The three-dimensional organization of the genome plays important roles in regulating the functional output of the genome and even in the maintenance of epigenetic inheritance and genome stability. Here, we review and compare a number of newly developed methods-especially those that utilize the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated protein 9) system-that enable the direct visualization of specific, endogenous DNA sequences in living cells. We also discuss the practical considerations in implementing the CRISPR imaging technique to achieve sufficient signal-to-background levels, high specificity, and high labeling efficiency. These DNA labeling methods enable tracking of the copy number, localization, and movement of genomic elements, and we discuss the potential applications of these methods in understanding the searching and targeting mechanism of the Cas9-sgRNA complex, investigating chromosome organization, and visualizing genome instability and rearrangement.

Live imaging of genome has offered important insights into the dynamics of the genome organization and gene expression. The demand to image simultaneously multiple genomic loci has prompted a flurry of exciting advances in multicolor CRISPR imaging, although color-based multiplexing is limited by the need for spectrally distinct fluorophores. Here we introduce an approach to achieve highly multiplexed live recording via correlative CRISPR imaging and sequential DNA fluorescence in situ hybridization (FISH). This approach first performs one-color live imaging of multiple genomic loci and then uses sequential rounds of DNA FISH to determine the loci identity. We have optimized the FISH protocol so that each round is complete in 1 min, demonstrating the identification of seven genomic elements and the capability to sustain reversible staining and washing for up to 20 rounds. We have also developed a correlation-based algorithm to faithfully register live and FISH images. Our approach keeps the rest of the color palette open to image other cellular phenomena of interest, as demonstrated by our simultaneous live imaging of genomic loci together with a cell cycle reporter. Furthermore, the algorithm to register faithfully between live and fixed imaging is directly transferrable to other systems such as multiplex RNA imaging with RNA-FISH and multiplex protein imaging with antibody-staining.

Strong and tough epoxy composites are developed using a less-studied fibre reinforcement, that of natural silk. Two common but structurally distinct silks from the domestic B. mori/Bm and the wild A. pernyi/Ap silkworms are selected in fabric forms. We show that the toughening effects on silk-epoxy composites or SFRPs are dependent on the silk species and the volume fraction of silk. Both silks enhance the room-temperature tensile and flexural mechanical properties of the composite, whereas the more resilient Ap silk shows a more pronounced toughening effect and a lower critical reinforcement volume for the brittle-ductile transition. Specifically, our 60 vol.% Ap-SFRP displays a three-fold elevation in tensile and flexural strength, as compared to pure epoxy resin, with an order of magnitude higher breaking energy via a distinct, ductile failure mode. Importantly, the 60 vol.% Ap-SFRP remains ductile with 7% flexural elongation at lower temperatures (-50 °C). Under impact, these SFRPs show significantly improved energy absorption, and the 60 vol.% Ap-SFRP has an impact strength some eight times that of pure epoxy resin. The findings demonstrate both marked toughening and strengthening effects for epoxy composites from natural silk reinforcements, which presents opportunities for mechanically superior and "green" structural composites.

High-performance, fast-growing natural materials with sustainable and functional features currently arouse significant attention. Here, facile processing, involving delignification, in situ hydrothermal synthesis of TiO₂ and pressure densification, is employed to transform natural bamboo into a high-performance structural material. The resulting TiO₂-decorated densified bamboo exhibits high flexural strength and elastic stiffness, with both properties more than double that of natural bamboo. Real-time acoustic emission reveals the key role of the TiO₂ nanoparticles in enhancing the flexural properties. The introduction of nanoscale TiO₂ is found to markedly increase the degree of oxidation and the formation of hydrogen bonds in bamboo materials, leading to extensive interfacial failure between the microfibers, a micro-fibrillation process that results in substantial energy consumption and high fracture resistance. This work furthers the strategy of the synthetic reinforcement of fast-growing natural materials, which could lead to the expanded applications of sustainable materials for high-performance structural applications.

High stiffness and strength carbon fibres are commonly used to reinforce epoxy-resin composites. While wild Antheraea pernyi silk fibres exhibit high toughness originating from their α-helix/random coil conformation structures and their micro-fibre morphology, their insufficient strength and stiffness hinders them from being used in similar structural composites. In this work, we use interply hybridization of silk and carbon fibres to reinforce epoxy-matrix composites. With increased carbon fibre content, the quasi-static tensile/flexural stiffness and strength increases following the rule of mixtures while more silk fibre acts to increase ductility and impact strength. This results in a composite comprising equal volumes of carbon and silk fibres achieving an impact strength of 98 kJ m^-2, which is twice that of purely carbon-fibre reinforced composites (44 kJ m^-2). This work shows tough natural silk fibres and strong synthetic fibres can be successfully integrated into epoxy-resin composites for tailored mechanical properties.

Enhanced telomere maintenance is evident in malignant cancers. While telomeres are thought to be inherently heterochromatic, detailed mechanisms of how epigenetic modifications impact telomere protection and structures are largely unknown in human cancers. Here we develop a molecular tethering approach to experimentally enrich heterochromatin protein HP1α specifically at telomeres. This results in increased deposition of H3K9me3 at cancer cell telomeres. Telomere extension by telomerase is attenuated, and damage-induced foci at telomeres are reduced, indicating augmentation of telomere stability. Super-resolution STORM imaging shows an unexpected increase in irregularity of telomeric structure. Telomere-tethered chromo shadow domain (CSD) mutant I165A of HP1α abrogates both the inhibition of telomere extension and the irregularity of telomeric structure, suggesting the involvement of at least one HP1α-ligand in mediating these effects. This work presents an approach to specifically manipulate the epigenetic status locally at telomeres to uncover insights into molecular mechanisms underlying telomere structural dynamics.

Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.

Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or "junk DNA." The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ESC self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA, and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1, and peri-nucleolar chromatin in the regulation of transcription, developmental potency, and ESC self-renewal.