Pulupa Joan, McArthur Natalie G, Stathi Olga, Wang Miao, Zazhytska Marianna, Pirozzolo Isabella D, Nayar Ahana, Shapiro Lawrence, Lomvardas Stavros
Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY, USA.
Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, USA.
Nature. 2025 May 14. doi: 10.1038/s41586-025-09043-6.
Ultra-long-range genomic contacts, which are key components of neuronal genome architecture, constitute a biochemical enigma. This is because regulatory DNA elements make selective and stable contacts with DNA sequences located hundreds of kilobases away, instead of interacting with proximal sequences occupied by the exact same transcription factors. This is exemplified in olfactory sensory neurons (OSNs), in which only a fraction of LHX2-, EBF1- and LDB1-bound sites interact with each other, converging into highly selective multi-chromosomal enhancer hubs. To obtain biochemical insight into this process, here we assembled olfactory receptor (OR) enhancer hubs in vitro with recombinant proteins and enhancer DNA. Cell-free reconstitution of enhancer hubs revealed that OR enhancers form nucleoprotein condensates with unusual, solid-like characteristics. Assembly of these solid condensates is orchestrated by specific DNA motifs enriched in OR enhancers, which are likely to confer distinct homotypic properties on their resident LHX2-EBF1-LDB1 complexes. Single-molecule tracking and pulse-chase experiments in vivo confirmed that LHX2 and EBF1 assemble OR-transcription-competent condensates with solid properties in OSN nuclei, under physiological concentrations of protein. Thus, homophilic nucleoprotein interactions that are influenced by DNA sequence generate new types of biomolecular condensate, which might provide a generalizable explanation for the stability and specificity of long-range genomic contacts across cell types.
超长距离基因组接触是神经元基因组结构的关键组成部分，构成了一个生化谜团。这是因为调控性DNA元件与位于数百千碱基之外的DNA序列形成选择性和稳定的接触，而不是与由完全相同的转录因子占据的近端序列相互作用。嗅觉感觉神经元（OSN）就是一个例子，其中只有一小部分与LHX2、EBF1和LDB1结合的位点相互作用，汇聚成高度选择性的多染色体增强子枢纽。为了深入了解这一过程的生化机制，我们在这里用重组蛋白和增强子DNA在体外组装了嗅觉受体（OR）增强子枢纽。增强子枢纽的无细胞重建显示，OR增强子形成具有不寻常的、类似固体特性的核蛋白凝聚物。这些固体凝聚物的组装由富含OR增强子的特定DNA基序精心编排，这些基序可能赋予其驻留的LHX2-EBF1-LDB1复合物独特的同型特性。体内的单分子追踪和脉冲追踪实验证实，在生理浓度的蛋白质条件下，LHX2和EBF1在OSN细胞核中组装具有固体特性的OR转录活性凝聚物。因此，受DNA序列影响的同源核蛋白相互作用产生了新型的生物分子凝聚物，这可能为跨细胞类型的长距离基因组接触的稳定性和特异性提供一个可推广的解释。
