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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2013)

The spatial organization of the genome is linked to its biological function. However, the relationship between specific gene regulatory networks that govern cell identity and large-scale organization of genomes remains unclear. To investigate the basis of distal chromatin interactions occurring between genomic regions mega-bases away on the same or different chromosomes, we mapped long-range chromatin interactions in embryonic stem cells (ESCs) using 4C-seq, and examined the genomic features of the interacting regions. Confirming previous results, we show that open, accessible versus closed chromatin character is the primary determinant of distal chromatin interaction preferences, where interacting regions exhibit very similar open/closed chromatin character. We extend these results by demonstrating that genomic regions highly enriched for binding by the pluripotency transcription factors Oct4, Sox2, and Nanog preferentially co-localize, as do regions strongly enriched for Polycomb proteins and trimethylation of histone H3 at lysine 27 (H3K27me3), which include the Hox clusters. Consistent with a spatial segregation of these transcriptional networks, we find that Nanog and Polycomb proteins occupy distinct spaces in the nucleus. Importantly, loss of the Polycomb protein Eed and H3K27me3 diminishes the preferential interactions between regions normally highly enriched for Polycomb proteins and H3K27me3 without dramatically changing long-range chromatin interactions related to the open/closed chromatin state. Finally, a comparison of interactomes in ESCs and fibroblasts uncovered an ESC-specific spatial organization to the mouse genome that is gradually re-established upon reprogramming to induced pluripotent stem cells (iPSCs). Together, our data suggest that transcriptional networks that govern ESC identity play a role in determining genome-organization. We propose the existence of a hierarchy in the organization of chromatin contacts wherein, at the largest scale, the open/closed chromatin character defines an interaction space and overall chromosome conformation; on a finer scale, cell type-specific transcriptional networks direct preferential distal interactions, which we speculate are critical for efficient regulation of transcription and establishment of local chromatin environments.

  • 3 supplemental files
Cover page: Long-range chromatin contacts reveal a role for the pluripotency and Polycomb networks in genome organization
  • Article
  • Peer Reviewed
UCLA Previously Published Works (2014)
The organization of chromatin within the nucleus and the regulation of transcription are tightly linked. Recently, mechanisms underlying this relationship have been uncovered. By defining the organizational hierarchy of the genome, determining changes in chromatin organization associated with changes in cell identity, and describing chromatin organization within the context of linear genomic features (such as chromatin modifications and transcription factor binding) and architectural proteins (including Cohesin, CTCF, and Mediator), a new paradigm in genome biology was established wherein genomes are organized around gene regulatory factors that govern cell identity. As such, chromatin organization plays a central role in establishing and maintaining cell state during development, with gene regulation and genome organization being mutually dependent effectors of cell identity.
    Cover page: A mechanistic link between gene regulation and genome architecture in mammalian development
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2020)
    The transition from the follicular B to the plasma cell stage is associated with large-scale changes in cell morphology. Here, we examine whether plasma cell development is also associated with changes in nuclear architecture. We find that the onset of plasma cell development is concomitant with a decline in remote genomic interactions; a gain in euchromatic character at loci encoding for factors that specify plasma cell fate, including Prdm1 and Atf4; and establishment of de novo inter-chromosomal hubs. We find that, in developing plasma cells and concurrent with transcriptional silencing, the Ebf1 locus repositions from an euchromatic to peri-centromeric heterochromatic environment. Finally, we find that inter-chromosomal hubs are enriched for the deposition of either H3K27Ac or H3K27me3. These data indicate that plasma cell fate is orchestrated by elaborate changes in genome topology and that epigenetic marks, linked with super-enhancers or transcriptionally repressed regions, are enriched at inter-chromosomal hubs.
      Cover page: Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs.
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2013)
      The relationship between 3D organization of the genome and gene-regulatory networks is poorly understood. Here, we examined long-range chromatin interactions genome-wide in mouse embryonic stem cells (ESCs), iPSCs, and fibroblasts and uncovered a pluripotency-specific genome organization that is gradually reestablished during reprogramming. Our data confirm that long-range chromatin interactions are primarily associated with the spatial segregation of open and closed chromatin, defining overall chromosome conformation. Additionally, we identified two further levels of genome organization in ESCs characterized by colocalization of regions with high pluripotency factor occupancy and strong enrichment for Polycomb proteins/H3K27me3, respectively. Underlining the independence of these networks and their functional relevance for genome organization, loss of the Polycomb protein Eed diminishes interactions between Polycomb-regulated regions without altering overarching chromosome conformation. Together, our data highlight a pluripotency-specific genome organization in which pluripotency factors such as Nanog and H3K27me3 occupy distinct nuclear spaces and reveal a role for cell-type-specific gene-regulatory networks in genome organization.
        Cover page: Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2017)
        It is now established that Bcl11b specifies T cell fate. Here, we show that in developing T cells, the Bcl11b enhancer repositioned from the lamina to the nuclear interior. Our search for factors that relocalized the Bcl11b enhancer identified a non-coding RNA named ThymoD (thymocyte differentiation factor). ThymoD-deficient mice displayed a block at the onset of T cell development and developed lymphoid malignancies. We found that ThymoD transcription promoted demethylation at CTCF bound sites and activated cohesin-dependent looping to reposition the Bcl11b enhancer from the lamina to the nuclear interior and to juxtapose the Bcl11b enhancer and promoter into a single-loop domain. These large-scale changes in nuclear architecture were associated with the deposition of activating epigenetic marks across the loop domain, plausibly facilitating phase separation. These data indicate how, during developmental progression and tumor suppression, non-coding transcription orchestrates chromatin folding and compartmentalization to direct with high precision enhancer-promoter communication.
          Cover page: Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate
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