Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription

Transcription through chromatin by RNA polymerase II (Pol II) is accompanied by the formation of small intranucleosomal DNA loops containing the enzyme (i-loops) that are involved in survival of core histones on the DNA and arrest of Pol II during the transcription of damaged DNA. However, the structures of i-loops have not been determined. Here, the structures of the intermediates formed during transcription through a nucleosome containing intact or damaged DNA were studied using biochemical approaches and electron microscopy. After RNA polymerase reaches position +24 from the nucleosomal boundary, the enzyme can backtrack to position +20, where DNA behind the enzyme recoils on the surface of the histone octamer, forming an i-loop that locks Pol II in the arrested state. Since the i-loop is formed more efficiently in the presence of SSBs positioned behind the transcribing enzyme, the loop could play a role in the transcription-coupled repair of DNA damage hidden in the chromatin structure.

Automated summary

Transcription by RNA polymerase II in chromatin involves the formation of small intranucleosomal DNA loops (i-loops) containing the enzyme, which are important for histone survival and transcription arrest during the transcription of damaged DNA. This study determined the structures of i-loops formed during transcription through nucleosomes with intact or damaged DNA using biochemical methods and electron microscopy. The results showed that i-loop formation is more efficient in the presence of single-strand DNA-binding proteins behind the transcribing enzyme, suggesting a potential role in transcription-coupled repair of hidden DNA damage in chromatin structure.