Topoisomerases, chromatin and transcription termination

Abstract

In eukaryotes transcription is complicated by the DNA being packed in nucleosomes and by supercoils induced by opening of the DNA double helix during elongation. Here we discuss our recent genome-wide work regarding topoisomerases and their role in chromatin remodeling during the transcription cycle and we report a novel function for topoisomerases in transcription termination.

Figure 1

Topoisomerases are required for the global formation of 3′NFR and transcription termination. (A) Histone H3 occupancy in wild-type cells is dependent on the proximity to the adjacent gene, (B) H3 occupancy in top1Δ top2-191^ts mutant relative to levels in wild-type cells, (C) RNA levels in top1Δ top2-191^ts mutant relative to levels in wild-type cells, (D) Pol II occupancy in top1Δ top2-191^ts mutant relative to levels in wild-type cells. Genes making up the green lines have no other transcript <1 kb downstream, genes making up the orange line have another transcript between 500 and 1,000 bp away. The genomic data are aligned at the transcript termination site (TTS). Error bars represent the 99% confidence intervals. Graphs were generated in Podbat (www.podbat.org). (E) Transcription from the forward strand is shown in black and transcription from the reverse strand is shown in red. The green boxes highlight the aberrant transcript in the top1Δ top2-191^ts mutant. Blue boxes indicate the increased level of H3 in the intergenic regions. Dotted arrows indicate cDNA primer position and blue arrows indicate the qRT-PCR primer positions used in (F). Browser views are generated in Podbat. (F) qRT-PCR reveals aberrant transcript elongation in top1Δ top2-191^ts cells. The primers specifically detect read-through transcripts from the indicated gene. Data are normalized to endogenous control.

Figure 2

A model of transcriptional regulation by Top1, Top2 and chromatin remodelers. All stages of the transcription cycle are affected by Top1 and Top2.