Transcription challenges the integrity of replicating chromosomes by generating topological stress and conflicts with forks^1,2. The DNA topoisomerases Top1 and Top2 and the HMGB family protein Hmo1 assist DNA replication and transcription^3,4,5,6. Here we describe the topological architecture of genes in Saccharomyces cerevisiae during the G1 and S phases of the cell cycle. We found under-wound DNA at gene boundaries and over-wound DNA within coding regions. This arrangement does not depend on Pol II or S phase. Top2 and Hmo1 preserve negative supercoil at gene boundaries, while Top1 acts at coding regions. Transcription generates RNA–DNA hybrids within coding regions, independently of fork orientation. During S phase, Hmo1 protects under-wound DNA from Top2, while Top2 confines Pol II and Top1 at coding units, counteracting transcription leakage and aberrant hybrids at gene boundaries. Negative supercoil at gene boundaries prevents supercoil diffusion and nucleosome repositioning at coding regions. DNA looping occurs at Top2 clusters. We propose that Hmo1 locks gene boundaries in a cruciform conformation and, with Top2, modulates the architecture of genes that retain the memory of the topological arrangements even when transcription is repressed.

转录通过产生拓扑应力和与叉^1,2冲突来挑战复制染色体的完整性。DNA 拓扑异构酶 Top1 和 Top2 以及 HMGB 家族蛋白 Hmo1 有助于 DNA 复制和转录^3,4,5,6。在这里，我们描述了酿酒酵母中基因的拓扑结构在细胞周期的 G1 期和 S 期。我们在基因边界处发现了伤口不足的 DNA，而在编码区域内发现了过度伤口的 DNA。这种安排不依赖于 Pol II 或 S 相。Top2 和 Hmo1 在基因边界处保留负超螺旋，而 Top1 作用于编码区。转录在编码区内产生 RNA-DNA 杂合体，与叉的方向无关。在 S 期，Hmo1 保护伤口下的 DNA 免受 Top2 的伤害，而 Top2 将 Pol II 和 Top1 限制在编码单元，抵消基因边界处的转录泄漏和异常杂交。基因边界处的负超螺旋防止超螺旋扩散和核小体在编码区重新定位。DNA 循环发生在 Top2 簇。我们建议 Hmo1 将基因边界锁定在十字形构象中，并且与 Top2 一起，