The application of an external pressure on Metal Halide Perovskite (MHPs) has become a fascinating way of tuning their optical properties, achieving also novel features. Here, the pressure response of 2D MHPs including a long alkyl chain made of ten carbon atoms, namely decylammonium (DA), has been investigated as a function of the central atom in DA2PbI4 and DA2GeI4. The two systems share a common trend in the phase stability, displaying a transition from an orthorhombic to a monoclinic phase around 2 GPa, followed by a phase separation in two monoclinic phases characterized by different c-axis. The optical properties show rather different behavior due to the presence of Pb or Ge. DA2PbI4 shows a progressive red shift of the band gap from 2.28 eV at ambient conditions, to 1.64 eV at 11.5 GPa, with a narrow PL emission composed by two components, with the second one appearing in concomitance with the phase separation and significantly shifted to lower energy. On the other hand, DA2GeI4, changes from a non-PL system at ambient pressure, to a clear broadband emitter centered around 730 nm (FWHM ~ 170 nm), with a large stoke shift, and an intensity maximum at about 3.7 GPa. This work sheds light on the structural stability of 2D perovskites characterized by extended alkyl chains, to date limited to four carbon atoms, and shows the pressure-induced emergence of broad emission in a novel lead-free perovskite, DA2GeI4. The evidence of wide emission by a moderate pressure in a germanium-based 2D MHP represents a novel result which may open the design, by chemical pressure, of efficient wide or even white lead-free emitters.

The computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods used to infer sub-compartments from Hi-C data fail to address the cell population heterogeneity. Here we describe a model-based method, called CscoreTool-M, which uses probabilistic modeling to build multiple 3D genome sub-compartments from Hi-C data. The compartment scores inferred using CscoreTool-M directly represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring local sub-compartment containing heterochromatin marked by Histone lysine trimethylation (H3K27me3) surrounded by the actively transcribed euchromatic regions. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations for different genomic regions. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can further identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions.

In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence and live-cell imaging revealed that lamin C but not the other lamin isoforms rapidly accumulated at sites of NE rupture induced by laser microirradiation in mouse embryonic fibroblasts. The immunoglobulinlike fold domain and the NLS were required for the recruitment from the nucleoplasm to the rupture sites with the Barrier-to-autointegration factor (BAF). The accumulation of nuclear BAF and cytoplasmic cyclic GMP-AMP (cGAMP) synthase (cGAS) at the rupture sites was in part dependent on lamin A/C. These results suggest that nucleoplasmic lamin C, BAF and cGAS concertedly accumulate at sites of NE rupture for repair.

A large fraction of heterochromatin in the metazoan genome is associated with the nuclear lamina (NL) in interphase nuclei. This heterochromatin is often referred to as Lamina-Associated Domains (LADs) and are often mapped from cell populations asynchronously progressing through the cell cycle. We and others have recently reported that LADs are largely stable during G1, S, or G2 phases of the cell cycle, and appear similar to LADs mapped from bulk cell populations. LADs in senescent cells, however, are reported to be quite different from proliferating cells, and it remains unclear how senescent cell LADs are established. As cells finish mitosis and re-enter G1, reassembly of the nuclear envelope and NL appears to precede mitotic chromosome decondensation. Therefore, the initial NL interactions with the decondensing chromatin may be quite different from those reported in asynchronous or FACS isolated G1, S, or G2 populations. By developing a modified version of the Tyramide-Signal Amplification sequencing (TSA-seq), which we call chromatin pull down-based Tyramide Signal Amplification-sequencing (cTSA-seq), we uncover a dynamic NL-chromatin interaction as cells progress through G1. The appearance of stable LADs coincides with sufficient chromatin decondensation and active gene expression in G1. Interestingly, early G1 NL-chromatin interactions, which are found toward the telomeric ends of human chromosomes, are similar to those found in oncogene-induced senescent cells. We find that the assembly of LADs during the formation of the G1 nucleus is gradual and that the arrest of NL-chromatin interactions in early G1 may contribute to genome disorganization of senescence cells.

The nuclear lamina (NL) is a proteinaceous network found beneath the inner nuclear membrane. The NL is linked to a number of dynamic cellular activities including chromatin organization, transcription and RNA/protein trafficking through nuclear pores. Our understanding of the NL has been hindered in part by the general insolubility and low extractability of proteins from this region. This has spurred the development of proximity ligation methods that label proteins and/or DNA near the NL for systematic identification (Bar et al., 2018; Chen et al., 2018b; Guelen et al., 2008; Roux et al., 2012). To simplify labeling and improve temporal resolution, we fused APEX2 (Hung et al., 2014; Lam et al., 2015) to the nuclear lamina protein lamin-B1 to map proteins, RNA and DNA associated with the NL. We show that APEX2 labeling of the NL is robust and requires as little as 20 seconds. In addition to identifying the NL proteome, this method revealed NL-proximal RNA species that were largely spliced. These NL-proximal RNAs show a bias toward long 3 UTRs, suggesting an RNA-regulatory role of the NL. This is further supported by the finding of a bias toward longer 3 UTRs in genes deregulated in lamin-null cells. Interestingly, these RNAs share a sequence motif in their 3 UTRs. Finally, we demonstrate that the APEX2 method can reliably map lamina-associated domains (LADs) at different stages of the cell cycle, revealing a variability of short LADs regions enriched for histone lysine 27 trimethylation (H3K27me3). Thus the APEX2 method report here is a useful addition to the molecular toolbox for the study of the NL and permits the identification of proteome, transcriptome, and genome elements associated with this nuclear substructure.

Many hard and soft corals harbor algae for photosynthesis. The algae live inside coral cells in a specialized membrane compartment called symbiosome, which shares the photosynthetically fixed carbon with coral host cells, while host cells provide inorganic carbon for photosynthesis1. This endosymbiotic relationship is critical for corals, but increased environmental stresses are causing corals to expel their endosymbiotic algae, i.e. coral bleaching, leading to coral death and degradation of marine ecosystem2. To date, the molecular pathways that orchestrate algal recognition, uptake, and maintenance in coral cells remain poorly understood. We report chromosome-level genome assembly of a fast-growing soft coral, Xenia species (sp.)3, and its use as a model to decipher the coral-algae endosymbiosis. Single cell RNA-sequencing (scRNA-seq) identified 13 cell types, including gastrodermis and cnidocytes, in Xenia sp. Importantly, we identified the endosymbiotic cell type that expresses a unique set of genes implicated in the recognition, phagocytosis/endocytosis, maintenance of algae, and host coral cell immune modulation. By applying scRNA-seq to investigate algal uptake in our new Xenia sp.. regeneration model, we uncovered a dynamic lineage progression from endosymbiotic progenitor state to mature endosymbiotic and post-endosymbiotic cell states. The evolutionarily conserved genes associated with the endosymbiotic process reported herein open the door to decipher common principles by which different corals uptake and expel their endosymbionts. Our study demonstrates the potential of single cell analyses to examine the similarities and differences of the endosymbiotic lifestyle among different coral species.

Many corals form a mutually beneficial relationship with the dinoflagellate algae called Symbiodiniaceae. Cells in the coral gastrodermis recognize, phagocytose, and house the algae in an organelle called symbiosome, which supports algae photosynthesis and nutrient exchange with corals1-3. Rising ocean temperature disrupts this endosymbiotic relationship, leading to alga loss, coral bleaching and death, and the degradation of marine ecosystems4-6. Mitigation of coral death requires a mechanistic understanding of coral-algal endosymbiosis. We have developed genomic resources to enable the use of a soft coral Xenia species as a model to study coral-algal endosymbiosis7. Here we report an effective RNA interference (RNAi) method and its application in the functional studies of genes involved in early steps of endosymbiosis. We show that an endosymbiotic cell marker called LePin (for its Lectin and kazal Protease inhibitor domains) is a secreted lectin that binds to algae to initiate the formation of alga-containing endosymbiotic cells. The evolutionary conservation of LePin among marine endosymbiotic anthozoans suggests a general role in coral-algal recognition. Coupling bioinformatics analyses with RNAi and single cell (sc)-RNA-seq, we uncover three gene expression programs (GEP) influenced by LePin during the early and middle stages of endosymbiotic lineage development. Further studies of genes in these GEPs lead to the identification of two scavenger receptors that support the formation of alga-containing endosymbiotic cells, most likely by initiating phagocytosis and modulating coral immune response. We also identify two actin regulators for endosymbiosis, which shed light on the phagocytic machinery and a possible mechanism for symbiosome formation. Our findings should usher in an era of mechanistic studies of coral-algal endosymbiosis.

Hepatic cysts are fluid-filled lesions in the liver that are estimated to occur in 5% of the population. They may cause hepatomegaly and abdominal pain. Progression to secondary fibrosis, cirrhosis, or cholangiocarcinoma can lead to morbidity and mortality. Previous studies of patients and rodent models have associated hepatic cyst formation with increased proliferation and fluid secretion in cholangiocytes, which are partially due to impaired primary cilia. Congenital hepatic cysts are thought to originate from faulty bile duct development, but the underlying mechanisms are not fully understood. In a forward genetic screen, we identified a zebrafish mutant that develops hepatic cysts during larval stages. Cyst formation in these mutants is not due to changes in biliary cell proliferation, bile secretion, or impairment of primary cilia. Instead, time-lapse live imaging data showed that the mutant biliary cells failed to form interconnecting bile ducts because of defects in motility and protrusive activity. Accordingly, immunostaining revealed an excessive and disorganized actin and microtubule cytoskeleton in the mutant biliary cells. By whole-genome sequencing, we determined that the cystic phenotype in the mutant was caused by a missense mutation in the furinb gene which encodes a proprotein convertase. The mutation alters Furinb localization and causes endoplasmic reticulum (ER) stress. The cystic phenotype could be suppressed by treatment with the ER stress inhibitor 4-phenylbutyric acid and exacerbated by treatment with the ER stress inducer tunicamycin. The mutant livers also exhibited increased mTOR signaling and treatment with the mTOR inhibitor rapamycin partially blocked cyst formation by reducing ER stress. Our study has established a novel vertebrate model for studying hepatic cystogenesis and illustrated the role of ER stress in the disease pathogenesis.

Cytoplasmic lipid droplets are highly dynamic storage organelles; their rapid synthesis, expansion, and degradation, as well as their varied interactions with other organelles allow cells to maintain lipid homeostasis. While the molecular details of lipid droplet dynamics are currently a very active area of investigation, this work has been primarily performed in cultured cells and in vitro systems. By taking advantage of the powerful transgenic and in vivo imaging opportunities afforded by the zebrafish model system, we have built a suite of tools to allow lipid droplets to be studied in real-time from the subcellular to the whole organism level. Fluorescently-tagging the lipid droplet associated proteins, perilipin 2 and perilipin 3, in the endogenous loci, permits visualization of lipid droplets in the intestine, liver, lateral line and adipose tissue. Using these transgenic lines we have found that perilipin 3 is rapidly loaded on intestinal lipid droplets following a high fat meal and then largely replaced by perilipin 2 a few hours later. These powerful new tools will facilitate studies on the role of lipid droplets in different tissues and under different genetic and physiological manipulations.

As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, allow frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of genomic compensation by means of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of genomic adaptations that can occur may inform the strategies of mutant generation.Author summaryThe recent rise of reverse genetic, gene targeting methods has allowed researchers to readily generate mutations in any gene of interest with relative ease. Should these mutations have the predicted effect on the mRNA and encoded protein, we would expect many more abnormal phenotypes than are typically being seen in reverse genetic screens. Here we set out to explore some of the reasons for this discrepancy by studying seven separate mutations in zebrafish. We present evidence that thorough cDNA sequence analysis is a key step in assessing the likelihood that a given mutation will produce hypomorphic or null alleles. This study reveals that alternative mRNA processing in the mutant background often produces transcripts that escape nonsense-mediated decay, thereby potentially preserving gene function. By understanding the ways that cells avoid the deleterious consequences of mutations, researchers can better design reverse genetic strategies to increase the likelihood of gene disruption.