The 3D genome in transcriptional regulation and pluripotency

Abstract

It can be convenient to think of the genome as simply a string of nucleotides, the linear order of which encodes an organism's genetic blueprint. However, the genome does not exist as a linear entity within cells where this blueprint is actually utilized. Inside the nucleus, the genome is organized in three-dimensional (3D) space, and lineage-specific transcriptional programs that direct stem cell fate are implemented in this native 3D context. Here, we review principles of 3D genome organization in mammalian cells. We focus on the emerging relationship between genome organization and lineage-specific transcriptional regulation, which we argue are inextricably linked.

Figure 1. Different levels of genome organization

[From top to bottom] Level 1: Chromosomes occupy distinct sub-regions of the nucleus known as chromosome territories (CTs). Individual chromosomes are indicated by different colors. Level 2: Transcriptionally inactive regions are enriched at the nuclear periphery where they contact the nuclear lamina (red). Actively transcribed genes often co-localize at RNA polymerase II transcription factories (yellow). These and other instances of co-localization between regions with similar transcriptional activity may provide the physical basis for the observations of A and B compartments in C-data. Level 3: Topological domains, or Topologically-Associating Domains (TADs) are regions of frequent local interactions separated by boundaries across which interactions are less frequent. CTCF binding sites and other sequence features (TSS, SINEs; not depicted here) are enriched at TAD boundaries. Note that CTCF also binds within TADs. Cohesin is often present at TAD boundaries, although it is not shown here. Level 4: Transcriptional regulation depends on long-range Interactions between cis-regulatory elements such as enhancers (light red) and promoters (light yellow). These cis-regulatory interactions are facilitated by proteins including Transcription Factors (“TFs”; blue), co-factors such as Mediator (“Med”; red) and Cohesin (purple ring), and RNA Polymerase II (“Pol II”; yellow).

Figure 2. TADs and A/B compartments

A) Diagrammatic representation of two neighboring TADs. B) UCSC genome browser view of the region chr11:115,470,000-116,770,000 which contains two adjacent TADs. [Top] Scale bar and refseq genes. [Middle] C-data from IMR90 fibroblasts. Tracks show pairwise interaction frequencies (red; 40 kb bins), TADs (black bars), and compartments A and B (green). Dashed line marks the boundary between TAD 1 and TAD 2. Note that TAD 2 contains far more genes than TAD 1, and is in the inactive compartment A in IMR90, while TAD 1 is in the inactive compartment A. [Bottom] C-data from human ESCs. Tracks are arranged as above for IMR90. Note that overall TAD structure and location of TAD boundaries do not differ significantly between IMR90 and ESCs. However, TAD1 is in the active compartment A in ESCs. Association of this gene-poor TAD with compartment A in ESCs may be related to the global pervasiveness of open chromatin in pluripotent cells (see section “Genome organization and pluripotency” for further discussion). All C-data taken from Dixon et al. (2012).

Figure 3. Molecular machinery of cis-regulatory interactions

[Top] Enhancer-promoter interactions. TFs (blue) bind to enhancers and promoters. RNA polymerase II (yellow) is recruited to the promoter, and Mediator (red) and Cohesin (purple ring) are recruited to the enhancer. Cohesin stabilizes the interaction, perhaps by forming a ring around interacting loci (although there is little experimental evidence to support this at present). [Bottom] ncRNA-mediated interactions. ncRNA-a (orange) have enhancer-like function: they upregulate genes in cis, dependent on Mediator and coincident with 3D interactions between the ncRNA locus and target gene promoter. Involvement of Cohesin in these interactions has not been demonstrated to date.