Evolution, biogenesis and function of promoter-associated RNAs

Abstract

Transcription initiation is a tightly controlled process that involves chromatin modifications and nucleosome remodelling, transcription factor binding, and the assembly and recruitment of the RNA Polymerase II (RNAPII) complex. Recent studies have reported a diversity of long and short RNAs derived from eukaryotic promoters, which may be involved in transcription regulation. Here we review these species with particular attention to the features and biogenesis of transcription initiation RNAs (tiRNAs), a class of 18 nucleotide small RNA conserved from insects to mammals. We also report and discuss the observation that tiRNAs are not present in plants and are not clearly expressed in the nematode C. elegans. We suggest that tiRNAs may be intimately connected RNAPII backtracking, nucleosome marking and gene regulation.