Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape

Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acquisition are balanced in this process is not well understood. Here we use single cell Hi-C to map chromosomal conformations in post-gastrulation mouse embryo cells and study their distributions and correlations with matching embryonic transcriptional atlases. We find that embryonic chromosomes show a remarkably strong cell cycle signature. Despite that, replication timing, chromosome compartment structure, topological associated domains (TADs) and promoter-enhancer contacts are shown to be variable between distinct epigenetic states. About 10% of the nuclei are identified as primitive erythrocytes, showing exceptionally compact and organized compartment structure. The remaining cells are broadly associated with ectoderm and mesoderm identities, showing only mild differentiation of TADs and compartment structures, but more specific localized contacts in hundreds of ectoderm and mesoderm promoter-enhancer pairs. The data suggest that while fully committed embryonic lineages can rapidly acquire specific chromosomal conformations, most embryonic cells are showing plastic signatures driven by complex and intermixed enhancer landscapes.

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus

Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.

The intrinsic and extrinsic effects of TET proteins during gastrulation

Mice deficient for all ten-eleven translocation (TET) genes exhibit early gastrulation lethality. However, separating cause and effect in such embryonic failure is challenging. To isolate cell-autonomous effects of TET loss, we used temporal single-cell atlases from embryos with partial or complete mutant contributions. Strikingly, when developing within a wild-type embryo, Tet-mutant cells retain near-complete differentiation potential, whereas embryos solely comprising mutant cells are defective in epiblast to ectoderm transition with degenerated mesoderm potential. We map de-repressions of early epiblast factors (e.g., Dppa4 and Gdf3) and failure to activate multiple signaling from nascent mesoderm (Lefty, FGF, and Notch) as likely cell-intrinsic drivers of TET loss phenotypes. We further suggest loss of enhancer demethylation as the underlying mechanism. Collectively, our work demonstrates an unbiased approach for defining intrinsic and extrinsic embryonic gene function based on temporal differentiation atlases and disentangles the intracellular effects of the demethylation machinery from its broader tissue-level ramifications.

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Chimeras with full or partial Tet deficiency are mapped over the course of gastrulation

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Tet-TKO cells disrupt signaling, leading to skewed whole-embryo mutant gastrulation

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Tet-TKO cells retain near-complete differentiation potential in a chimera context

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Loss of TET leads to pervasive hypermethylation and mildly perturbed gene expression

Dissection of floral transition by single-meristem transcriptomes at high temporal resolution

The vegetative-to-floral transition is a dramatic developmental change of the shoot apical meristem, promoted by the systemic florigen signal. However, poor molecular temporal resolution of this dynamic process has precluded characterization of how meristems respond to florigen induction. Here, we develop a technology that allows sensitive transcriptional profiling of individual shoot apical meristems. Computational ordering of hundreds of tomato samples reconstructed the floral transition process at fine temporal resolution and uncovered novel short-lived gene expression programs that are activated before flowering. These programs are annulled only when both florigen and a parallel signalling pathway are eliminated. Functional screening identified genes acting at the onset of pre-flowering programs that are involved in the regulation of meristem morphogenetic changes but dispensable for the timing of floral transition. Induced expression of these short-lived transition-state genes allowed us to determine their genetic hierarchies and to bypass the need for the main flowering pathways. Our findings illuminate how systemic and autonomous pathways are integrated to control a critical developmental switch.

Early metazoan cell type diversity and the evolution of multicellular gene regulation

A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programs remain largely uncharacterized. Here, we use whole-organism single-cell RNA-seq to map cell type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programs of these cell types reveal variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell type-specific programs. In contrast, the generation of a higher diversity of cell types in ctenophores is associated to lower specificity of promoter sequences and to the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of TFs and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.

Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C

The development of niches for tissue-specific stem cells is an important aspect of stem cell biology. Determination of niche size and niche numbers during organogenesis involves precise control of gene expression. How this is achieved in the context of a complex chromatin landscape is largely unknown. Here we show that the nuclear protein Combgap (Cg) supports correct ovarian niche formation in Drosophila by controlling ecdysone-Receptor (EcR)- mediated transcription and long-range chromatin contacts in the broad locus (BR-C). Both cg and BR-C promote ovarian growth and the development of niches for germ line stem cells. BR-C levels were lower when Combgap was either reduced or over-expressed, indicating an intricate regulation of the BR-C locus by Combgap. Polytene chromosome stains showed that Cg co-localizes with EcR, the major regulator of BR-C, at the BR-C locus and that EcR binding to chromatin was sensitive to changes in Cg levels. Proximity ligation assay indicated that the two proteins could reside in the same complex. Finally, chromatin conformation analysis revealed that EcR-bound regions within BR-C, which span ~30 KBs, contacted each other. Significantly, these contacts were stabilized in an ecdysone- and Combgap-dependent manner. Together, these results highlight Combgap as a novel regulator of chromatin structure that promotes transcription of ecdysone target genes and ovarian niche formation.

Germ line stem cells (GSCs) supply either eggs or sperm throughout the life- time of many organisms, including mammals. For their function, GSCs require input from somatic niche cells. Understanding how niches form during development is an important initial step in understanding how stem cell units form, and by extension, how they may regenerate. In this work we describe a new function for the chromatin binding protein Combgap in ovarian niche formation of the model organism Drosophila melanogaster. Combgap is required for the correct expression of another factor, BR-C, in somatic ovarian cells. BR-C is one of the central target genes of the steroid hormone ecdysone, and its expression is controlled by the ecdysone receptor (EcR). Interestingly, EcR-enriched regions within the BR-C locus are engaged in long-range contacts that are stabilized by ecdysone in a Combgap-depended manner. We also found that EcR binding to chromatin depends on WT levels of Combgap. BR-C regulates GSC unit establishment, intestinal stem cells, immune responses, and many other processes. Understanding Combgaps’ function in shaping the BR-C chromatin landscape is a first step towards better appreciation of how this important locus is controlled, and the general machinery coupling gene expression to 3D chromatin structure.

Derivation of novel human ground state naive pluripotent stem cells

Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3β signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, and global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters. Upon withdrawal of 2i/LIF, naive mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. Although human ES cells share several molecular features with naive mouse ES cells, they also share a variety of epigenetic properties with primed murine epiblast stem cells (EpiSCs). These include predominant use of the proximal enhancer element to maintain OCT4 expression, pronounced tendency for X chromosome inactivation in most female human ES cells, increase in DNA methylation and prominent deposition of H3K27me3 and bivalent domain acquisition on lineage regulatory genes. The feasibility of establishing human ground state naive pluripotency in vitro with equivalent molecular and functional features to those characterized in mouse ES cells remains to be defined. Here we establish defined conditions that facilitate the derivation of genetically unmodified human naive pluripotent stem cells from already established primed human ES cells, from somatic cells through induced pluripotent stem (iPS) cell reprogramming or directly from blastocysts. The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells. This includes competence in the generation of cross-species chimaeric mouse embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas. Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo.

Deterministic direct reprogramming of somatic cells to pluripotency

Somatic cells can be inefficiently and stochastically reprogrammed into induced pluripotent stem (iPS) cells by exogenous expression of Oct4 (also called Pou5f1), Sox2, Klf4 and Myc (hereafter referred to as OSKM). The nature of the predominant rate-limiting barrier(s) preventing the majority of cells to successfully and synchronously reprogram remains to be defined. Here we show that depleting Mbd3, a core member of the Mbd3/NuRD (nucleosome remodelling and deacetylation) repressor complex, together with OSKM transduction and reprogramming in naive pluripotency promoting conditions, result in deterministic and synchronized iPS cell reprogramming (near 100% efficiency within seven days from mouse and human cells). Our findings uncover a dichotomous molecular function for the reprogramming factors, serving to reactivate endogenous pluripotency networks while simultaneously directly recruiting the Mbd3/NuRD repressor complex that potently restrains the reactivation of OSKM downstream target genes. Subsequently, the latter interactions, which are largely depleted during early pre-implantation development in vivo, lead to a stochastic and protracted reprogramming trajectory towards pluripotency in vitro. The deterministic reprogramming approach devised here offers a novel platform for the dissection of molecular dynamics leading to establishing pluripotency at unprecedented flexibility and resolution.

Hypomethylation marks enhancers within transposable elements

Transposable elements (TEs) make up 50% of the human genome and are usually considered a mutational burden. A new study uses signatures of DNA hypomethylation to identify tissue-specific enhancers within TEs, providing fresh evidence that mobile DNA has a non-negligible role in genome regulation and evolution.

Modeling the functional genomics of autism using human neurons

Human neural progenitors from a variety of sources present new opportunities to model aspects of human neuropsychiatric disease in vitro. Such in vitro models provide the advantages of a human genetic background combined with rapid and easy manipulation, making them highly useful adjuncts to animal models. Here, we examined whether a human neuronal culture system could be utilized to assess the transcriptional program involved in human neural differentiation and to model some of the molecular features of a neurodevelopmental disorder, such as autism. Primary normal human neuronal progenitors (NHNPs) were differentiated into a post-mitotic neuronal state through addition of specific growth factors and whole-genome gene expression was examined throughout a time course of neuronal differentiation. After 4 weeks of differentiation, a significant number of genes associated with autism spectrum disorders (ASDs) are either induced or repressed. This includes the ASD susceptibility gene neurexin 1, which showed a distinct pattern from neurexin 3 in vitro, and which we validated in vivo in fetal human brain. Using weighted gene co-expression network analysis, we visualized the network structure of transcriptional regulation, demonstrating via this unbiased analysis that a significant number of ASD candidate genes are coordinately regulated during the differentiation process. As NHNPs are genetically tractable and manipulable, they can be used to study both the effects of mutations in multiple ASD candidate genes on neuronal differentiation and gene expression in combination with the effects of potential therapeutic molecules. These data also provide a step towards better understanding of the signaling pathways disrupted in ASD.

Association and mutation analyses of 16p11.2 autism candidate genes

Background

Autism is a complex childhood neurodevelopmental disorder with a strong genetic basis. Microdeletion or duplication of a ∼500–700-kb genomic rearrangement on 16p11.2 that contains 24 genes represents the second most frequent chromosomal disorder associated with autism. The role of common and rare 16p11.2 sequence variants in autism etiology is unknown.

Methodology/Principal Findings

To identify common 16p11.2 variants with a potential role in autism, we performed association studies using existing data generated from three microarray platforms: Affymetrix 5.0 (777 families), Illumina 550 K (943 families), and Affymetrix 500 K (60 families). No common variants were identified that were significantly associated with autism. To look for rare variants, we performed resequencing of coding and promoter regions for eight candidate genes selected based on their known expression patterns and functions. In total, we identified 26 novel variants in autism: 13 exonic (nine non-synonymous, three synonymous, and one untranslated region) and 13 promoter variants. We found a significant association between autism and a coding variant in the seizure-related gene SEZ6L2 (12/1106 autism vs. 3/1161 controls; p = 0.018). Sez6l2 expression in mouse embryos was restricted to the spinal cord and brain. SEZ6L2 expression in human fetal brain was highest in post-mitotic cortical layers, hippocampus, amygdala, and thalamus. Association analysis of SEZ6L2 in an independent sample set failed to replicate our initial findings.

Conclusions/Significance

We have identified sequence variation in at least one candidate gene in 16p11.2 that may represent a novel genetic risk factor for autism. However, further studies are required to substantiate these preliminary findings.

Death-associated protein 3 localizes to the mitochondria and is involved in the process of mitochondrial fragmentation during cell death

Death-associated protein 3 (DAP3) was previously isolated in our laboratory as a positive mediator of cell death. It is a 46-kDa protein containing a GTP binding domain that was shown to be essential for the induction of cell death. DAP3 functions downstream of the receptor signaling complex, and its death-promoting effects depend on caspase activity. Recent reports have suggested that DAP3 is localized to the mitochondria, but no functional significance of this localization has been reported so far. Here, we study the sub-cellular localization and cellular function of human DAP3 (hDAP3). We found that hDAP3 is localized to the mitochondria and, in contrast to cytochrome c, is not released to the cytoplasm following several cell death signals. Overexpression of hDAP3 induced dramatic changes in the mitochondrial structure involving increased fragmentation of the mitochondria. Both the mitochondrial localization of hDAP3 and its GTP-binding activity were essential for the fragmentation. The punctiform mitochondrial morphology was similar to that observed upon treatment of HeLa cells with staurosporine. In fact, reduction of endogenous hDAP3 protein by RNA interference partially attenuated staurosporine-induced mitochondrial fission. Thus, hDAP3 is a necessary component in the molecular pathway that culminates in fragmented mitochondria, probably reflecting its involvement in the fission process. These results, for the first time, provide a specific functional role for hDAP3 in mitochondrial maintenance.