Transcription initiation at promoters requires the assemblyofgeneral transcription factors (GTFs) and RNA polymerase(Pol) II. Recent works have shown that Pol II can also berecruited to, and transcribe distal regulatory regions.

We have analyzed initiation and elongation through genome-widelocalization of Pol II isoforms, GTFs and active chromatin marksin developing T-cells. We show that Pol II and GTFs are recruitedto known, highly T-cell specific enhancers and we extend thisobservation to many new putative enhancers, a fraction of whichis transcribed. Importantly, we also identify new genomic featurescharacterized by large Pol II/GTFs recruitment and transcriptionalinitiation platforms (TIPs), not only at promoters but also atintergenic and intragenic regions. TIPs are characterized byvariable widths ranging from 0.2 to 10 Kb, and correlate with highCpG content and tissue-specificity at promoters. We proposethat TIPs represent important novel regulatory hallmarks of thegenome.