Structural analysis of nucleosomal barrier to transcription

Abstract

Thousands of human and Drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. However, the molecular mechanisms of formation of the nucleosomal barrier to transcribing RNA polymerase II (Pol II) and nucleosome survival during/after transcription remain unknown. Here we show that both DNA-histone interactions and Pol II backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely occurs through allosterically stabilized histone-histone interactions. Structural analysis indicates that after Pol II encounters the barrier, the enzyme backtracks and nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state. DNA is displaced from one of the H2A/H2B dimers that remains associated with the octamer. The data reveal the importance of intranucleosomal DNA-protein and protein-protein interactions during conformational changes in the nucleosome structure on transcription. Mechanisms of nucleosomal barrier formation and nucleosome survival during transcription are proposed.

Nucleosomal Barrier to Transcription: Structural Determinants and Changes in Chromatin Structure

“…Insert: A model of yeast RNA polymerase II elongation complex (PDB 1Y1W) with the active center at the position +42 bp in the nucleosome (PDB 1KX5). The model was built using the published structure of the +42 complex with E. coli RNA polymerase [18] where the bacterial enzyme was replaced by Pol II. Dotted line indicates direction of transcription by Pol II.…”

“…Formation of the Ø-loop induces uncoiling of the ~100-bp DNA region in front of the enzyme allowing further transcription through the nucleosome and efficient survival of nearly all histones (with exception of one H2A/H2B dimer that is displaced by Pol II) during this process [12,15]. The high efficiency of histone survival during transcription is explained in part by allosterically stabilized intranucleosomal histone-histone interactions [18]. Recent structural analysis indicates that after Pol II encounters the strong +50 barrier, the enzyme backtracks and nucleosomal DNA re-coils on the octamer, locking Pol II in the arrested state (Fig.…”

“…Recent structural analysis indicates that after Pol II encounters the strong +50 barrier, the enzyme backtracks and nucleosomal DNA re-coils on the octamer, locking Pol II in the arrested state (Fig. 1, [18]).…”

Histone chaperones: Variety and functions

“…Показано также, что FACT по-могает димерам гистонов Н2А-Н2В встроиться в репарируемые участки хроматина. Шапероны гистонов участвуют в транскрипции хроматина В ходе работы РНК-полимеразы нарушают структуру хроматина, нуклеосомная организация которого является барьером для их продвижения по ДНК [30]. ШГ участвуют в процессе транскрип-ции хроматина.…”

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

“…[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.…”