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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 92,928 bioRxiv papers from 396,821 authors.

Most downloaded bioRxiv papers, all time

in category developmental biology

2,709 results found. For more information, click each entry to expand.

61: Brd4 and P300 regulate zygotic genome activation through histone acetylation
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Posted to bioRxiv 13 Jul 2018

Brd4 and P300 regulate zygotic genome activation through histone acetylation
2,023 downloads developmental biology

Shun Hang Chan, Yin Tang, Liyun Miao, Hiba Darwich-Codore, Charles E. Vejnar, Jean-Denis Beaudoin, Damir Musaev, Juan P. Fernandez, Miguel A. Moreno-Mateos, Antonio J. Giraldez

The awakening of the zygote genome, signaling the transition from maternal transcriptional control to zygotic control, is a watershed in embryonic development, but the factors and mechanisms controlling this transition are still poorly understood. By combining CRISPR-Cas9-mediated live imaging of the first transcribed genes (miR-430), chromatin and transcription analysis during zebrafish embryogenesis, we observed that genome activation is gradual and stochastic, and the active state is inherited in daughter cells. We discovered that genome activation is regulated through both translation of maternal mRNAs and the effects of these factors on the chromatin. We show that chemical inhibition of H3K27Ac writer (P300) and reader (Brd4) block genome activation, while induction of a histone acetylation prematurely activates transcription, and restore genome activation in embryos where translation of maternal mRNAs is impaired, demonstrating that they are limiting factors for the activation of the genome. In contrast to current models, we do not observe triggering of genome activation by a reduction of the nuclear-cytoplasmic(N/C) ratio or slower cell division. We conclude that genome activation is controlled by a time-dependent mechanism involving the translation of maternal mRNAs and the regulation of histone acetylation through P300 and Brd4. This mechanism is critical to initiating zygotic development and developmental reprogramming.

62: Single-cell RNA-Seq Resolves Cellular Heterogeneity and Transcriptional Dynamics in Spermatogonial Stem Cells Establishment
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Posted to bioRxiv 30 Dec 2017

Single-cell RNA-Seq Resolves Cellular Heterogeneity and Transcriptional Dynamics in Spermatogonial Stem Cells Establishment
2,016 downloads developmental biology

Jinyue Liao, Shuk Han Ng, Jiajie Tu, Alfred Chun Shui Luk, Yan Qian, Jacqueline Fung, Nelson Leung Sang Tang, Bo Feng, Wai-Yee Chan, Pierre Fouchet, Tin-Lap Lee

The transition of gonocytes to spermatogonia and subsequent differentiation provide the foundation of spermatogenesis. However, systematic understanding on the cellular and molecular basis of this process is still limited, mainly impeded by the asynchrony in development and the lack of stage-specific markers. Using single-cell RNA sequencing on Oct4-GFP+/KIT- cells isolated from PND5.5 mice, we dissected the cellular heterogeneity and established molecular regulations. We demonstrated that gonocyte-spermatogonial transition was characterized by gene expression change related to apoptosis, cell cycle progression, and regulation of migration processes. Pseudotime analysis reconstructed developmental dynamics of the spermatogonial populations and unraveled sequential cellular and molecular transitions. We also identified CD87 as a neonatal stem cell marker which are potentially involved in the intial establishment of SSC pool. Lastly, we uncovered an unexpected subpopulation of spermatogonia primed to differentiation within the undifferentiated compartment, which is characterized by the lack of self-renewal genes and enhanced Oct4 expression and retinoic acid signaling response. Our study thus provides a novel understanding of cellular and molecular changes during spermatogonial establishment.

63: Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
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Posted to bioRxiv 19 Dec 2018

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
2,010 downloads developmental biology

Alex A. Pollen, Aparna Bhaduri, Madeline G. Andrews, Tomasz J. Nowakowski, Olivia S Meyerson, Mohammed A. Mostajo-Radji, Elizabeth Di Lullo, Beatriz Alvarado, Melanie Bedolli, Max L Dougherty, Ian T. Fiddes, Zev N. Kronenberg, Joe Shuga, Anne A Leyrat, Jay A West, Marina Bershteyn, Craig B Lowe, Bryan Pavlovic, Sofie R. Salama, David Haussler, Evan E. Eichler, Arnold R. Kriegstein

Direct comparisons of human and non-human primate brain tissue have the potential to reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is largely inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. First, we systematically evaluated the fidelity of organoid models to primary human and macaque cortex, finding organoid models preserve gene regulatory networks related to cell types and developmental processes but exhibit increased metabolic stress. Second, we identified 261 genes differentially expressed in human compared to chimpanzee organoids and macaque cortex. Many of these genes overlap with human-specific segmental duplications and a subset suggest increased PI3K/AKT/mTOR activation in human outer radial glia. Together, our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.

64: Emergence of neuronal diversity during vertebrate brain development
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Posted to bioRxiv 12 Nov 2019

Emergence of neuronal diversity during vertebrate brain development
1,982 downloads developmental biology

Bushra Raj, Jeffrey A. Farrell, Aaron McKenna, Jessica L Leslie, Alexander F. Schier

Neurogenesis in the vertebrate brain comprises many steps ranging from the proliferation of progenitors to the differentiation and maturation of neurons. Although these processes are highly regulated, the landscape of transcriptional changes and progenitor identities underlying brain development are poorly characterized. Here, we describe the first developmental single-cell RNA-seq catalog of more than 200,000 zebrafish brain cells encompassing 12 stages from 12 hours post-fertilization to 15 days post-fertilization. We characterize known and novel gene markers for more than 800 clusters across these timepoints. Our results capture the temporal dynamics of multiple neurogenic waves from embryo to larva that expand neuronal diversity from ~20 cell types at 12 hpf to ~100 cell types at 15 dpf. We find that most embryonic neural progenitor states are transient and transcriptionally distinct from long-lasting neural progenitors of post-embryonic stages. Furthermore, we reconstruct cell specification trajectories for the retina and hypothalamus, and identify gene expression cascades and novel markers. Our analysis reveal that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo, while hypothalamic neural progenitors become progressively distinct with developmental time. These data provide the first comprehensive single-cell transcriptomic time course for vertebrate brain development and suggest distinct neurogenic regulatory paradigms between different stages and tissues.

65: Single-Cell RNA-seq Reveals a Subpopulation of Cells Underlying β Cell Expansion in the Postnatal Islets
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Posted to bioRxiv 17 Apr 2018

Single-Cell RNA-seq Reveals a Subpopulation of Cells Underlying β Cell Expansion in the Postnatal Islets
1,976 downloads developmental biology

Jingli A Zhang, Chunyan Gu, Derek K Smith, Monica K. Beltran, Noelyn Kljavin, Hai Ngu, Rowena Suriben, Jeremy Stinson, Zora Modrusan, Andrew S. Peterson

Pancreatic β cells undergo significant expansion and maturation during human and rodent postnatal development. Here, we used single-cell RNA-seq to characterize gene expression patterns at various stages of mouse islet cell development and uncovered a population of cells that is most abundant during the early postnatal period. This cell population lacks expression of FLTP and expresses PDGF receptors. Each of these conditions have previously been associated with proliferative capacity in β cells suggesting that we have identified the proliferative competent of β cell mass expansion. The subpopulation co-express many endocrine lineage-specific genes and exhibits a downregulation of genes associated with mitochondrial oxidative phosphorylation and global protein synthesis. It has upregulated activity of genes in the Wnt, Hippo, PDGF, and Notch pathways and has a significantly higher proliferation potential than the more mature β population. We show that activity of the Notch pathway is required in postnatal β cell expansion where it serves to maintain an undifferentiated endocrine state in the polyhormonal cell population. Collectively, our study identifies a proliferative, progenitor-like cell subpopulation in the postnatal islet as the source of postnatal β cell expansion.

66: Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive demethylation in mammals
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Posted to bioRxiv 15 May 2018

Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive demethylation in mammals
1,973 downloads developmental biology

Christopher B. Mulholland, Atsuya Nishiyama, Joel Ryan, Ryohei Nakamura, Merve Yiğit, Ivo M. Glück, Carina Trummer, Weihua Qin, Michael D. Bartoschek, Franziska R Traube, Edris Parsa, Enes Ugur, Miha Modic, Aishwarya Acharya, Paul Stolz, Christoph Ziegenhain, Michael Wierer, Wolfgang Enard, Thomas Carell, Don C. Lamb, Hiroyuki Takeda, Makoto Nakanashi, Sebastian Bultmann, Heinrich Leonhardt

Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. So far, it was unclear how mammals specifically achieve global DNA hypomethylation, given the high conservation of the DNA (de-)methylation machinery among vertebrates. We found that DNA demethylation requires TET activity but mostly occurs at sites where TET proteins are not bound suggesting a rather indirect mechanism. Among the few specific genes bound and activated by TET proteins was the naïve pluripotency and germline marker Dppa3 ( Pgc7, Stella ), which undergoes TDG dependent demethylation. The requirement of TET proteins for genome-wide DNA demethylation could be bypassed by ectopic expression of Dppa3 . We show that DPPA3 binds and displaces UHRF1 from chromatin and thereby prevents the recruitment and activation of the maintenance DNA methyltransferase DNMT1. We demonstrate that DPPA3 alone can drive global DNA demethylation when transferred to amphibians ( Xenopus ) and fish (medaka), both species that naturally do not have a Dppa3 gene and exhibit no post-fertilization DNA demethylation. Our results show that TET proteins are responsible for active and - indirectly also for - passive DNA demethylation; while TET proteins initiate local and gene-specific demethylation in vertebrates, the recent emergence of DPPA3 introduced a unique means of genome-wide passive demethylation in mammals and contributed to the evolution of epigenetic regulation during early mammalian development.

67: Mbd3/NuRD is a Key Inhibitory Module During the Induction and Maintenance of Naïve Pluripotency
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Posted to bioRxiv 06 Mar 2015

Mbd3/NuRD is a Key Inhibitory Module During the Induction and Maintenance of Naïve Pluripotency
1,952 downloads developmental biology

Asaf Zviran, Yoach Rais, Nofar Mor, Noa Novershtern, Jacob H Hanna

Our group has published a study on induced pluripotent stem cell (iPSC) reprogramming (Rais et al. Nature 20131) that reached the following conclusions: a) Mbd3/NuRD is a repressor of inducing naïve pluripotency from mouse Epiblast stem cells (EpiSCs), primordial germ cells (PGCs), murine somatic cells and human secondary fibroblasts; b) Up to 100% iPSC formation efficiency can be achieved via optimized Mbd3/NuRD depletion, in concert with optimized OKSM delivery and naïve pluripotency conditions (2i supplement applied only after 48 hours, human LIF, hypoxia and Vitamin C containing Knockout serum replacement)1. This represented the first proof for deterministic/near-deterministic iPSC reprogramming, and highlighted a previously unappreciated role for Mbd3/NuRD in hampering the re-establishment of pluripotency. Recent reports have seemingly provided contradictory results and attempted to dispute our iPSC efficiency quantifications and/or the role of Mbd3/NuRD in blocking reprogramming2,3. Here we provide a detailed response to these reports based on extended discussions and providing new data. The synthesis presented herein disagrees with claims made by Silva, Hendrich, Bertone and colleagues2,3, and reconfirms that Mbd3/NuRD is a major pathway that inhibits the maintenance and induction of pluripotency1. Further, we foresee that its controlled manipulation is likely to become an integral pathway for inducing and maintaining naïve pluripotency in a variety of species.

68: Contact-dependent cell communications drive morphological invariance during ascidian embryogenesis
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Posted to bioRxiv 24 Dec 2017

Contact-dependent cell communications drive morphological invariance during ascidian embryogenesis
1,942 downloads developmental biology

Léo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Emmanuel Faure, Julien Laussu, Lars Hufnagel, Grégoire Malandain, Christophe Godin, Patrick Lemaire

Canalization of developmental processes ensures the reproducibility and robustness of embryogenesis within each species. In its extreme form, found in ascidians, early embryonic cell lineages are invariant between embryos within and between species, despite rapid genomic divergence. To resolve this paradox, we used live light-sheet imaging to quantify individual cell behaviors in digitalized embryos and explore the forces that canalize their development. This quantitative approach revealed that individual cell geometries and cell contacts are strongly constrained, and that these constraints are tightly linked to the control of fate specification by local cell inductions. While in vertebrates ligand concentration usually controls cell inductions, we found that this role is fulfilled in ascidians by the area of contacts between signaling and responding cells. We propose that the duality between geometric and genetic control of inductions contributes to the counterintuitive inverse correlation between geometric and genetic variability during embryogenesis.

69: Gastruloids develop the three body axes in the absence of extraembryonic tissues and spatially localised signalling
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Posted to bioRxiv 31 Jan 2017

Gastruloids develop the three body axes in the absence of extraembryonic tissues and spatially localised signalling
1,906 downloads developmental biology

D.A. Turner, L. Alonso-Crisostomo, M. Girgin, P. Baillie-Johnson, C. R. Glodowski, P. C. Hayward, J. Collignon, C. Gustavsen, P. Serup, Ben Steventon, M. Lutolf, A. Martinez Arias

Establishment of the three body axes is a critical step during animal development. In mammals, genetic studies have shown that a combination of precisely deployed signals from extraembryonic tissues position the anteroposterior axis (AP) within the embryo and lead to the emergence of the dorsoventral (DV) and left-right (LR) axes. We have used Gastruloids, embryonic organoids, as a model system to understand this process and find that they are able to develop AP, DV and LR axes as well as to undergo axial elongation in a manner that mirror embryos. The Gastruloids can be grown for 160 hours and form derivatives from ectoderm, mesoderm and endoderm. We focus on the AP axis and show that in the Gastruloids this axis is registered in the expression of T/Bra at one pole that corresponds to the tip of the elongation. We find that localisation of T/Bra expression depends on the combined activities of Wnt/β-Catenin and Nodal/Smad2,3 signalling, and that BMP signalling is dispensable for this process. Furthermore, AP axis specification occurs in the absence of both extraembryonic tissues and of localised sources of signalling. Our experiments show that Nodal, together with Wnt/β-Catenin signalling, is essential for the expression of T/Bra but that Wnt signalling has a separable activity in the elongation of the axis. The results lead us to suggest that, in the embryo, the role of the extraembryonic tissues might not be to induce the axes but to bias an intrinsic ability of the embryo to break its initial symmetry and organise its axes.

70: Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions
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Posted to bioRxiv 11 Apr 2018

Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions
1,902 downloads developmental biology

Daniel Strebinger, Cédric Deluz, Elias T Friman, Subashika Govindan, Andrea B Alber, David M. Suter

SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self-renewal and differentiation. However, how temporal fluctuations in their expression levels bias lineage commitment is unknown. Here we generated knock-in reporter fusion ES cell lines allowing to monitor endogenous SOX2 and OCT4 protein fluctuations in living cells and to determine their impact on mesendodermal and neuroectodermal commitment. We found that small differences in SOX2 and OCT4 levels impact cell fate commitment in G1 but not in S phase. Elevated SOX2 levels modestly increased neuroectodermal commitment and decreased mesendodermal commitment upon directed differentiation. In contrast, elevated OCT4 levels strongly biased ES cell towards both neuroectodermal and mesendodermal fates. Using ATAC-seq on ES cells gated for different endogenous SOX2 and OCT4 levels, we found that high OCT4 levels increased chromatin accessibility at differentiation-associated enhancers. This suggests that small endogenous fluctuations of pioneer transcription factors can bias cell fate decisions by concentration-dependent priming of differentiation-associated enhancers.

71: Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development
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Posted to bioRxiv 06 Jun 2018

Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development
1,897 downloads developmental biology

Morgan Oatley, Özge Vargel Bölükbasi, Valentine Svensson, Maya Shvartsman, Kerstin Ganter, Katharina Zirngibl, Polina V. Pavlovich, Vladislava Milchevskaya, Vladimira Foteva, Kedar N Natarajan, Bianka Baying, Vladimir Benes, Kiran R. Patil, Sarah A. Teichmann, Christophe Lancrin

The endothelial to haematopoietic transition (EHT) is the process whereby haemogenic endothelium differentiates into haematopoietic stem and progenitor cells (HSPCs). The intermediary steps of this process are unclear, in particular the identity of endothelial cells that give rise to HSPCs is unknown. Using single-cell transcriptome analysis and antibody screening we identified CD44 as a new marker of EHT enabling us to isolate robustly the different stages of EHT in the aorta gonad mesonephros (AGM) region. This allowed us to provide a very detailed phenotypical and transcriptional profile for haemogenic endothelial cells, characterising them with high expression of genes related to Notch signalling, TGFbeta/BMP antagonists (Smad6, Smad7 and Bmper) and a downregulation of genes related to glycolysis and the TCA cycle. Moreover, we demonstrated that by inhibiting the interaction between CD44 and its ligand hyaluronan we could block EHT, identifying a new regulator of HSPC development.

72: Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos
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Posted to bioRxiv 02 Apr 2018

Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos
1,894 downloads developmental biology

Fernando Biase, Qiuyang Wu, Riccardo Calandrelli, Marcelo Rivas-Astroza, Shuigeng Zhou, Sheng Zhong

Single-cell RNA-seq experiments cannot record cell division history and therefore cannot directly connect intercellular differences at a later developmental stage to their progenitor cells. We developed Rainbow-seq to combine cell division lineage tracing with single-cell RNA-seq. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA-seq experiment to simultaneously read single-cell transcriptomes and decode the lineage marker genes. We traced the lineages deriving from each blastomere in two-cell mouse embryos and observed inequivalent contributions to the embryonic and abembryonic poles in 72% of the blastocysts evaluated. Rainbow-seq on four- and eight-cell embryos with lineage tracing triggered at two-cell stage exhibited remarkable transcriptome-wide differences between the two cell lineages at both stages, including genes involved in negative regulation of transcription and signaling. These data provide critical insights on cell fate choices in cleavage embryos. Rainbow-seq bridged a critical gap between cellular division history and single-cell RNA-seq assays.

73: Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility
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Posted to bioRxiv 23 Jul 2018

Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility
1,876 downloads developmental biology

Mehdi Goudarzi, Kathryn Berg, Lindsey M Pieper, Alexander F. Schier

Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs are dispensable for embryogenesis, viability and fertility.

74: Embryonic organoids recapitulate early heart organogenesis
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Posted to bioRxiv 14 Oct 2019

Embryonic organoids recapitulate early heart organogenesis
1,866 downloads developmental biology

Giuliana Rossi, Andrea Boni, Romain Guiet, Mehmet Girgin, Robert G. Kelly, Matthias P. Lutolf

Organoids are powerful models for studying tissue development, physiology, and disease. However, current culture systems disrupt the inductive tissue-tissue interactions needed for the complex morphogenetic processes of native organogenesis. Here we show that mouse embryonic stem cells (mESCs) can be coaxed to robustly undergo the fundamental steps of early heart organogenesis with an in vivo -like spatiotemporal fidelity. These axially patterned embryonic organoids support the generation of cardiovascular progenitors, as well as first and second heart field compartments. The cardiac progenitors self-organize into an anterior domain reminiscent of a cardiac crescent before forming a beating cardiac tissue near a putative primitive gut-like tube, from which it is separated by an endocardial-like layer. These findings unveil the surprising morphogenetic potential of mESCs to execute key aspects of organogenesis through the coordinated development of multiple tissues. This platform could be an excellent tool for studying heart development in unprecedented detail and throughput.

75: Modeling the Human Segmentation Clock with Pluripotent Stem Cells
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Posted to bioRxiv 27 Feb 2019

Modeling the Human Segmentation Clock with Pluripotent Stem Cells
1,857 downloads developmental biology

Mitsuhiro Matsuda, Yoshihiro Yamanaka, Maya Uemura, Mitsujiro Osawa, Megumu K. Saito, Ayako Nagahashi, Megumi Nishio, Long Guo, Shiro Ikegawa, Satoko Sakurai, Shunsuke Kihara, Michiko Nakamura, Tomoko Matsumoto, Hiroyuki Yoshitomi, Makoto Ikeya, Takuya Yamamoto, Knut Woltjen, Miki Ebisuya, Junya Toguchida, Cantas Alev

Pluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types experimental model systems that can recapitulate more complex biological features of human mesoderm development and patterning are largely missing. Here, we utilized induced pluripotent stem cells (iPSCs) for the stepwise in vitro induction of presomitic mesoderm (PSM) and its derivatives to model distinct aspects of human somitogenesis. We focused initially on modeling the human segmentation clock, a major biological concept believed to underlie the rhythmic and controlled emergence of somites, which give rise to the segmental pattern of the vertebrate axial skeleton. We succeeded to observe oscillatory expression of core segmentation clock genes, including HES7 and DKK1, and identified novel oscillatory genes in human iPSC-derived PSM. We furthermore determined the period of the human segmentation clock to be around five hours and showed the presence of dynamic traveling wave-like gene expression within in vitro induced human PSM. Utilizing CRISPR/Cas9-based genome editing technology, we then targeted genes, for which mutations in patients with abnormal axial skeletal development such as spondylocostal dysostosis (SCD) (HES7, LFNG and DLL3) or spondylothoracic dysostosis (STD) (MESP2) have been reported. Subsequent analysis of patient-like iPSC knock-out lines as well as patient-derived iPSCs together with their genetically corrected isogenic controls revealed gene-specific alterations in oscillation, synchronization or differentiation properties, validating the overall utility of our model system, to recapitulate not only key features of human somitogenesis but also to provide novel insights into diseases associated with the formation and patterning of the human axial skeleton.

76: Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene
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Posted to bioRxiv 31 May 2018

Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene
1,826 downloads developmental biology

Augusto Berrocal, Nicholas C Lammers, Hernan G Garcia, Michael B. Eisen

We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its iconic seven stripe expression pattern forms. We developed a rigorous quantitative framework for analyzing and visualizing these data, that allows us to infer the temporal dynamics of the transcriptional state of roughly 3,000 nuclei, and characterize how the process varies over time and space. We show that despite being created by the largely independent activity of five discrete enhancers, the seven eve stripes are sculpted by the same basic kinetic phenomena: the suppression of bursting outside of stripes, a coupled increase of burst frequency and burst duration within stripes over time and across stripes from their margins to their centers, and the exchange of active nuclei from the posterior to anterior flanks to reposition stripes over time.

77: Single-Cell Sequencing of Primate Preimplantation Embryos Reveals Chromosome Elimination Via Cellular Fragmentation and Blastomere Exclusion
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Posted to bioRxiv 02 Jan 2018

Single-Cell Sequencing of Primate Preimplantation Embryos Reveals Chromosome Elimination Via Cellular Fragmentation and Blastomere Exclusion
1,821 downloads developmental biology

Brittany L. Daughtry, Jimi L. Rosenkrantz, Nathan H. Lazar, Suzanne S. Fei, Nash Redmayne, Kristof A. Torkenczy, Andrew C. Adey, Lina Gao, Byung Park, Kimberly A. Nevonen, Lucia Carbone, Shawn L. Chavez

Aneuploidy that arises during meiosis and/or mitosis is a major contributor to early embryo loss. We previously demonstrated that human preimplantation embryos encapsulate mis-segregated chromosomes into micronuclei while undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a non-human primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254 blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N=50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the frequency of aneuploidy and micronucleation is conserved between humans and macaques and that cellular fragments encapsulate whole and/or partial chromosomes lost from blastomeres. Single-cell/fragment genotyping demonstrated that these chromosome-containing cellular fragments (CCFs) can be either maternal or paternal in origin and display DNA damage via double-stranded breaks. Chromosome breakage and abnormal cytokinesis resulted in reciprocal losses/gains at the terminal ends of chromosome arms, uniparental genome segregation, and mixoploidy between blastomeres. Combining time-lapse imaging with scDNA-seq, we also determined that multipolar divisions at the zygote or 2-cell stage generated chaotic aneuploidy encompassing a complex mixture of maternal and paternal chromosomes. Despite frequent chromosomal mis-segregation at the cleavage-stage, we show that CCFs and non-dividing aneuploid blastomeres exhibiting extensive DNA damage are prevented from incorporation at the blastocyst stage. These findings suggest that embryos respond to chromosomal errors by encapsulation into micronuclei, elimination by cellular fragmentation, and selection against highly aneuploid blastomeres to overcome chromosome instability during preimplantation development.

78: In vitro induction and in vivo engraftment of lung bud tip progenitor cells derived from human pluripotent stem cells
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Posted to bioRxiv 15 Feb 2017

In vitro induction and in vivo engraftment of lung bud tip progenitor cells derived from human pluripotent stem cells
1,817 downloads developmental biology

Alyssa J. Miller, David R. Hill, Melinda S. Nagy, Yoshiro Aoki, Briana R. Dye, Alana M Chin, Sha Huang, Felix Zhu, Eric S. White, Vibha Lama, Jason R. Spence

The bud tip epithelium of the branching mouse and human lung contains multipotent progenitors that are able to self-renew and give rise to all mature lung epithelial cell types. The current study aimed to understand the developmental signaling cues that regulate bud tip progenitor cells in the human fetal lung, which are present during branching morphogenesis, and to use this information to induce a bud tip progenitor-like population from human pluripotent stem cells (hPSCs) in vitro. We identified that FGF7, CHIR-99021 and RA maintained isolated human fetal lung epithelial bud tip progenitor cells in an undifferentiated state in vitro, and led to the induction of a 3-dimensional lung-like epithelium from hPSCs. 3-dimensional hPSC-derived lung tissue was initially patterned, with airway-like interior domains and bud tip-like progenitor domains at the periphery. Epithelial bud tip-like domains could be isolated, expanded and maintained as a nearly homogeneous population by serial passaging. Comparisons between human fetal lung epithelial bud tip cells and hPSC-derived bud tip-like cells were carried out using immunostaining, in situ hybridization and transcriptome-wide analysis, and revealed that in vitro derived tissue was highly similar to native lung. hPSC-derived epithelial bud tip-like structures survived in vitro for over 16 weeks, could be easily frozen and thawed and maintained multi-lineage potential. Furthermore, hPSC-derived epithelial bud tip progenitors successfully engrafted in the proximal airways of injured immunocompromised NSG mouse lungs, where they persisted for up to 6 weeks and gave rise to several lung epithelial lineages.

79: Chemically-defined induction of a primitive endoderm and epiblast-like niche supports post-implantation progression from blastoids
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Posted to bioRxiv 02 Jan 2019

Chemically-defined induction of a primitive endoderm and epiblast-like niche supports post-implantation progression from blastoids
1,809 downloads developmental biology

Erik J Vrij, Yvonne S. Scholte op Reimer, Javier Frias Aldeguer, Isabel Misteli Guerreiro, Jop Kind, Bon-Kyoung Koo, Clemens A van Blitterswijk, Nicolas C Rivron

The early mammalian conceptus (blastocyst) contains two supporting extraembryonic tissues - the trophectoderm and the primitive endoderm (PrE) - that encase and guide the epiblast (Epi) to eventually form the all body. Modifications of the conceptus exposed key genes regulating these tissues co-development. However, the combinations of signalling pathways underlying the interplay of PrE and Epi remains elusive. Stem cell-based models including embryoid bodies and blastoids can be generated in large numbers and subjected to high-content screens. Here, we use combinatorial screens of proteins, GPCR ligands and small molecules to rapidly (72 hours) and efficiently (80%) guide embryoid bodies to form a three-dimensional PrE-/Epiblast-like niche in chemically-defined conditions (gel-free, serum-free). This bipotent niche spontaneously progresses, without growth factors, to form a pro-amniotic cavity surrounded by a polarized Epi covered with parietal and visceral endoderm-like cells. In blastoids, these molecules enhance the ratio and number of Gata6+/Nanog+ cells and promote the survival, expansion and morphogenesis of a post-implantation-like Epi in vitro . Altogether, modelling early development in chemically-defined conditions delineates the pathways sufficient to form a functional PrE/Epiblast niche that fuels post-implantation development.

80: Multimodal transcriptional control of pattern formation in embryonic development
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Posted to bioRxiv 31 May 2018

Multimodal transcriptional control of pattern formation in embryonic development
1,808 downloads developmental biology

Nicholas C Lammers, Vahe Galstyan, Armando Reimer, Sean A Medin, Chris H Wiggins, Hernan G Garcia

Predicting developmental outcomes from regulatory DNA sequence and transcription factor patterns remains an open challenge in physical biology. Using stripe 2 of the even-skipped gene in Drosophila embryos as a case study, we dissect the regulatory forces underpinning a key step along the developmental decision-making cascade: the generation of cytoplasmic mRNA patterns via the control of transcription in individual cells. Using live imaging and computational approaches, we found that the transcriptional burst frequency is modulated across the stripe to control the mRNA production rate. However, we discovered that bursting alone cannot quantitatively recapitulate the formation of the stripe, and that control of the window of time over which each nucleus transcribes even-skipped plays a critical role in stripe formation. Theoretical modeling revealed that these regulatory strategies—bursting and the time window—obey different kinds of regulatory logic, suggesting that the stripe is shaped by the interplay of two distinct underlying molecular processes.

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