Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

Abstract

Transcription of eukaryotic genes by RNA polymerase II (Pol II) is typically accompanied by nucleosome survival and minimal exchange of histones H3/H4. The mechanism of survival and recovery of chromatin structure remains obscure. Here we show how transcription through chromatin by Pol II is uniquely coupled with nucleosome survival. Structural modeling and functional analysis of the intermediates of transcription through a nucleosome was conducted. When Pol II approaches the area of strong DNA-histone interactions, a small intranucleosomal DNA loop (zero-size or Ø-loop) containing transcribing enzyme is formed. During formation of the Ø-loop, the recovery of DNA-histone interactions behind Pol II is tightly coupled with their disruption ahead of the enzyme. This coupling is a distinct feature of the Pol II-type mechanism that allows further transcription through the nucleosome, prevents nucleosome translocation and minimizes displacement of H3/H4 histones from DNA during enzyme passage.

Partially Assembled Nucleosome Structures at Atomic Detail

“…The fine details of the histone-DNA contacts may be important because transcription through the tightly packed nucleosome carried out by RNA polymerase unassisted by chromatin remodeling factors and histone chaperones can depend on specific protein-DNA contacts. In vitro experiments detailing the progression of RNA polymerase (RNAP or Pol II) through nucleosomes show strong pausing at approximately -60 bp and -30 bp from the dyad (69,70), and a distinct periodicity of~10 bp pause sites (71). Thus, positions of polymerase strong pausing sites tend to occur in the transient accessibility regions (Fig.…”

Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription

“…9 The i-loops formed 24, 34 and 44 bp within the nucleosome are opened behind the enzyme, whereas the i-loop formed at 49 bp is opened ahead of Pol II. 8,9 It should be noted that a nucleosome with an i-loop formed at 49 bp contains more DNA-histone interactions in front of the enzyme than behind it, yet the i-loop is disrupted in front of Pol II. 8 Thus, DNA-histone interactions are more efficiently destabilized by positive DNA supercoiling accumulated ahead of Pol II (discussed in ref.…”

“…Formation of i-loops is especially important before position C49, where the loop forms for the last time and resolves in front of the transcribing complex, resulting in nucleosome recovery and further efficient transcription along DNA uncoiled from the surface of the histone octamer. 8 In vivo and in vitro studies have revealed that chromatin remodeling is also accompanied by formation of DNA loops. 23 Thus, i-loops could facilitate nucleosome survival and/or progression of other processive enzymes (e.g., eukaryotic replisome) along DNA.…”

“…[8][9][10] These loops play a major role in the progression of RNA polymerase through nucleosomes. Furthermore, they may facilitate detection of DNA damage hidden within nucleosomes.…”

“…1C). 8 I-loops forming during transcription represent topologically locked domains with an enclosed molecular motor. Progression of Pol II within an i-loop likely leads to accumulation of supercoiling in the looped DNA ahead of and behind the enzyme (Fig.…”