3D GENOME DYNAMICS · Unraveling the Molecular Basis And Regulatory Function Of Genome Architecture By Monitoring Its Dynamic Makeup During Differentiation And In Differentiated Cells
FP7 — People (Marie Curie Actions)
- Duration
- 2013-09-01 → 2017-08-31
- EU contribution
- €100,000
- Participants
- 1
- Scheme
- MC-CIG
Lines connect the coordinator with its partners.
Results in brief
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.
Data: CORDIS, © European Union
Project objective
This proposed study addresses a major issue in the field of genome biology: how cells adopt specific genome configuration during differentiation, how is it maintained, and how properties of nuclear architecture relate to cell function.Although spatial clustering of genes and regulatory elements is correlated with transcription status and epigenetic states, it is not clear which mechanisms drive, which features follow, and what is the regulatory role of nuclear organization.Our studies in numerous cell types have identified the enrichment for transcription factor (TF) binding loci as the salient feature of genomic loci residing in active sub-nuclear environments. Surprisingly, the coordinated chromosomal associations were not correlated with transcription response. Thus, we hypothesize that TF interactions with the genome are key for the establishment of genome three-dimensional organization.To understand how nuclear architecture is modulated during differentiation we propose to study the coupled dynamics of genomic association networks together with multiple genomic layers of genome regulation (transcription, transcription factor binding, and epigenetic states) during adipogenic differentiation in high temporal resolution. Moreover, genome architecture data will be combined with DHS-seq profiles for unbiased examinations and discovery of nuclear organizing factors. To understand how genome organization is maintained we will study differentiated mammary cells. We will validate our findings with molecular perturbations, and combine genomics with single cell analysis by imaging. Lastly, to understand genome organization transitions, we will study the dynamics of genome organization throughout the cell cycle in high molecular and temporal resolutions. Importantly, we will link nuclear organization to cellular function by studying functional and terminal differentiation.
Original text from CORDIS.
Participants
- BAR ILAN UNIVERSITY · Ramat GanCoordinatorIsrael
Links
Data: CORDIS, © European Union