1.5 Dynamics of chromatin structure

Proximity ligation experiments, like Hi-C, measure contact frequencies as average over millions of cells in the sample. Therefore, identified contacts might be present only in a subset of cells. Furthermore, specific contacts could be very dynamic over short time-scales in individual cells. While recent methodological advances allow studying of variation across individual cells (discussed in section 6.6.4), initial studies focused on the differences of genome folding across cell cycle and cell differentiation.

1.5.1 Dynamics across the cell cycle

It is important to keep in mind how chromosome folding changes during cell division. Spatial organization is generally studied in non-synchronous cells, of which interphase cells make up the biggest proportion (Bouwman and Laat 2015). In interphase, chromosomes are decondensed and hierarchically organized into territories, compartments, and TADs as described above. To prepare for cell division chromosomes untangle and condense, while transcription ceases almost entirely. Mitotic chromosomes do not show preferential organization, such as compartments or TADs (Naumova et al. 2013). Enhancer-promoter looping might be absent as well (Dekker 2014). After cell division, chromosomes decondense and fold into the interphase hierarchy. While individual genes are relatively mobile during the early G1 phase, they become quickly constrained to a small nuclear sub-volume, after which genome folding is relatively stable for the rest of the interphase (Chubb et al. 2002; Walter et al. 2003). These dynamics during cell-cycle raise the question of how the pattern of 3D organization is re-established with each cell division.

1.5.2 Dynamics across cell types and differntiation

  The primary domain architecture of chromatin is mostly preserved in different cell types and even across species (Dixon et al. 2012; Rao et al. 2014). However, chromatin dynamics specify distinct gene expression programs and biological functions (Bonev and Cavalli 2016). One example of dynamic chromatin organization is dosage compensation, in which the X chromosome is transcriptionally inactivated in human female cells. Whereas typical TAD structures were observed on the active X chromosome, only two huge domains were identified on the inactive X chromosome in Drosophila and human (Deng et al. 2015; Rao et al. 2014). Other examples include differences in terminally differentiated post-mitotic cells. For example, rod photoreceptor cells in nocturnal mammals have an unusual, inverted nuclear architecture, in which heterochromatin is enriched in the center of the nucleus and is absent from the periphery (Solovei et al. 2013; Falk et al. 2018). Further biological processes related to cell cycle exit strongly affect three-dimensional chromatin organization. These are quiescence in yeast, where intrachromosomal contacts increase (Rutledge et al. 2015), and senescence, where heterochromatin relocalizes from the nuclear periphery to the interior (Chandra et al. 2015). However, A/B compartments and TADs seems to be mostly unaffected in these processes (Criscione et al. 2016).

Subtler effects of changes in chromatin reorganization are observed during biological processes such as cell differentiation and signaling (Bonev and Cavalli 2016). During the transition of embryonal stem cells (ESC) from ground-state of pluripotency to a primed state for differentiation, a gradual and reversible establishment of long-range contacts was observed between bivalent gene promoters (Joshi et al. 2015). These changes depended on Polycomb repressive complex 2, underscoring its role in establishing 3D genome organization in early development, as was previously shown for Drosophila (Bantignies et al. 2011). To address the question of how nuclear architecture change during lineage specification, a recent Hi-C study produced Hi-C interaction maps in ESCs and four ESC-derived lineages representing early developmental stages (Dixon et al. 2015). Interestingly, TADs are mostly unchanged during lineage specification, but intra-TAD interactions in some domains were strongly altered, and these changes correlate with active chromatin state (Dixon et al. 2015). Furthermore, often entire TADs relocate from one compartment to another, which was also associated with transcriptional changes of genes in these TADs. Also in B cell differentiation, several regions change compartment identity and relocate from the nuclear periphery to the interior (Lin et al. 2012).

The dynamics of chromatin architecture were also studied in response to stimuli, such as hormone signaling by progestin or estradiol. Despite substantial changes in the transcriptional activity, only small differences were observed in the domain organization of chromatin (Le Dily et al. 2014). However, often the entire TAD responded as a unit by changing histone modifications and switching between A and B compartment. This suggests that transcription status is coordinated within TADs. Overall, TADs seems to be mostly cell-type invariant, whereby local regulatory interactions within TADs and global differences in compartment type change between cell types and correlate with differential gene expression.