Christopher A Penfold

University of Cambridge | Cam · Wellcome Trust/Cancer Research UK Gurdon Institute

Gastrulation controls the emergence of cellular diversity and axis patterning in the early embryo. In mammals, this transformation is orchestrated by dynamic signalling centres at the interface of embryonic and extraembryonic tissues1–3. Elucidating the molecular framework of axis formation in vivo is fundamental for our understanding of human deve...

Nuclear transfer systems represent the efficient means to reprogram a cell and in theory provide a basis for investigating the development of endangered species. However, conventional nuclear transfer using oocytes of laboratory animals does not allow reprogramming of cross-species nuclei owing to defects in cell divisions and activation of embryon...

The uterus is the organ for embryo implantation and fetal development. Most current models of the uterus are centred around capturing its function during later stages of pregnancy to increase the survival in pre-term births. However, in vitro models focusing on the uterine tissue itself would allow modelling of pathologies including endometriosis a...

Motivation A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may under-go further branching; the contrary is true during recombination, where two or more statistical processes conve...

Primate germ cell development remains largely unexplored due to limitations in sample collection and the long duration of development. In mice, primordial germ cell-like cells (PGCLCs) derived from pluripotent stem cells (PSCs) can develop into functional gametes by in vitro culture or in vivo transplantation. Such PGCLC-mediated induction of matur...

In mammals, pluripotent cells transit through a continuum of distinct molecular and functional states en route to initiating lineage specification. Capturing pluripotent stem cells (PSCs) mirroring in vivo pluripotent states provides accessible in vitro models to study the pluripotency program and mechanisms underlying lineage restriction. Here, we...

Human germline-soma segregation occurs during weeks 2-3 in gastrulating embryos. Although direct studies are hindered, here, we investigate the dynamics of human primordial germ cell (PGCs) specification using in vitro models with temporally resolved single-cell transcriptomics and in-depth characterisation using in vivo datasets from human and non...

Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs)...

Primate germ cell development remains largely unexplored due to limitations in sample collection and the long duration of development. In mice, primordial germ cell-like cells (PGCLCs) derived from pluripotent stem cells (PSCs) can develop into functional gametes by in vitro culture or in vivo transplantation. Such PGCLC-mediated induction of matur...

The early specification and rapid growth of extraembryonic membranes are distinctive hallmarks of primate embryogenesis. These complex tasks are resolved through an intricate combination of signals controlling the induction of extraembryonic lineages and, at the same time, safeguarding the pluripotent epiblast. Here, we delineate the signals orches...

Human germline-soma segregation occurs during weeks 2-3 in gastrulating embryos. While direct studies are hindered, here we investigate the dynamics of human primordial germ cell (PGCs) specification using in vitro models with temporally resolved single-cell transcriptomics and in-depth characterisation to in vivo datasets from human and non-human...

The trophoblast lineage safeguards fetal development by mediating embryo implantation, immune tolerance, nutritional supply and gas exchange. Human trophoblast stem cells (hTSCs) provide a platform to study lineage specification of placental tissues; however, the regulatory network controlling self-renewal remains elusive. Here, we present a single...

Mammalian embryogenesis relies on glycolysis and oxidative phosphorylation to balance the generation of biomass with energy production. However, the dynamics of metabolic regulation in the postimplantation embryo in vivo have remained elusive due to the inaccessibility of the implanted conceptus for biochemical studies. To address this issue, we co...

Reprogramming of somatic nuclei toward the embryonic state has been studied using nuclear transfer (NT) to an oocyte at the metaphase II (MII) stage. In this NT, a somatic nucleus transplanted into an MII oocyte of the same species undergoes DNA replication and cell division before activating embryonic genes. Here, we describe a direct NT protocol...

Germline–soma segregation is a fundamental event during mammalian embryonic development. Here we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced remodelling of mesendoderm enhancers transiently confers the compet...

Platelet deficiency, known as thrombocytopenia, can cause hemorrhage and is treated with platelet transfusions. We developed a system for the production of platelet precursor cells, megakaryocytes, from pluripotent stem cells. These cultures can be maintained for >100 days, implying culture renewal by megakaryocyte progenitors (MKPs). However, it i...

The photosynthetic capacity of mature leaves increases after several days’ exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast-level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL-dependen...

Platelet deficiency, known as thrombocytopenia, can cause haemorrhage and is treated with platelet transfusions. We developed a system for the production of platelet precursor cells, megakaryocytes, from pluripotent stem cells. These cultures can be maintained for >100 days, implying culture renewal by megakaryocyte progenitors (MKPs). However, it...

The photosynthetic capacity of mature leaves increases after several days’ exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. This is termed dynamic acclimation but how it is initiated and controlled is unknown. From fully expanded Arabidopsis leaves, we determined HL-d...

Gaussian process dynamical systems (GPDS) represent Bayesian nonparametric approaches to inference of nonlinear dynamical systems, and provide a principled framework for the learning of biological networks from multiple perturbed time series measurements of gene or protein expression. Such approaches are able to capture the full richness of complex...

During the cell-cycle and meiosis, during development, or in response to stress, chromosomes undertake dramatic programs of reorganisation, which can result in major changes to genomic architecture, as well as local changes to chromatin structure via chromatin remodelling and epigenetic modification. The biophysical properties of the genome may the...

Motivation A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may undergo further branching; the contrary is true during recombination, where two or more statistical processes conver...

Leaf senescence involves degenerative but active biological processes that require balanced regulation of pro- and anti-senescing activities. Ethylene and cytokinin are major antagonistic regulatory hormones that control the timing and progression rate of leaf senescence. To identify the roles of these hormones in the regulation of leaf senescence...

During embryonic development, cells undertake a series of cell fate decisions to form a complete organism, epitomising a branching process; in some instances, these decisions may be reversible, particularly during the onset of disease, exemplifying a recombination process. Single cell transcriptomics provide a rich resource to explore the temporal...

List of gene ontology terms enriched in differentially expressed genes between WT and KO 2-cell embryos.Gene ontology terms enriched for biological processes were calculated using DAVID software (version 6.7).DOI: http://dx.doi.org/10.7554/eLife.22345.011

Gene counts for WT and KO oocyte, 1-cell and 2-cell embryos.Gene counts for 66 samples from single cell / embryo RNA-seq experiments. Removal of Unwanted Variation analysis has been performed to control for potentially confounding technical factors.DOI: http://dx.doi.org/10.7554/eLife.22345.004

List of differentially expressed genes between WT and KO samples at oocyte, 1-cell and 2-cell stage, from single cell/embryo RNA-seq analysis.ENSEMBL ID and names of genes identified as significantly differentially expressed with adjusted P-value (padj) <0.05. Log2FoldChange=Log2(WT/KO). Stage indicates the developmental stage that is analysed.DOI:...

List of zygotically activated genes (ZAG), WT class = EU, which are differentially expressed in KO samples.‘E’ denotes equally expressed, ‘D’ denotes downregulated or ‘U’ denotes upregulated at a later time point. Adjusted p-value (padj) shows significant differential expression between WT and KO class.DOI: http://dx.doi.org/10.7554/eLife.22345.007

Uniquely and multi-mapped transposable element (TE) counts.TE counts for 66 samples from single cell/embryo RNA-seq experiments. Uniquely and multi-mapped reads.DOI: http://dx.doi.org/10.7554/eLife.22345.016

Stella ChIP-seq enriched peaks. DOI: http://dx.doi.org/10.7554/eLife.22345.025

A list of primer sequences used in this study. DOI: http://dx.doi.org/10.7554/eLife.22345.026

List of maternal transcripts, WT class = ED, which are differentially expressed in KO samples.‘E’ denotes equally expressed, ‘D’ denotes downregulated or ‘U’ denotes upregulated at a later time point. Adjusted p-value (padj) shows significant differential expression between WT and KO class.DOI: http://dx.doi.org/10.7554/eLife.22345.006

Genome-wide Dppa3 co-expression network analysis.Table shows ensemble ID and official names of genes exhibiting significant expression correlation with Dppa3 (Pearson Correlation |r| > 0.9).DOI: http://dx.doi.org/10.7554/eLife.22345.012

Uniquely mapped transposable element (TE) counts.TE counts for 66 samples from single cell / embryo RNA-seq experiments. Uniquely mapped reads only.DOI: http://dx.doi.org/10.7554/eLife.22345.015

Sample details for single-cell / embryo RNA sequencing. DOI: http://dx.doi.org/10.7554/eLife.22345.024

The maternal-to-zygotic transition (MZT) marks the period when the embryonic genome is activated and acquires control of development. Maternally inherited factors play a key role in this critical developmental process, which occurs at the 2-cell stage in mice. We investigated the function of the maternally inherited factor Stella (encoded by Dppa3)...

Motivation: Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do not provide a pri...

Water availability is the biggest single limitation on plant productivity worldwide. In Arabidopsis, changes in metabolism and gene expression drive increased drought tolerance and initiate diverse drought avoidance and escape responses. To address regulatory processes that link these responses together, we set out to identify novel genes that gove...

Motivation: Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do not provide a pr...

Transcriptional reprogramming is integral to effective plant defense. Pathogen effectors act transcriptionally and posttranscriptionally to suppress defense responses. A major challenge to understanding disease and defense responses is discriminating between transcriptional reprogramming associated with microbial-associated molecular pattern (MAMP)...

The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast amount of legacy data obtained in model organisms to inform the GRNs of more complex, or economically or medically relevant counterparts. Examples include transferring information from Arabidopsis thaliana into related crop...

Here we introduce the causal structure identification (CSI) package, a Gaussian process based approach to inferring gene regulatory networks (GRNs) from multiple time series data. The standard CSI approach infers a single GRN via joint learning from multiple time series datasets; the hierarchical approach (HCSI) infers a separate GRN for each datas...

Motivation: There are a number of algorithms to infer causal regulatory networks from time series (gene expression) data. Here we analyse the phenomena of regulator interference, where regulators with similar dynamics mutually suppress both the probability of regulating a target and the associated link strength; for instance, interference between t...

Deciphering the networks that underpin complex biological processes using experimental data remains a significant, but promising, challenge, a task made all the harder by the added complexity of host-pathogen interactions. The aim of this article is to review the progress in understanding plant immunity made so far by applying network modeling algo...

The process of leaf senescence is induced by an extensive range of developmental and environmental signals and controlled by multiple, cross-linking pathways, many of which overlap with plant stress-response signals. Elucidation of this complex regulation requires a step beyond a traditional one-gene-at-a-time analysis. Application of a more global...

Oligonucleotides used to generate promoter fragment clones for Y1H screens.

Gene expression patterns of selected genes representing GO terms identified as being enriched at one or more timepoints during the experiment.

Genes differentially expressed in the anac055 mutant compared to Col-0 WT control over the whole time course were identified using GP2S sampling (Stegle et al., 2010) and genes with a GP2S score >5 were retained.

Identification of putative binding locations for transcription factors that interact with fragments of the ANAC019 promoter in Y1H assays.

Identification of putative binding locations for transcription factors that interact with fragments of the ANAC055 promoter in Y1H assays.

Identification of putative binding locations for transcription factors that interact with fragments of the ANAC072 promoter in Y1H assays.

Genes differentially expressed in the anac019 mutant compared to Col-5 WT control over the whole time course were identified using GP2S sampling (Stegle et al., 2010) and genes with a GP2S score >5 were retained.

Hierarchical CSI modeling was used to identify a treatment- specific subnetwork for various stress datasets (developmental senescence, Botrytis cinerea infection, salt, osmotic and cold stresses) based upon the core Y1H network.

Expression of MYB2 and MYB108 is positively correlated with that of ANAC019, ANAC055 and ANAC072 during B. cinerea infection and developmental senescence.

Oligonucleotides used to generate mutations in the DRE motif.

A model describing the gene regulatory network surrounding three similar NAC transcription factors that have roles in Arabidopsis leaf senescence and stress responses is presented. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions id...

Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a si...

The generation of time series transcriptomic datasets collected under multiple experimental conditions has proven to be a powerful approach for disentangling complex biological processes, allowing for the reverse engineering of gene regulatory networks (GRNs). Most methods for reverse engineering GRNs from multiple datasets assume that each of the...

Sample trajectories for chromosome XVI homologues with centromeres tethered. Conditions are as described for Fig. S1. (BZ2)

Sample trajectories for chromosome I homologues with centromeres tethered. Flexible means persistence length 0.2 µm and rigid means persistence length 2.0 µm, nu refers to the clustering parameter ν (see Materials and Methods). (BZ2)

Sample trajectories for chromosome I homologues with telomeres tethered. Conditions are as described for Fig. S1. (BZ2)

Convergence of measured statistics to the continuous wormlike chain (WLC). In the above graphs the average pairwise distance between loci (averaged over all loci on the same chromosome and 1000 sample trajectories) is indicated on the Y-axis, plotted as a function of the discretisation number (X-axis; the number of segments the chromosome is divide...

Sample trajectories for chromosome XVI homologues with telomeres tethered. Conditions are as described for Fig. S1. (BZ2)

Sample trajectories for chromosome IV homologues with centromeres tethered. Conditions are as described for Fig. S1. (BZ2)

Sample trajectories for chromosome IV homologues with telomeres tethered. Conditions are as described for Fig. S1. (BZ2)

Sample trajectories for untethered chromosomes. Conditions are as described for Fig. S1. (BZ2)

The influence of excluded volume terms (within chromosome only) was found to have negligible influence on chromosome trajectories. In particular, the excluded volume terms were modeled as an additional (repulsive) potential between all pairwise loci in the same chromosome with magnitude exp(100) if those loci approached within 40 nm of one another...

Meiosis is the cell division that halves the genetic component of diploid cells to form gametes or spores. To achieve this, meiotic cells undergo a radical spatial reorganisation of chromosomes. This reorganisation is a prerequisite for the pairing of parental homologous chromosomes and the reductional division, which halves the number of chromosom...

Inferring the topology of a gene-regulatory network (GRN) from genome-scale time-series measurements of transcriptional change has proved useful for disentangling complex biological processes. To address the challenges associated with this inference, a number of competing approaches have previously been used, including examples from information the...

Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is li...