Rabuffo Claudia, Schmidt Markus R, Yadav Prateek, Tong Pin, Carloni Roberta, Barcons-Simon Anna, Cosentino Raúl O, Krebs Stefan, Matthews Keith R, Allshire Robin C, Siegel T Nicolai
Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
Biomedical Center Munich, Division of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
Nat Commun. 2024 Dec 23;15(1):10716. doi: 10.1038/s41467-024-55285-9.
The eukaryotic nucleus exhibits a highly organized 3D genome architecture, with RNA transcription and processing confined to specific nuclear structures. While intra-chromosomal interactions, such as promoter-enhancer dynamics, are well-studied, the role of inter-chromosomal interactions remains poorly understood. Investigating these interactions in mammalian cells is challenging due to large genome sizes and the need for deep sequencing. Additionally, transcription-dependent 3D topologies in mixed cell populations further complicate analyses. To address these challenges, we used high-resolution DNA-DNA contact mapping (Micro-C) in Trypanosoma brucei, a parasite with continuous RNA polymerase II (RNAPII) transcription and polycistronic transcription units (PTUs). With approximately 300 transcription start sites (TSSs), this genome organization simplifies data interpretation. To minimize scaffolding artifacts, we also generated a highly contiguous phased genome assembly using ultra-long sequencing reads. Our Micro-C analysis revealed an intricate 3D genome organization. While the T. brucei genome displays features resembling chromosome territories, its chromosomes are arranged around polymerase-specific transcription hubs. RNAPI-transcribed genes cluster, as expected from their localization to the nucleolus. However, we also found that RNAPII TSSs form distinct inter-chromosomal transcription hubs with other RNAPII TSSs. These findings highlight the evolutionary significance of inter-chromosomal transcription hubs and provide new insights into genome organization in T. brucei.
真核细胞核呈现出高度组织化的三维基因组结构，RNA转录和加工局限于特定的核结构。虽然染色体内部的相互作用，如启动子-增强子动态变化，已得到充分研究，但染色体间相互作用的作用仍知之甚少。由于基因组规模庞大且需要深度测序，在哺乳动物细胞中研究这些相互作用具有挑战性。此外，混合细胞群体中转录依赖的三维拓扑结构进一步使分析复杂化。为应对这些挑战，我们在布氏锥虫中使用了高分辨率DNA-DNA接触图谱（Micro-C），布氏锥虫是一种具有连续RNA聚合酶II（RNAPII）转录和多顺反子转录单元（PTU）的寄生虫。该基因组约有300个转录起始位点（TSS），这种基因组组织简化了数据解读。为尽量减少支架假象，我们还使用超长测序读段生成了高度连续的分阶段基因组组装。我们的Micro-C分析揭示了一种复杂的三维基因组组织。虽然布氏锥虫基因组显示出类似于染色体区域的特征，但其染色体围绕着聚合酶特异性转录中心排列。RNAPI转录的基因如预期那样聚集在核仁中。然而，我们还发现RNAPII TSS与其他RNAPII TSS形成了不同的染色体间转录中心。这些发现突出了染色体间转录中心的进化意义，并为布氏锥虫的基因组组织提供了新的见解。
