Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

• DOI: 10.1371/journal.pgen.1001274
• Publication Date: 2011-01-13T16:26:02Z
• Authors: Elizabeth A. Rach; Deborah R. Winter; Ashlee M. Benjamin; David L. Corcoran; Ting Ni; Jun Zhu; Uwe Ohler
• Keywords: CTCF; RNA polymerase II; CpG site; ChIA-PET; Transcription

The application of deep sequencing to map 5′ capped transcripts has confirmed the existence at least two distinct promoter classes in metazoans: "focused" promoters with transcription start sites (TSSs) that occur a narrowly defined genomic span and "dispersed" TSSs are spread over larger window. Previous studies have explored presence features, such as CpG islands sequence motifs, these classes, but virtually no directly investigated relationship chromatin features. Here, we show significantly differentiated by nucleosome organization structure. Dispersed display higher associations well-positioned nucleosomes downstream TSS more clearly free region upstream, while focused less organized structure, yet RNA polymerase II. These differences extend histone variants (H2A.Z) marks (H3K4 methylation), well insulator binding (such CTCF), independent expression levels affected genes. Notably, conserved across mammals flies, they provide for clearer separation architectures than absence or occurrence stalled polymerase. Computational models support stronger contribution features definition dispersed compared sites. Our results from not only reflect initiation process core also indicative divergent transcriptional programs established within gene-proximal organization.