Structural basis of transcription reduction by a promoter-proximal+1 nucleosome

At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucle-osome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.

Automated summary

At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II pre-initiation complex. Inactive genes have the +1 nucleosome positioned further upstream, at a promoter-proximal location. A model system shows that a promoter-proximal +1 nucleosome can inhibit RNA synthesis, and this is attributed to the structural basis of the pre-initiation complex. The position of the nucleosome edge relative to the transcription start site determines the assembly and activity of the pre-initiation complex, with a closer proximity resulting in inhibition.