAs transcribed by RNA polymerase II, has enabled obtaining fine-grained pictures of transcription initiation
How are genes transcribed at the right levels and under the right conditions? Transcription regulation in eukaryotes has long been proposed to work by a division of labor: ubiquitous DNA sequence features in the core promoter region, close to the transcription start site (TSS) of genes, were thought to generically encode information to recruit RNA polymerase to initiate transcription, while specific sequence features, often distal from the genes, were thought to boost expression under the right conditions
Linking these patterns to chromatin maps, we find distinct core promoter classes, those in which the TSS location is defined broadly on the chromatin level and those in which the TSS is defined by precisely positioned sequence features
Summary
The development of high-throughput sequencing strategies, which generate millions of 59 sequence tags from capped RNAs transcribed by RNA polymerase II (pol II), has enabled obtaining fine-grained pictures of transcription initiation. Each of the tags originates from a transcription start site (TSSs), and mapping the tags to the genome identifies tag clusters for individual genes. The application of Cap Analysis of Gene Expression (CAGE) produced comprehensive data sets for mammalian promoters [1], and an extension of this methodology to Paired End Analysis of Transcription Start Sites (PEAT) was used to map and cluster millions of paired reads from Drosophila melanogaster embryos [2]. Tag clusters exhibit different initiation patterns, i.e. distributions of tags within a cluster, and have been used to define distinct promoter classes, generally falling into two basic groups: Both flies and mammals have focused promoters in which transcription occurs within a narrow genomic window of a few nucleotides, and dispersed promoters in which TSSs spread out over a larger genomic region on the order of a hundred nucleotides. Data on frequent modifications to the Nterminal histone tails have supported a histone code specifying functional domains in the genome; for instance, the tri-
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