Formation Of Heterochromatin Domains Research Articles

New Aspects of Magnesium Function: A Key Regulator in Nucleosome Self-Assembly, Chromatin Folding and Phase Separation.

Metal cations are associated with many biological processes. The effects of these cations on nucleic acids and chromatin were extensively studied in the early stages of nucleic acid and chromatin research. The results revealed that some monovalent and divalent metal cations, including Mg2+, profoundly affect the conformations and stabilities of nucleic acids, the folding of chromatin fibers, and the extent of chromosome condensation. Apart from these effects, there have only been a few reports on the functions of these cations. In 2007 and 2013, however, Mg2+-implicated novel phenomena were found: Mg2+ facilitates or enables both self-assembly of identical double-stranded (ds) DNA molecules and self-assembly of identical nucleosomes in vitro. These phenomena may be deeply implicated in the heterochromatin domain formation and chromatin-based phase separation. Furthermore, a recent study showed that elevation of the intranuclear Mg2+ concentration causes unusual differentiation of mouse ES (embryonic stem) cells. All of these phenomena seem to be closely related to one another. Mg2+ seems to be a key regulator of chromatin dynamics and chromatin-based biological processes.

Phase Separation Drives Heterochromatin Domain Formation

HP1a can nucleate into foci that display liquid properties during the early stages of heterochromatin domain formation in Drosophila embryos, suggesting that the repressive action of heterochromatin may be mediated in part by emergent properties of phase separation. The gene-silencing action of heterochromatin is thought to arise from the spread of proteins such as HP1 that compact the underlying chromatin and recruit repressors. Two papers in this issue demonstrate that HP1α has the ability to form phase-separated droplets. Gary Karpen and colleagues show that HP1α can nucleate into foci that display liquid properties during the early stages of heterochromatin domain formation in Drosophila embryos. Geeta Narlikar and colleagues demonstrate that human HP1α protein also forms phase-separated droplets. Phosphorylation or DNA binding promotes the physical partitioning of HP1α out of the soluble aqueous phase into droplets. These related findings suggest that the repressive action of heterochromatin may be in part mediated by the phase separation of HP1, with the droplets being initiated or dissolved by various ligands depending on nuclear context. 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.

Phase separation drives heterochromatin domain formation.

Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. 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 DNA. 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 compartments. 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.

144 EPIGENETIC ASYMMETRY IN HISTONE H3 LYSINE 9 DIMETHYLATION STATUS IN PRONUCLEAR STAGE PORCINE EMBRYOS

Covalent modification of specific residues on the tail regions of core histone proteins has been shown to play a key role in regulation of the genome. Methylation of lysine 9 on histone H3 (H3K9) is associated with repression of transcription and formation of heterochromatin domains. The maternal- and paternal-derived pronuclei from pronuclear stage murine embryos have an asymmetric distribution of H3K9 dimethylation between the 2 pronuclei; maternal pronuclei have the H3K9 dimethylation, whereas the paternal pronuclei lack this modification. The aim of this study was to characterize the H3K9 dimethylation pattern in cleavage stage porcine embryos. Indirect immunocytochemical staining was performed using a commercially available antibody from Upstate (Charlottesville, VA) that recognizes the dimethylated form of lysine 9 on histone H3 and fluorescein isothiocyanate (FITC)-conjugated secondary antibody on germinal vesicle (GV) stage porcine oocytes and cleavage stage porcine embryos. Germinal vesicle stage oocytes were matured in vitro for 44 h in a chemically defined maturation medium (TCM 199 supplemented with 0.1% PVA, 0.069 mg/mL cysteine, 10 ng/mL EGF 0.5 IU/mL LH, and 0.5 IU/mL FSH) at 39�C in 5% CO2. Following in vitro fertilization, presumptive zygotes were cultured in NCSU23 medium containing 4 mg/mL BSA at 39�C in 5% CO2, 5% O2. Embryos were fixed in 3.7% paraformaldehide for 2 h and washed in PBS and 0.1% Tween20. H3K9 dimethylation is present in the nuclei of GV-stage oocytes (n = 24) and pronuclear (n = 13), 2-cell (n = 4), 4-cell (n = 9), blastocyst (n = 8) stage embryos. The analysis revealed 2 interesting findings. First, examination of thin optical sections through the nuclei of processed embryos on a confocal microscope revealed that in GV-stage oocytes and pronuclear, 2-cell and 4-cell stage embryos the dimethylated form of H3K9 was distributed throughout the nuclei at these developmental time points, whereas in blastocyst stage embryos, the dimethylated H3K9 was restricted to the nuclear periphery. Second, not all pronuclei within pronuclear stage embryos were positive for the dimethylated form of H3K9. To determine if differential H3K9 methylation pattern observed among pronuclei in 1-cell stage embryos was due to parental origin, we produced parthenogenic porcine embryos by electrically activating porcine oocytes in calcium containing activation medium and processed them as indicated above for fertilized oocytes (n = 13). All pronuclei found in pronuclear stage parthenogenic porcine embryos were positive for dimethylation of H3K9. Chi square analysis revealed this pattern to be different from that observed in pronuclear embryos produced by fertilization (P < 0.05). In summary we conclude that the pronuclei in 1-celled embryos produced by in vitro fertilization are differentially dimethylated at H3K9 and that the localization of dimethylated H3K9 changes during cleavage development.