Oncins Anna, Zaurin Roser, Toukabri Houyem, Quililan Kimberly, Hernández Mora José R, Karpinska Magdalena A, Wernersson Erik, Smith Alastair, Bianchi Agostina, Albinati Leone, Cozzuto Luca, Rivero Andrea, Gulliver Chloe, Velten Jessica, Denkena Johanna, Serra François, Gómez Raúl, López Cristina, Beà Sílvia, Paulsen Jonas, Halidi Nadia, Valencia Alfonso, Bienko Magda, Oudelaar A Marieke, Beekman Renée
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), C. Dr. Aiguader 88, Barcelona 08003, Spain.
Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
Nucleic Acids Res. 2025 Aug 11;53(15). doi: 10.1093/nar/gkaf677.
Chromosomal translocations have largely been implicated in tumor development. However, beyond the consequences of aberrant gene expression near the breakpoint, their effects remain underexplored. In this work, we characterize the interplay between translocations, chromatin organization and gene expression using mantle cell lymphoma (MCL) as a model. We show by in vitro genomic engineering and in MCL patient samples that translocations can drive transcriptional changes at entire chromosome arms affecting multiple genes in a regulon-like fashion. Moreover, we demonstrate a clear link between the translocation-induced transcriptional alterations and genome organization, with genes most susceptible to change expression forming pre-existing ultra-long-range interactions spanning 50 megabases. The translocation involves the strong immunoglobulin enhancer into this 3D interaction, allowing the spread of its regulatory potential over the entire affected chromosome arm. Finally, we show that translocation-induced effects mainly represent expression enhancement of genes already active prior to translocation formation, highlighting the importance of the epigenetic state of the cell in which this initial hit occurs. In summary, by studying genome organization principles in the context of translocations, we describe a new principle of gene regulation, showing that strong enhancers can induce substantial gene expression enhancement through ultra-long-range interactions affecting entire chromosome arms, representing an important new mechanism in health and disease.
染色体易位在很大程度上与肿瘤发展有关。然而,除了断点附近异常基因表达的后果外,它们的影响仍未得到充分探索。在这项工作中,我们以套细胞淋巴瘤(MCL)为模型,描述了易位、染色质组织和基因表达之间的相互作用。我们通过体外基因组工程和MCL患者样本表明,易位可以以类似调控子的方式驱动整个染色体臂上的转录变化,影响多个基因。此外,我们证明了易位诱导的转录改变与基因组组织之间存在明确的联系,最易发生表达变化的基因形成了跨越50兆碱基的预先存在的超长程相互作用。易位将强大的免疫球蛋白增强子纳入这种三维相互作用,使其调控潜能扩展到整个受影响的染色体臂。最后,我们表明易位诱导的效应主要表现为易位形成前已活跃的基因的表达增强,突出了初始命中发生时细胞表观遗传状态的重要性。总之,通过在易位背景下研究基因组组织原则,我们描述了一种新的基因调控原则,表明强大的增强子可以通过影响整个染色体臂的超长程相互作用诱导大量基因表达增强,这是健康和疾病中的一种重要新机制。