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Abstract 3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we presentMethyltransferaseTargeting-based chromosomeArchitectureCapture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization. 

Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes are clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion. 

Abstract We investigate the validity of the “Einstein relations” in the general setting of unimodular random networks. These are equalities relating scaling exponents:$$\begin{aligned} d_{w} &= d_{f} + \tilde{\zeta }, \\ d_{s} &= 2 d_{f}/d_{w}, \end{aligned}$$whered_wis the walk dimension,d_fis the fractal dimension,d_sis the spectral dimension, and$$\tilde{\zeta }$$is the resistance exponent. Roughly speaking, this relates the mean displacement and return probability of a random walker to the density and conductivity of the underlying medium. We show that ifd_fand$$\tilde{\zeta } \geqslant 0$$exist, thend_wandd_sexist, and the aforementioned equalities hold. Moreover, our primary new estimate$$d_{w} \geqslant d_{f} + \tilde{\zeta }$$is established for all$$\tilde{\zeta } \in \mathbb{R}$$. For the uniform infinite planar triangulation (UIPT), this yields the consequenced_w=4 usingd_f=4 (Angel in Geom. Funct. Anal. 13(5):935–974, 2003) and$$\tilde{\zeta }=0$$(established here as a consequence of the Liouville Quantum Gravity theory, following Gwynne-Miller 2020 and (Ding and Gwynne in Commun. Math. Phys. 374(3):1877–1934, 2020)). The conclusiond_w=4 had been previously established by Gwynne and Hutchcroft (2018) using more elaborate methods. A new consequence is thatd_w=d_ffor the uniform infinite Schnyder-wood decorated triangulation, implying that the simple random walk is subdiffusive, sinced_f>2.