Two models of preinitiation complex (PIC) positioning at promoters. The nucleosome organization and sequences features found in ubiquitous, germline-specific, and somatic tissue–specific promoters suggest that two models of PIC recruitment exist. (A) In ubiquitous and germline-specific promoters (i.e., germline-active promoters), nucleosomes flank a narrow 120- to 140-bp-wide NDR. Positioning of these nucleosomes is facilitated by the underlying DNA sequence, which harbors highly periodic WW (mainly TT) dinucleotides. Thus, the PIC assembling at the NDR is physically constrained by the +1 nucleosome edge, resulting in transcription initiation ∼20 bp upstream of the +1 nucleosome edge. Many of these promoters lead to bidirectional elongative transcription. Otherwise, upstream-antisense RNA (uaRNA) are transcribed. (B) In soma-restricted promoters, NDRs are wider (>200 bp), and flanking nucleosomes are weakly positioned and not reproducibly aligned relative to the TSS. Core and transcription factors recruited to the NDR facilitate assembly and positioning of the PIC, resulting in transcription initiation −45 to −50 bp downstream.
