Genome architecture is the arrangement of functional elements within the genome [1] and can be thought of in a linear fashion, or in the three-dimensional arrangement found in nuclei [2]. The architecture of genomes differs greatly across the tree of life. For example, bacteria tend to have ...
CTCF loops and loop domains, and enhancer–promoter (E–P) interactions (Fig.1b). Hi-C experiments were performed in triplicates which clearly clustered by group (Fig.1c). Considering the high correlation between the replicates
With millions of candidate regulatory elements and ∼20,000 regulated genes in the human genome, these limitations preclude the comprehensive dissection of the cis-regulatory architecture of even a single cell line. Here, we introduce a framework (Figure 1A) designed to overcome both limitations. ...
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. https://doi.org/10.1038/cr.2016.137 (2016). Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973–1237973 ...
Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton Article Open access 27 December 2024 Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance...
Recently, tilted light sheet microscopy combined with PSF engineering was able to map out the whole mammalian cell nuclear envelope [19] and may become a powerful future technique for 3D genome architecture. Besides optical advances, a novel experimental PSF-fitter software has been developed, which...
and HSR may allow the tumor to adapt to changing environment, e.g. targetted drug application. As a result, understanding the architecture of the focal amplifications is important to gain insights into cancer biology. AmpliconArchitect (AA) is a tool which can reconstruct the structure of focal...
Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell. 2016;167:1369–1384.e19. Article CAS PubMed PubMed Central Google Scholar Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;...
The analysis comprised 41 proteins with pQTLs in two populations.aShared genetic architecture among two populations. EAS, East Asian; EUR, European.bEffect of BMI on cardiometabolic disease risk. The effect sizes are present as odds ratios per 1 kg/m2increase in BMI. The dots represent the es...
The purpose of the deep learning model is to (1) predict the mutation rateμRand (2) quantify prediction uncertainty\(\sigma _R^2\)conditioned on the epigenetic organization of the regionR. The architecture was previously described31. In brief, the network consists of a convolutional neural ne...