Yao Qian, Zhu Linying, Shi Zhen, Banerjee Subhadra, Chen Chongyi
Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Nat Struct Mol Biol. 2025 Jan;32(1):48-61. doi: 10.1038/s41594-024-01377-5. Epub 2024 Aug 16.
DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.
DNA超螺旋是双螺旋的一种生物物理特征，在生物过程中起着关键作用。然而，对染色质中DNA超螺旋的理解仍然有限。在此，我们开发了叠氮化物-三甲基补骨脂素测序（ATMP-seq），这是一种DNA超螺旋检测方法，在最大限度减少基因组偏差和背景噪声的同时提供定量准确性。使用ATMP-seq，我们直接可视化了基因周围转录依赖性的负向和正向双超螺旋结构域，并绘制了整个人类基因组中千碱基分辨率的DNA超螺旋图谱。值得注意的是，我们在所有染色体上发现了兆碱基规模的超螺旋结构域（SDs），其主要由拓扑异构酶I和IIβ调节。转录活性而非局部区域随后的超螺旋积累有助于SD的形成，这表明转录产生的超螺旋具有长程传播。全基因组的SDs在人类和果蝇细胞中均与A/B区室共定位，但与拓扑相关结构域（TADs）不同，在TAD边界处有负超螺旋积累。此外，全基因组的DNA超螺旋在细胞状态和类型之间存在差异，并调节人类基因表达，强调了超螺旋动力学在染色质调控和功能中的重要性。
