Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability1, and silencing of transposon and gene expression2. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA3. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments4. We show that Drosophila HP1a protein undergoes liquid–liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

Monomeric near-infrared (NIR) fluorescent proteins (FPs) are in high demand as protein tags and components of biosensors for deep-tissue imaging and multicolour microscopy. We report three bright and spectrally distinct monomeric NIR FPs, termed miRFPs, engineered from bacterial phytochrome, which can be used as easily as GFP-like FPs. miRFPs are 2–5-fold brighter in mammalian cells than other monomeric NIR FPs and perform well in protein fusions, allowing multicolour structured illumination microscopy. miRFPs enable development of several types of NIR biosensors, such as for protein–protein interactions, RNA detection, signalling cascades and cell fate. We demonstrate this by engineering the monomeric fluorescence complementation reporters, the IκBα reporter for NF-κB pathway and the cell cycle biosensor for detection of proliferation status of cells in culture and in animals. miRFPs allow non-invasive visualization and detection of biological processes at different scales, from super-resolution microscopy to in vivo imaging, using the same probes.

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multiple cell types, with gene-rich euchromatin more centrally disposed of than gene-poor heterochromatin. Such territories are not randomly positioned and both gene-density-based and size-based radial positioning schemes have been proposed to describe the data. We propose that any realistic model of these and other large-scale features of nuclear architecture must account for ATP-fueled non-equilibrium activity, associated with transcriptional processes that are inhomogeneous within and across chromosomes. We describe a biophysical model for human cell nuclei which incorporates such activity. The model predicts the statistics of the shapes, positioning, and contact maps of individual chromosomes, with the differential positioning of the inactive and active X chromosomes in female (XX), cells emerging as a natural consequence, and our results compare favorably to a broad spectrum of experimental data. We argue that the consequences, in mechanical terms, of the distribution of transcriptional activity across chromosomes should be the primary determinant of a chromosome positioning code. Constitutive heterochromatin is made of repetitive sequences and is epigenetically identified by methylation of H3K9 and binding of Heterochromatin Protein 1a (HP1a). In cells, repetitive sequences from multiple chromosomes are organized into spherical domains important for maintaining transcriptional silencing and preventing aberrant recombination. Canonically, these functions of heterochromatin are attributed to tight compaction of nucleosomes and consequent exclusion of large protein complexes like polymerases and recombinases. However, proteins within the domain are mobile, and size is not the only factor that defines whether a protein can enter heterochromatin. We investigated whether the heterochromatin domain is similar to other membraneless cellular compartments like nucleoli in that it is formed via phase separation. We purified recombinant Drosophila HP1a and found that in vitro, this protein is able to demix from aqueous solution to form droplets that fuse and flow like a liquid. In vivo, we observe similar droplet formation and fusion during the initial establishment of heterochromatin in the early Drosophila embryo. We used Fluorescence Correlation Spectroscopyderived imaging methods to observe bulk movement of HP1a at the heteroeuchromatin interface, and found that proteins exhibit specific dynamic properties associated with phase interfaces, indicating they are held in the heterochromatin domain by surface tension. Additionally, an inert probe (three tandem YFPs) is excluded from the domain in a similar manner, indicating that physicochemical properties of the heterochromatin domain define access to these sequences. The phase separation model we propose here is consistent with historical data about heterochromatin domains, including the tendency for distal regions of heterochromatin to loop back and contact the main domain. We believe this work represents a shift in perspective of how we should view the nucleus; as a...

The organization of chromatin affects all aspects of nuclear DNA metabolism in eukaryotes. H3.3 is an evolutionarily conserved histone variant and a key substrate for replication-independent chromatin assembly. Elimination of chromatin remodeling factor CHD1 in Drosophila embryos abolishes incorporation of H3.3 into the male pronucleus, renders the paternal genome unable to participate in zygotic mitoses, and leads to the development of haploid embryos. Furthermore, CHD1, but not ISWI, interacts with HIRA in cytoplasmic extracts. Our findings establish CHD1 as a major factor in replacement histone metabolism in the nucleus and reveal a critical role for CHD1 in the earliest developmental instances of genome-scale, replication-independent nucleosome assembly. Furthermore, our results point to the general requirement of adenosine triphosphate (ATP)-utilizing motor proteins for histone deposition in vivo.H istone-DNA interactions constantly change during various processes of DNA metabolism. Recent studies have highlighted the importance of histone variants, such as H3.3, CENP-A (centromere protein A), or H2A.Z, in chromatin dynamics (1, 2). Incorporation of replacement histones into chromatin occurs throughout the cell cycle, whereas nucleosomes containing canonical histones are assembled exclusively during DNA replication. A thorough understanding of the replication-independent mechanisms of chromatin assembly, however, is lacking.In vitro, chromatin assembly requires the action of histone chaperones and adenosine triphosphate (ATP)-utilizing factors (3). Histone chaperones may specialize for certain histone variants. For example, H3.3 associates with a complex containing HIRA, whereas canonical H3 is in a complex with CAF-1 (chromatin assembly factor 1) (4). The molecular motors known to assemble nucleosomes are ACF (ATP-utilizing chromatin assembly and remodeling factor), CHRAC (chromatin accessibility complex), and RSF (nucleosome-remodeling and spacing factor), which contain the Snf2 family member ISWI as the catalytic subunit (5-7), and CHD1, which belongs to the CHD subfamily of Snf2-like adenosine triphosphatases (ATPases) (8). These factors have not been shown to mediate deposition of histones in vivo. We previously demonstrated that CHD1, together with the chaperone NAP-1, assembles nucleosome arrays from DNA and histones in vitro (9). Here, we investigated the role of CHD1 in chromatin assembly in vivo in Drosophila.We generated Chd1 alleles by P elementmediated mutagenesis (Fig. 1A) (10). Two exci- 2] with Df(2L)Exel7014 affect both copies of the Chd1 gene only (Fig. 1B). We also identified a single point mutation that results in premature translation termination of Chd1 (Q1394*) in a previously described lethal allele, l(2)23Cd[A7-4] (11). Hence, l(2)23Cd[A7-4] was renamed Chd1 [3].sions, Df(2L)Chd1[1] and Df(2L)Chd1[2], deleted fragments of the Chd1 gene and fragments of unrelated adjacent genes. Heterozygous combinations, however, of Chd1[1] or Chd1[Analysis of Western blots of embryos from heterozyg...