Higher-order chromatin organization such as A/B compartments, TADs, and chromatin loops are temporarily disrupted during mitosis 1,2. Since these structures are thought to influence gene regulation, it is important to understand how they are re-established after mitosis. We examined the dynamics of chromosome reorganization by Hi-C after mitosis in highly purified, synchronous cell populations. We observed rapid establishment, gradual intensification, and expansion of A/B compartments. Contact domains form from the "bottom-up" with smaller subTADs forming initially, followed by convergence into multi-domain TAD structures. CTCF is partially retained on mitotic chromosomes and immediately resumes full binding at ana/telophase. In contrast, cohesin is completely evicted from mitotic chromosomes and regains focal binding with delayed Reprints and permissions information is available at www.nature.com/reprints.Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://

More than 25 inherited human disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas thousands of repeat tracts across the human genome are relatively stable. Here, we discover that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains. We identify a subset of boundaries with markedly higher CpG island density compared to the rest of the genome. daSTRs specifically localize to ultra-high-density CpG island boundaries, suggesting they might be hotspots for epigenetic misregulation or topological disruption linked to STR expansion. Fragile X syndrome patients exhibit severe boundary disruption in a manner that correlates with local loss of CTCF occupancy and the degree of FMR1 silencing. Our data uncover higher-order chromatin architecture as a new dimension in understanding repeat expansion disorders.

Summary BET (bromodomain and extraterminal motif) proteins are pharmacologic targets for the treatment of diverse diseases, yet the roles of individual BET family members remain unclear. We find that BRD2 but not BRD4 colocalizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites, whereas BRD2 is dispensable for CTCF occupancy. Disruption of a CTCF/BRD2-occupied element positioned between two unrelated genes enables regulatory influence to spread from one gene to another, suggesting that CTCF and BRD2 form a transcriptional boundary. Accordingly, single molecule mRNA FISH reveals that upon site-specific CTCF disruption or BRD2 depletion, expression of the two genes becomes increasingly correlated. HiC shows that BRD2 depletion weakens boundaries co-occupied by CTCF and BRD2, but not those that lack BRD2. These findings indicate that BRD2 supports boundary activity and raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function.

Summary Pluripotent genomes are folded in a topological hierarchy that reorganizes during differentiation. The extent to which chromatin architecture is reconfigured during somatic cell reprogramming is poorly understood. Here we integrate fine-resolution architecture maps with epigenetic marks and gene expression in embryonic stem (ES) cells, neural progenitor cells (NPCs) and NPC-derived induced pluripotent stem (iPS) cells. We find that most pluripotency genes reconnect to target enhancers during reprogramming. Unexpectedly, some NPC interactions around pluripotency genes persist in our iPS clone. Pluripotency genes engaged in both ‘fully-reprogrammed-ES’ and ‘persistent-NPC’ interactions exhibit over/undershooting of target expression levels in iPS. Additionally, we identify a subset of ‘poorly-reprogrammed’ interactions that do not reconnect in iPS and display only partially recovered, ES-specific CTCF occupancy. 2i/LIF can abrogate ‘persistent-NPC’ interactions, recover ‘poorly-reprogrammed’ interactions, re-instate CTCF occupancy and restore expression levels. Our results demonstrate that iPS genomes can exhibit imperfectly rewired 3D-folding linked to inaccurately reprogrammed gene expression.

Mammalian genomes are folded into tens of thousands of long-range looping interactions. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which loops are dynamic on short time scales remains an unanswered question. Here we engineer a new class of synthetic architectural proteins for directed rearrangement of the 3-D genome using blue light. We target our light-activated-dynamic-looping (LADL) system to two genomic anchors with CRISPR guide RNAs and induce their spatial co-localization via light-induced heterodimerization of cryptochrome 2 and a dCas9-CIBN fusion protein. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Using single molecule RNA FISH, we demonstrate that de novo formation of the Zfp462-SE loop correlates with a modest but significant increase in Zfp462 expression. LADL facilitates co-localization of genomic loci without exogenous chemical cofactors and will enable future efforts to engineer reversible and oscillatory loops on short time scales.