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Unraveling the Molecular Basis And Regulatory Function Of Genome Architecture By Monitoring Its Dynamic Makeup During Differentiation And In Differentiated Cells

Final Report Summary - 3D GENOME DYNAMICS (Unraveling the Molecular Basis And Regulatory Function Of Genome Architecture By Monitoring Its Dynamic Makeup During Differentiation And In Differentiated Cells)

The non-random folding of mammalian genomes is an important regulatory layer of genome function. Importantly, the large-scale genome architecture is cell-type specific and hard to convert, suggesting that it is important for cell-specific functions and identity. Our goal is to understand the mechanisms driving the co-localization of active chromosomal domains and the regulatory function of this organization. We found that the most prominent feature of genomic loci from across the entire genome that meet together in the nuclear space is the enrichment for transcription factors (TF) binding events. Moreover during cellular differentiation the genome is reorganized according to changes in binding of lineage-specific TFs and less by changes in gene expression programs. Thus we proposed that lineage-specific TF via their direct genome association play a key role in coordinating clustering of cell-type specific active chromatin compartments. However, given the complexity and interdependencies that involve multiple TFs, transcription machinery, and histone modifying enzymes in the active compartments it is challenging to determine which factors drive, which follow, and how transcription is regulated by nuclear organization. Thus we took the approach of measuring the dynamic progression of genome high-order architecture in high temporal resolution during differentiation of 3T3-L1 fibroblasts to adipocytes as a model system, and integrating this data with multiple genomic profiles (transcription, transcription factor binding, and epigenetic states). Importantly, analysis of mature adipocytes revealed a strong link between nuclear organization and cellular function as adipogenic genes from across the genome cluster together in adipocyte-specific nuclear topology. Analyzing the coordinated dynamics of genome architecture with multiple linear profiles revealed unexpected hierarchy within the adipogenic factors C/EBPβ, RXR, and PPARγ. Although all these TFs are essential for adipogenesis, RXR is the dominant genome "organizer" at the initiation of adipogenesis, while later the other TFs are equally associated with genome reorganization. Surprisingly, at the last stage of adipogenesis the binding of these TFs is negatively associated with genome reorganization, while the adipogenic hub is shifted to H3K27me3 repressive environment in conjunction with attenuation of gene transcription. We propose that the repositioning to H3K27me3 environment in the end of the differentiation may contribute to stabilize gene expression levels and diminish the developmental plasticity of the specialize cell.

Findings of this study provide important insights about stage-specific hierarchy among the orchestra of transcription factors contributing to the establishment of the adipogenic genome architecture that brings together the adipogenic transcription program and how it may be altered to accommodate with obesity, one of the world looming epidemics.