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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 70,415 bioRxiv papers from 307,444 authors.

Most downloaded bioRxiv papers, all time

in category developmental biology

2,072 results found. For more information, click each entry to expand.

61: Identification and Functional Characterization of Muscle Satellite Cells in Drosophila
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Posted to bioRxiv 25 Jan 2016

Identification and Functional Characterization of Muscle Satellite Cells in Drosophila
1,612 downloads developmental biology

Dhananjay Chaturvedi, Heinrich Reichert, Rajesh Gunage, K VijayRaghavan

Work on genetic model systems such as Drosophila and mouse has shown that the fundamental mechanisms of myogenesis are remarkably similar in vertebrates and invertebrates. Strikingly however, satellite cells, the adult muscle stem cells that are essential for the regeneration of damaged muscles in vertebrates, have not been reported in invertebrates. In this study we show that lineal descendants of muscle stem cells are present in adult muscle of Drosophila as small, unfused cells located superficially and in close proximity to the mature muscle fibers. Normally quiescent, following muscle fiber injury, we show that these cells express Zfh1- cells and engage in Notch-Delta dependent proliferative activity and generate lineal descendant populations, which fuse with the injured muscle fiber. In view of strikingly similar morphological and functional features, we consider these novel cells to be the Drosophila equivalent of vertebrate muscle satellite cells.

62: 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
1,600 downloads developmental biology

Augusto Berrocal, Nicholas 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.

63: Hydraulic control of embryo size, tissue shape and cell fate
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Posted to bioRxiv 10 Aug 2018

Hydraulic control of embryo size, tissue shape and cell fate
1,581 downloads developmental biology

Chii Jou Chan, Maria Costanzo, Teresa Ruiz-Herrero, Gregor Mönke, Ryan J. Petrie, L. Mahadevan, Takashi Hiiragi

Size control is fundamental in tissue development and homeostasis. While the role of cell proliferation in this process has been widely studied, the mechanisms of organ size control and how it impacts cell fates remain elusive. Here, we use mouse blastocyst development as a model to unravel a key role of fluid-filled lumen in embryonic size control and cell fate specification. We find that during blastocyst expansion, there is a two-fold increase in the pressure of the lumen that translates into a concomitant increase in the cortical tension of trophectoderm (TE) cells lining the lumen. Increased cortical tension leads to vinculin mechanosensing and maturation of the functional tight junctions, thereby establishing a positive feedback loop to accommodate lumenal growth. However, when the cortical tension reaches a critical threshold, cell-cell adhesion cannot be sustained, and mitotic entry leads to a rupture of TE epithelium, fluid leakage and collapse of the blastocyst cavity. A simple theory of hydraulically-gated oscillations that integrates these feedback interactions recapitulates the evolution of cavity size and predicts the scaling of embryonic size with the tissue volume. Our theory further predicts that reduced cortical tension or disrupted tight junctions, and increased tissue stiffness lead to smaller embryonic size. These predictions are verified experimentally by embryological, pharmacological and genetic manipulations of the embryos. Remarkably, these changes to lumenal size, without a change in the tissue volume, lead to alteration of tissue architecture and cell fate. Overall, our study reveals how lumenal pressure and tissue mechanics control embryonic size at the tissue scale, that in turn couples to cell position and fate at the cellular scale.

64: 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
1,560 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.

65: Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution
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Posted to bioRxiv 15 Nov 2018

Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution
1,559 downloads developmental biology

Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Lui, Vidur Garg, Roshan Sharma, Claire S Simon, Nestor Saiz, Rui Gardner, Stéphane C Boutet, Deanna M Church, Pamela A Hoodless, Anna-Katerina Hadjantonakis, Dana Pe’er

To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single-cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio-temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis.

66: 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
1,558 downloads developmental biology

Leo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Emmanuel Faure, Julien Laussu, Lars Hufnagel, Grégoire Malandain, Christophe Godin, P. 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.

67: Cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription
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Posted to bioRxiv 07 Dec 2017

Cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription
1,542 downloads developmental biology

Clayton E Friedman, Quan Nguyen, Samuel W. Lukowski, Han Sheng Chiu, Abbigail Helfer, Jason Miklas, Shengbao Suo Suo, Jing-Dong Jackie Han, Pierre Osteil, Guangdun Peng, Naihe Jing, Greg J Baillie, Anne Senabouth, Angelika N. Christ, Timothy J Bruxner, Charles E. Murry, Emily S Wong, Jun Ding, Yuliang Wang, James Hudson, Hannele Ruohola-Baker, Ziv Bar-Joseph, Patrick P L Tam, Joseph E. Powell, Nathan J. Palpant

Differentiation into diverse cell lineages requires the orchestration of gene regulatory networks guiding diverse cell fate choices. Utilizing human pluripotent stem cells, we measured expression dynamics of 17,718 genes from 43,168 cells across five-time points over a thirty-day time-course of in vitro cardiac- directed differentiation. Unsupervised clustering and lineage prediction algorithms were used to map fate choices and transcriptional networks underlying cardiac differentiation. We leveraged this resource to identify strategies for controlling in vitro differentiation as it occurs in vivo. HOPX, a non-DNA binding homeodomain protein essential for heart development in vivo was identified as dysregulated in vitro derived cardiomyocytes. Utilizing genetic gain and loss of function approaches, we dissect the transcriptional complexity of the HOPX locus and identify the requirement of hypertrophic signaling for HOPX transcription in hPSC-derived cardiomyocytes. This work provides a single cell dissection of the transcriptional landscape of cardiac differentiation for broad applications of stem cells in cardiovascular biology.

68: A genome-wide assessment of the ancestral neural crest gene regulatory network
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Posted to bioRxiv 12 Mar 2018

A genome-wide assessment of the ancestral neural crest gene regulatory network
1,540 downloads developmental biology

Dorit Hockman, Vanessa Chong-Morrison, Daria Gavriouchkina, Stephen Green, Chris T Amemiya, Jeramiah J. Smith, Marianne E. Bronner, Tatjana Sauka-Spengler

The neural crest is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional profiles and chromatin accessibility of neural crest cells in the basal sea lamprey, in order to gain insight into the ancestral state of the neural crest gene regulatory network (GRN) at the dawn of vertebrates. Transcriptome analyses reveal clusters of co-regulated genes during neural crest specification and migration that show high conservation across vertebrates for dynamic programmes like Wnt modulation during the epithelial to mesenchymal transition, but also reveal novel transcription factors and cell-adhesion molecules not previously implicated in neural crest migration. ATAC-seq analysis refines the location of known cis-regulatory elements at the Hox-α2 locus and uncovers novel cis-regulatory elements for Tfap2B and SoxE1. Moreover, cross-species deployment of lamprey elements in zebrafish reveals that the lamprey SoxE1 enhancer activity is deeply conserved, mediating homologous expression in jawed vertebrates. Together, our data provide new insight into the core elements of the GRN that are conserved to the base of the vertebrates, as well as expose elements that are unique to lampreys.

69: Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking
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Posted to bioRxiv 28 Feb 2017

Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking
1,530 downloads developmental biology

Carsten Wolff, Jean-Yves Tinevez, Tobias Pietzsch, Evangelia Stamataki, Benjamin Harich, Stephan Preibisch, Spencer Shorte, Philipp J. Keller, Pavel Tomancak, Anastasios Pavlopoulos

During development coordinated cell behaviors orchestrate tissue and organ morphogenesis to suit the lifestyle of the organism. We have used here the crustacean Parhyale hawaiensis to study the cellular basis of limb development. Transgenic Parhyale embryos with fluorescently labeled nuclei were imaged at high spatiotemporal resolution with multi-view light-sheet fluorescence microscopy over several days of embryogenesis spanning appendage morphogenesis from early specification up to late differentiation stages. Cell tracking with a new tool called Massive Multi-view Tracker (MaMuT) enabled the reconstruction of the complete cell lineage of an outgrowing thoracic limb with single-cell resolution. In silico clonal analyses suggested that the limb primordium becomes subdivided from an early stage first into anterior-posterior and then into dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb bud formation is associated with the spatial modulation of cell proliferation, while limb elongation is also driven by the preferential orientation of division of epidermal cells along the proximal-distal axis of growth. Cellular reconstructions were predictive of the expression patterns of limb development genes including the Decapentaplegic (Dpp) morphogen.

70: Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics
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Posted to bioRxiv 30 Jan 2017

Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics
1,528 downloads developmental biology

Andreas Sagner, Zachary B. Gaber, Julien Delile, Jennifer H. Kong, David L. Rousso, Caroline A. Pearson, Steven E. Weicksel, Manuela Melchionda, Neda S. Mousavy Gharavy, James Briscoe, Bennett G. Novitch

During tissue development, multipotent progenitors differentiate into specific cell types in characteristic spatial and temporal patterns. We address the mechanism linking progenitor identity and differentiation rate in the neural tube, where motor neuron (MN) progenitors differentiate more rapidly than other progenitors. Using single cell transcriptomics, we define the transcriptional changes associated with the transition of neural progenitors into MNs. Reconstruction of gene expression dynamics from these data indicate a pivotal role for the MN determinant Olig2 just prior to MN differentiation. Olig2 represses expression of the Notch signaling pathway effectors Hes1 and Hes5. Olig2 repression of Hes5 appears to be direct, via a conserved regulatory element within the Hes5 locus that restricts expression from MN progenitors. These findings reveal a tight coupling between the regulatory networks that control patterning and neuronal differentiation, and demonstrate how Olig2 acts as the developmental pacemaker coordinating the spatial and temporal pattern of MN generation.

71: A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation
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Posted to bioRxiv 21 Aug 2019

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation
1,522 downloads developmental biology

Celia Alda-Catalinas, Danila Bredikhin, Irene Hernando-Herraez, Oana Kubinyecz, Fátima Santos, Melanie A. Eckersley-Maslin, Oliver Stegle, Wolf Reik

Zygotic genome activation (ZGA) is a crucial developmental milestone that remains poorly understood. This first essential transcriptional event in embryonic development coincides with extensive epigenetic reprogramming processes and is orchestrated, in part, by the interplay of transcriptional and epigenetic regulators. Here, we developed a novel high-throughput screening method that combines pooled CRISPR-activation (CRISPRa) with single-cell transcriptomics to systematically probe candidate regulators of ZGA. We screened 230 epigenetic and transcriptional regulators by upregulating their expression with CRISPRa in mouse embryonic stem cells (ESCs). Through single-cell RNA-sequencing (scRNA-seq) of CRISPRa-perturbed cells, we generated approximately 200,000 single-cell transcriptomes, each transduced with a unique short-guide RNA (sgRNA) targeting a specific candidate gene promoter. Using integrative dimensionality reduction of the perturbation scRNA-seq profiles, we characterized molecular signatures of ZGA and uncovered 44 factors that promote a ZGA-like response in ESCs, both in the coding and non-coding transcriptome. Upon upregulation of these factors, including the DNA binding protein Dppa2, the chromatin remodeller Smarca5 and the transcription factor Patz1, ESCs adopt an early embryonic-like state. Supporting their roles as ZGA regulators, Dppa2 and Smarca5 knock-out ESCs lose expression of ZGA genes, however, overexpression of Dppa2 in Smarca5 knock-out ESCs, but not vice versa, rescues ZGA-like expression, suggesting that Smarca5 regulates ZGA upstream and via Dppa2. Together, our single-cell transcriptomic profiling of CRISPRa-perturbed cells provides comprehensive system-level insights into the molecular mechanisms that orchestrate ZGA.

72: Tracking the embryonic stem cell transition from ground state pluripotency
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Posted to bioRxiv 08 Dec 2016

Tracking the embryonic stem cell transition from ground state pluripotency
1,512 downloads developmental biology

Tüzer Kalkan, Nelly Olova, Mila Roode, Carla Mulas, Heather J. Lee, Isabelle Nett, Hendrik Marks, Rachael Walker, Hendrik G. Stunnenberg, Kathryn S. Lilley, Jennifer Nichols, Wolf Reik, Paul Bertone, Austin Smith

Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naive pluripotency. Here we examined the initial transition of ES cells. The population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naive status. Extinction of ES cell identity in single cells is acute. It occurs only after near-complete elimination of naive pluripotency factors, but precedes appearance of lineage specification markers. Cells newly departed from the ES cell state exhibit global transcriptome features consistent with features of early post-implantation epiblast and distinct from primed epiblast. They also exhibit a genome-wide increase in DNA methylation, intermediate between early and late epiblast. These findings are consistent with the proposition that naive cells transition to a discrete formative phase of pluripotency preparatory to lineage priming.

73: Hair-bearing human skin generated entirely from pluripotent stem cells
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Posted to bioRxiv 08 Jul 2019

Hair-bearing human skin generated entirely from pluripotent stem cells
1,507 downloads developmental biology

Jiyoon Lee, Cyrus Rabbani, Hongyu Gao, Matthew Steinhart, Benjamin M. Woodruff, Zachary Pflum, Alexander Kim, Stefan Heller, Yunlong Liu, Taha Z Shipchandler, Karl R Koehler

The skin is important for regulating bodily fluid retention and temperature, guarding against external stresses, and mediating touch and pain sensation. The skin is also susceptible to damage from burns, diseases, or genetic defects, which affect nearly one billion people worldwide. For the advancement of skin regenerative therapies, it remains challenging to construct new skin with hair follicles and nerves in tissue cultures and in bioengineered skin grafts. Here, we report an organoid culture system that generates complex skin from human pluripotent stem cells. We use step-wise modulation of the TGF and FGF signalling pathways to co-induce cranial epithelial cells and neural crest cells within a spherical cell aggregate. During 4-5 months incubation, we observe the emergence of a cyst-like skin organoid composed of stratified epidermis, fat-rich dermis, and pigmented hair follicles equipped with sebaceous glands. A network of sensory neurons and Schwann cells form nerve-like bundles that target Merkel cells in organoid hair follicles, mimicking human touch circuitry. Single-cell RNA sequencing and direct comparison to foetal specimens suggest that skin organoids are equivalent to human facial skin in the second-trimester of development. Moreover, we show that skin organoids produce planar hair-bearing skin when grafted on nude mice. Together, our results demonstrate the self-assembly of nearly complete skin tissue in vitro that can be used to reconstitute skin in vivo. We anticipate that our skin organoid model will be foundational to future studies of human skin development, disease modelling, or reconstructive surgery.

74: A conserved regulatory program drives emergence of the lateral plate mesoderm
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Posted to bioRxiv 07 Feb 2018

A conserved regulatory program drives emergence of the lateral plate mesoderm
1,501 downloads developmental biology

Karin D. Prummel, Christopher Hess, Susan Nieuwenhuize, Hugo J. Parker, Katherine W. Rogers, Iryna Kozmikova, Claudia Racioppi, Eline C. Brombacher, Anna Czarkwiani, Dunja Knapp, Alexa Burger, Elena Chiavacci, Gopi Shah, Alexa Burger, Jan Huisken, Maximina H. Yun, Lionel Christiaen, Lionel Christiaen, Patrick Müller, Marianne E. Bronner, Robb Krumlauf, Christian Mosimann

Cardiovascular lineages develop together with kidney, smooth muscle, and limb connective tissue progenitors from the lateral plate mesoderm (LPM). How the LPM initially emerges and how its downstream fates are molecularly interconnected remain unknown. Here, we isolated a pan-LPM enhancer in the zebrafish draculin (drl) gene that provides specific LPM reporter activity from early gastrulation. In toto live imaging and lineage tracing of drl-based reporters captured the dynamic LPM emergence as lineage-restricted mesendoderm field. The drl pan-LPM enhancer responds to the transcription factors EomesoderminA, FoxH1, and MixL1 that combined with Smad activity drive LPM emergence. We uncovered specific drl reporter activity in LPM-corresponding territories of several chordates including chicken, axolotl, lamprey, Ciona, and amphioxus, revealing a universal upstream LPM program. Altogether, our work provides a mechanistic framework for LPM emergence as defined progenitor field, possibly representing an ancient mesodermal cell state that predates the primordial vertebrate embryo.

75: Unlimited genetic switches for cell-type specific manipulation
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Posted to bioRxiv 14 Nov 2018

Unlimited genetic switches for cell-type specific manipulation
1,500 downloads developmental biology

Jorge Garcia-Marques, Ching-Po Yang, Isabel Espinosa-Medina, Kent Mok, Minoru Koyama, Ying-Jou Lee

Gaining independent genetic access to discrete cell types is critical to interrogate their biological functions, as well as to deliver precise gene therapy. Transcriptome analyses have allowed us to profile cell populations with extraordinary precision, revealing that cell types are typically defined by a unique combination of genetic markers. Given the lack of adequate tools to target cell types based on multiple markers, most cell types have remained inaccessible to genetic manipulation. Here, we present CaSSA, a platform to create unlimited genetic switches based on CRISPR/Cas9 (Ca) and the DNA repair mechanism known as single-strand annealing (SSA). CaSSA allows engineering of independent genetic switches that each respond to a specific gRNA. Expressing multiple gRNAs in specific patterns enables multiplex cell type-specific manipulations and combinatorial genetic targeting. CaSSA is thus a new genetic tool that conceptually works as an unlimited number of recombinases and will facilitate genetic access to cell types in diverse organisms.

76: Genome And Epigenome Engineering CRISPR Toolkit For Probing In Vivo cis-Regulatory Interactions In The Chicken Embryo
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Posted to bioRxiv 08 May 2017

Genome And Epigenome Engineering CRISPR Toolkit For Probing In Vivo cis-Regulatory Interactions In The Chicken Embryo
1,494 downloads developmental biology

Ruth M Williams, Upeka Senanayake, Mara Artibani, Gunes Taylor, Daniel Wells, Ahmed Ashour Ahmed, Tatjana Sauka-Spengler

CRISPR-Cas9 genome engineering has revolutionised all aspects of biological research, with epigenome engineering transforming gene regulation studies. Here, we present a highly efficient toolkit enabling genome and epigenome engineering in the chicken embryo, and demonstrate its utility by probing gene regulatory interactions mediated by neural crest enhancers. First, we optimise efficient guide-RNA expression from novel chick U6-mini-vectors, provide a strategy for rapid somatic gene knockout and establish protocol for evaluation of mutational penetrance by targeted next generation sequencing. We show that CRISPR/Cas9-mediated disruption of transcription factors causes a reduction in their cognate enhancer-driven reporter activity. Next, we assess endogenous enhancer function using both enhancer deletion and nuclease-deficient Cas9 (dCas9) effector fusions to modulate enhancer chromatin landscape, thus providing the first report of epigenome engineering in a developing embryo. Finally, we use the synergistic activation mediator (SAM) system to activate an endogenous target promoter. The novel genome and epigenome engineering toolkit developed here enables manipulation of endogenous gene expression and enhancer activity in chicken embryos, facilitating high-resolution analysis of gene regulatory interactions in vivo.

77: Establishment In Culture Of Expanded Potential Stem Cells
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Posted to bioRxiv 06 Apr 2017

Establishment In Culture Of Expanded Potential Stem Cells
1,493 downloads developmental biology

Jian Yang, David J. Ryan, Wei Wang, Jason Cheuk-Ho Tsang, Guocheng Lan, Hideki Masaki, Xuefei Gao, Liliana Antunes, Yong Yu, Zhexin Zhu, Juexuan Wang, Aleksandra A. Kolodziejczyk, Lia S Campos, Cui Wang, Fengtang Yang, Zhen Zhong, Beiyuan Fu, Melanie Eckersley-Maslin, Michael Woods, Yosuke Tanaka, Adam C. Wilkinson, James Bussell, Jacqui White, Ramiro Ramirez-Solis, Wolf Reik, Berthold Göttgens, Sarah A. Teichmann, Hiromitsu Nakauchi, Xiangang Zou, Liming Lu, Pentao Liu

Mouse embryonic stem cells are derived from in vitro explantation of blastocyst epiblasts and contribute to both the somatic lineage and germline when returned to the blastocyst but are normally excluded from the trophoblast lineage and primitive endoderm. Here, we report that cultures of expanded potential stem cells (EPSCs) can be established from individual blastomeres, by direct conversion of mouse embryonic stem cells (ESCs) and by genetically reprogramming somatic cells. Remarkably, a single EPSC contributes to the embryo proper and placenta trophoblasts in chimeras. Critically, culturing EPSCs in a trophoblast stem cell (TSC) culture condition permits direct establishment of TSC lines without genetic modification. Molecular analyses including single cell RNA-seq reveal that EPSCs share cardinal pluripotency features with ESCs but have an enriched blastomere transcriptomic signature and a dynamic DNA methylome. These proof-of-concept results open up the possibility of establishing cultures of similar stem cells in other mammalian species.

78: Single cell epigenomic atlas of the developing human brain and organoids
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Posted to bioRxiv 31 Dec 2019

Single cell epigenomic atlas of the developing human brain and organoids
1,488 downloads developmental biology

Ryan S Ziffra, Chang N Kim, Amy Wilfert, Tychele N. Turner, Maximilian Haeussler, Alex M Casella, Pawel F Przytycki, Anat Kreimer, Katherine S. Pollard, Seth A Ament, Evan E. Eichler, Nadav Ahituv, Tomasz J. Nowakowski

Dynamic changes in chromatin accessibility coincide with important aspects of neuronal differentiation, such as fate specification and arealization and confer cell type-specific associations to neurodevelopmental disorders. However, studies of the epigenomic landscape of the developing human brain have yet to be performed at single-cell resolution. Here, we profiled chromatin accessibility of >75,000 cells from eight distinct areas of developing human forebrain using single cell ATAC-seq (scATACseq). We identified thousands of loci that undergo extensive cell type-specific changes in accessibility during corticogenesis. Chromatin state profiling also reveals novel distinctions between neural progenitor cells from different cortical areas not seen in transcriptomic profiles and suggests a role for retinoic acid signaling in cortical arealization. Comparison of the cell type-specific chromatin landscape of cerebral organoids to primary developing cortex found that organoids establish broad cell type-specific enhancer accessibility patterns similar to the developing cortex, but lack many putative regulatory elements identified in homologous primary cell types. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

79: A high-resolution mRNA expression time course of embryonic development in zebrafish
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Posted to bioRxiv 10 Feb 2017

A high-resolution mRNA expression time course of embryonic development in zebrafish
1,484 downloads developmental biology

Richard J. White, John E Collins, Ian M. Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek Stemple, Daniel N Murphy, Thibaut Hourlier, Anja Füllgrabe, Matthew P. Davis, Anton J. Enright, Elisabeth M. Busch-Nentwich

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1-cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise the temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5,024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. The data reveal complex and widespread differential use of exons and previously unidentified 3′ ends across development, new primary microRNA transcripts and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data are accessible to browse and download at Expression Atlas and Ensembl.

80: A Transcriptional Lineage of the Early C. elegans Embryo
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Posted to bioRxiv 08 Apr 2016

A Transcriptional Lineage of the Early C. elegans Embryo
1,476 downloads developmental biology

Sophia C Tintori, Erin Osborne Nishimura, Patrick Golden, Jason D Lieb, Bob Goldstein

During embryonic development, cells must establish fates, morphologies and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell's fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify the abundance of every mRNA transcript in each cell of the C. elegans embryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify critical developmental genes previously unappreciated because of their partial redundancy. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fates of each cell, describes at a cellular resolution the mRNA landscape that guides development.

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