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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 220,095 papers from 870,669 authors.

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in category developmental biology

5,521 results found. For more information, click each entry to expand.

1: Reversing age: dual species measurement of epigenetic age with a single clock
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Posted 08 May 2020

Reversing age: dual species measurement of epigenetic age with a single clock
110,810 downloads bioRxiv developmental biology

Steve Horvath, Kavita Singh, Ken Raj, Shraddha Khairnar, Akshay Sanghavi, Agnivesh Shrivastava, Joseph Z Zoller, Caesar Z Li, Claudia B. Herenu, Martina Canatelli-Mallat, Marianne Lehmann, Leah C Solberg Woods, Angel Garcia Martinez, Tengfei Wang, Priscila Chiavellini, Andrew J. Levine, Hao Chen, Rodolfo G Goya, Harold L Katcher

Young blood plasma is known to confer beneficial effects on various organs in mice. However, it was not known whether young plasma rejuvenates cells and tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly-accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n=593 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain-, liver-, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n=850 human tissue samples to the training data. We employed these six clocks to investigate the rejuvenation effects of a plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers and behavioral responses to assess cognitive functions. Cellular senescence, which is not associated with epigenetic aging, was also considerably reduced in vital organs. Overall, this study demonstrates that a plasma-derived treatment markedly reverses aging according to epigenetic clocks and benchmark biomarkers of aging. ### Competing Interest Statement Several authors are founders, owners, employees (Harold Katcher and Akshay Sanghavi) or consultants of Nugenics Research (Steve Horvath and Agnivesh Shrivastava) which plans to commercialize the "Elixir" treatment. Other authors (Kavita Singh, Shraddha Khairnar) received financial support from Nugenics Research. The other authors do not have conflict of interest.

2: A rat model of pregnancy in the male parabiont
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Posted 10 Jun 2021

A rat model of pregnancy in the male parabiont
21,636 downloads bioRxiv developmental biology

Rongjia Zhang, Yuhuan Liu

Male pregnancy is a unique phenomenon in syngnathidae which refers to the incubation of embryos or fetuses by males. However, whether male mammalian animals have the potential to conceive and maintain pregnancy remains unclear. Here, we constructed a rat model of male pregnancy by a four-step strategy: a heterosexual parabiotic pair was firstly produced by surgically joining a castrated male rat and a female rat. Uterus transplantation (UTx) was then performed on the male parabiont 8 weeks later. After recovery, blastocyst-stage embryos were transplanted to the grafted uterus of male parabiont and the native uterus of female parabiont. Caesarean section was performed at embryonic day (ED) 21.5. The success rate of modeling was only 3.68%, but 10 pups could still be delivered from male parabionts and developed. Our experiment reveals the possibility of normal embryonic development in male mammalian animals, and it may have a profound impact on reproductive biology. One-sentence summaryA rat model of male pregnancy can be constructed in four steps. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/447686v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1a0146aorg.highwire.dtl.DTLVardef@9c4329org.highwire.dtl.DTLVardef@fd652borg.highwire.dtl.DTLVardef@1fd0120_HPS_FORMAT_FIGEXP M_FIG C_FIG

3: Microtubules promote intercellular contractile force transmission during tissue folding
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Posted 04 Feb 2019

Microtubules promote intercellular contractile force transmission during tissue folding
9,889 downloads bioRxiv developmental biology

Clint S. Ko, Vardges Tserunyan, Adam C Martin

During development, forces transmitted between cells are critical for sculpting epithelial tissues. Actomyosin contractility in the middle of the cell apex (medioapical) can change cell shape (e.g., apical constriction), but can also result in force transmission between cells via attachments to adherens junctions. How actomyosin networks maintain attachments to adherens junctions under tension is poorly understood. Here, we discovered that microtubules promote actomyosin intercellular attachments in epithelia during Drosophila mesoderm invagination. First, we used live imaging to show a novel arrangement of the microtubule cytoskeleton during apical constriction: medioapical Patronin (CAMSAP) foci formed by actomyosin contraction organized an apical non-centrosomal microtubule network. Microtubules were required for mesoderm invagination but were not necessary for initiating apical contractility or adherens junction assembly. Instead, microtubules promoted connections between medioapical actomyosin and adherens junctions. These results delineate a role for coordination between actin and microtubule cytoskeletal systems in intercellular force transmission during tissue morphogenesis.

4: Molecular architecture of the developing mouse brain
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Posted 03 Jul 2020

Molecular architecture of the developing mouse brain
9,712 downloads bioRxiv developmental biology

Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Christoffer Mattsson Langseth, Irina Khven, Anna Johnsson, Mats Nilsson, Peter Lönnerberg, Sten Linnarsson

The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions, and intrinsic genetic programs that result in the generation of likely more than a thousand distinct cell types. Therefore, a complete understanding of mammalian brain development requires systematic mapping of cell states covering the entire relevant spatiotemporal range. Here we report a comprehensive single-cell transcriptome atlas of mouse brain development spanning from gastrulation to birth. We identified almost a thousand distinct cellular states, including the initial emergence of the neuroepithelium, a rich set of region-specific secondary organizers and a complete developmental program for the functional elements of the brain and its enclosing membranes. We used the atlas to directly test the hypothesis that human glioblastoma reflects a return to a developmental cell state. In agreement, most aneuploid tumor cells matched embryonic rather than adult types, while karyotypically normal cells predominantly matched adult immune cell types. ### Competing Interest Statement The authors have declared no competing interest.

5: The Spatio-Temporal Control of Zygotic Genome Activation
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Posted 06 Dec 2018

The Spatio-Temporal Control of Zygotic Genome Activation
9,678 downloads bioRxiv developmental biology

George E. Gentsch, Nick D L Owens, James C Smith

One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the mid-blastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation, and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal and BMP signaling together generate most of the spatio-temporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.

6: Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development
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Posted 21 Jul 2017

Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development
9,498 downloads bioRxiv developmental biology

Andrey Vyshedskiy, Mahapatra Shreyas, Rita Dunn

We analyzed all published reports of individuals not exposed to syntactic language until puberty: two feral children, who grew up without hearing any language, and eight deaf linguistic isolates, who grew up communicating to their families using homesign or kitchensign, a system of gestures which allows them to communicate simple commands but lacks much in the way of syntax. A common observation in these individuals is the lifelong difficulty understanding syntax and spatial prepositions, even after many years of rehabilitation. This debilitating condition stands in stark contrast to linguistic isolates' performance on memory as well as semantic tests: they could easily remember hundreds of newly learned words and identify previously seen objects by name. The lack of syntactic language comprehension in linguistic isolates may stem from inability to understand words and/or grammar or inability to mentally synthesize known objects into novel configurations. We have previously shown that purposeful construction of novel mental images is the function of the lateral prefrontal cortex (LPFC) ability to dynamically control posterior cortex neurons [1]. Here we have ranked all tests performed on linguistic isolates by their reliance on the LPFC control of the posterior cortex: a) the amount of posterior cortex territory that needs to be recruited by the LPFC and b) the number of disparate objects that have to be combined together by the LPFC in order to answer the test question. According to our analysis, linguistic isolates performed well in all tests that did not involve the LPFC control of the posterior cortex, showed decreasing scores in tests that involved greater recruitment of the posterior cortex by the LPFC, and failed in tests that involved greatest recruitment of posterior cortex necessary for mental synthesis of multiple objects. This pattern is consistent with inadequate frontoposterior connections in linguistic isolates. We discuss implications of these findings for the importance of early syntactic language exposure in formation of frontoposterior connections.

7: Altering the temporal regulation of one transcription factor drives sensory trade-offs
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Posted 15 Jun 2018

Altering the temporal regulation of one transcription factor drives sensory trade-offs
9,279 downloads bioRxiv developmental biology

Ariane Ramaekers, Simon Weinberger, Annelies Claeys, Martin Kapun, Jiekun Yan, Reinhard Wolf, Thomas Flatt, Erich Buchner, Bassem A Hassan

Size trade-offs of visual versus olfactory organs is a pervasive feature of animal evolution. Comparing Drosophila species, we find that larger eyes correlate with smaller antennae, where olfactory organs reside, and narrower faces. We demonstrate that this trade-off arises through differential subdivision of the head primordium into visual versus non-visual fields. Specification of the visual field requires a highly-conserved eye development gene called eyeless in flies and Pax6 in humans. We discover that changes in the temporal regulation of eyeless expression during development is a conserved mechanism for sensory trade-offs within and between Drosophila species. We identify a natural single nucleotide polymorphism in the cis-regulatory region of eyeless that is sufficient to alter its temporal regulation and eye size. Because Pax6 is a conserved regulator of sensory placode subdivision, we propose that alterations in the mutual repression between sensory territories is a conserved mechanism for sensory trade-offs in animals.

8: Distinct RhoGEFs activate apical and junctional actomyosin contractility under control of G proteins during epithelial morphogenesis
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Posted 04 Mar 2019

Distinct RhoGEFs activate apical and junctional actomyosin contractility under control of G proteins during epithelial morphogenesis
9,175 downloads bioRxiv developmental biology

Alain Garcia De Las Bayonas, Jean-Marc Philippe, Annemarie C. Lellouch, Thomas Lecuit

Small RhoGTPases and Myosin-II direct cell shape changes and movements during tissue morphogenesis. Their activities are tightly regulated in space and time to specify the desired pattern of contractility that supports tissue morphogenesis. This is expected to stem from polarized surface stimuli and from polarized signaling processing inside cells. We examined this general problem in the context of cell intercalation that drives extension of the Drosophila ectoderm. In the ectoderm, G protein coupled receptors (GPCRs) and their downstream heterotrimeric G proteins (Gα and Gβγ) activate Rho1 both medial-apically, where it exhibits pulsed dynamics, and at junctions, where its activity is planar polarized (Kerridge et al., 2016; Munjal et al., 2015). However, the mechanisms responsible for polarizing Rho1 activity are unclear. In particular, it is unknown how Rho1 activity is controlled at junctions. We report a division of labor in the mechanisms of Rho1 activation in that distinct guanine exchange factors (GEFs), that serve as activators of Rho1, operate in these distinct cellular compartments. RhoGEF2 acts uniquely to activate medial-apical Rho1. Although RhoGEF2 is recruited both medial-apically and at junctions by Gα12/13-GTP, also called Concertina (Cta) in Drosophila, its activity is restricted to the medial-apical compartment. Furthermore, we characterize a novel RhoGEF, p114RhoGEF/Wireless (Wrl), and report its requirement for cell intercalation in the extending ectoderm. p114RhoGEF/Wireless activates Rho1 specifically at junctions. Strikingly it is restricted to adherens junctions and is under Gβ13F/Gγ1 control. Gβ13F/Gγ1 activates junctional Rho1 and exerts quantitative control over planar polarization of Rho1. In particular, overexpression of Gβ13F/Gγ1 leads to hyper planar polarization of Rho1 and MyoII. Finally, we found that p114RhoGEF/Wireless is absent in the mesoderm, arguing for a tissue-specific control over junctional Rho1 activity. These results shed light on the mechanisms of polarization of Rho1 activity in different cellular compartments and reveal that distinct GEFs are sensitive tuning parameters of cell contractility in remodeling epithelia.

9: Supercentenarians and remarkable age records exhibit patterns indicative of clerical errors and pension fraud
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Posted 16 Jul 2019

Supercentenarians and remarkable age records exhibit patterns indicative of clerical errors and pension fraud
9,091 downloads bioRxiv developmental biology

Saul Justin Newman

The observation of individuals attaining remarkable ages, and their concentration into geographic sub-regions or blue zones, has generated considerable scientific interest. Proposed drivers of remarkable longevity include high vegetable intake, strong social connections, and genetic markers. Here, we reveal new predictors of remarkable longevity and supercentenarian status. In the United States supercentenarian status is predicted by the absence of vital registration. In the UK, Italy, Japan, and France remarkable longevity is instead predicted by regional poverty, old-age poverty, material deprivation, low incomes, high crime rates, a remote region of birth, worse health, and fewer 90+ year old people. In addition, supercentenarian birthdates are concentrated on the first of the month and days divisible by five: patterns indicative of widespread fraud and error. As such, relative poverty and missing vital documents constitute unexpected predictors of centenarian and supercentenarian status, and support a primary role of fraud and error in generating remarkable human age records. ### Competing Interest Statement The authors have declared no competing interest.

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

Single cell epigenomic atlas of the developing human brain and organoids
8,264 downloads bioRxiv developmental biology

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

11: Hair regeneration by small molecules that activate autophagy
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Posted 18 Apr 2018

Hair regeneration by small molecules that activate autophagy
7,602 downloads bioRxiv developmental biology

Min Chai, Meisheng Jiang, Laurent Vergnes, Xudong Fu, Stéphanie C. de Barros, Jing Jiao, Harvey R Herschman, Gay M Crooks, Karen Reue, Jing Huang

Hair plays important roles, ranging from the conservation of body heat to the preservation of psychological well-being. Hair loss or alopecia affects millions worldwide and can occur because of aging, hormonal dysfunction, autoimmunity, or as a side effect of cancer treatment (Gilhar et al., 2012; Petukhova et al., 2010). Methods that can be used to regrow hair are highly sought after, but lacking. Here we report that hair regeneration can be stimulated by small molecules that activate autophagy, including the longevity metabolites α-ketoglutarate and α-ketobutyrate, and the prescription drugs rapamycin and metformin which impinge on TOR and AMPK signaling.

12: Universal DNA methylation age across mammalian tissues
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Posted 19 Jan 2021

Universal DNA methylation age across mammalian tissues
7,347 downloads bioRxiv developmental biology

Ake T Lu, Zhe Fei, Amin Haghani, Todd R. Robeck, Joseph A Zoller, Caesar Z Li, Robert Lowe, Qi Yan, Joshua Zhang, Ha T. H. Vu, Julia Ableava, Victoria A. Acosta-Rodriguez, Danielle M Adams, Javier Almunia, Ajoy Aloysius, Reza Ardehali, Adriana Arneson, C. Scott Baker, Gareth Banks, Katherine Belov, Nigel C. Bennett, Pete Black, Daniel T Blumstein, Eleanor K. Bors, Charles E. Breeze, Robert T. Brooke, Janine L. Brown, Gerald Carter, Alex Caulton, Julie M. Cavin, Lisa Chakrabarti, Ioulia Chatzistamou, Hao Chen, Kaiyang Cheng, Priscila Chiavellini, Oi-Wa Choi, Shannon Clarke, Lisa Noelle Cooper, Marie-Laurence Cossette, Joanna Day, Joseph DeYoung, Stacy DiRocco, Christopher Dold, Erin E. Ehmke, Candice K. Emmons, Stephan Emmrich, Ebru Erbay, Claire Erlacher-Reid, Chris G. Faulkes, Steven H. Ferguson, Carrie Finno, Jennifer E. Flower, Jean-Michel Gaillard, Eva Garde, Livia Gerber, Vadim N Gladyshev, Vera Gorbunova, Rodolfo G Goya, Matthew J Grant, Carla B. Green, Erin N. Hales, M. Bradley Hanson, Daniel W Hart, Martin Haulena, Kelsey Herrick, Andrew N. Hogan, Carolyn J Hogg, Timothy A Hore, Taosheng Huang, Juan Carlos Izpisua Belmonte, Anna J. Jasinska, Gareth Jones, Eve Jourdain, Olga Kashpur, Harold Katcher, Etsuko Katsumata, Vimala Kaza, Hippokratis Kiaris, Michael S. Kobor, Pawel Kordowitzki, William R. Koski, Michael Kruetzen, Soo Bin Kwon, Brenda Larison, Sang-Goo Lee, Marianne Lehmann, Jean-Francois Lemaitre, Andrew J. Levine, Cun Li, Xinmin Li, Andrea R. Lim, David TS Lin, Dana M. Lindemann, Thomas J. Little, Nicholas Macoretta, Dewey Maddox, Craig O. Matkin, Julie A. Mattison, Matthew McClure, June Mergl, Jennifer J. Meudt, Gisele A. Montano, Khyobeni Mozhui, Jason Munshi-South, Asieh Naderi, Martina Nagy, Pritika Narayan, Peter W. Nathanielsz, Ngoc B. Nguyen, Christof Niehrs, Justine K. O'Brien, Perrie O'Tierney Ginn, Duncan T Odom, Alexander G Ophir, Steve Osborn, Elaine A. Ostrander, Kim M. Parsons, Kimberly C Paul, Matteo Pellegrini, Katharina J. Peters, Amy B. Pedersen, Jessica L. Petersen, Darren W. Pietersen, Gabriela M. Pinho, Jocelyn Plassais, Jesse R. Poganik, Natalia A. Prado, Pradeep Reddy, Benjamin Rey, Beate R. Ritz, Jooke Robbins, Magdalena Rodriguez, Jennifer Russell, Elena Rydkina, Lindsay L. Sailer, Adam B Salmon, Akshay Sanghavi, Kyle M. Schachtschneider, Dennis Schmitt, Todd Schmitt, Lars Schomacher, Lawrence B Schook, Karen E Sears, Ashley W. Seifert, Andrei Seluanov, Aaron BA Shafer, Dhanansayan Shanmuganayagam, Anastasia V. Shindyapina, Melanie Simmons, Kavita Singh, Ishani Sinha, Jesse Slone, Russel G. Snell, Elham Soltanmaohammadi, Matthew L. Spangler, Maria C. Spriggs, Lydia Staggs, Nancy Stedman, Karen J. Steinman, Donald T. Stewart, Victoria J Sugrue, Balazs Szladovits, Joseph S. Takahashi, Masaki Takasugi, Emma C. Teeling, Michael J. Thompson, Bill Van Bonn, Sonja C. Vernes, Diego Villar Lozano, Harry V. Vinters, Mary C. Wallingford, Nan Wang, Robert K. Wayne, Gerald S. Wilkinson, Christopher K. Williams, Robert W Williams, X. William Yang, Mingjia Yao, Brent G. Young, Bohan Zhang, Zhihui Zhang, Peng Zhao, Yang Zhao, Wanding Zhou, Joerg Zimmermann, Jason Ernst, Ken Raj, Steve Horvath

Aging is often perceived as a degenerative process resulting from random accrual of cellular damage over time. Despite this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, we hypothesized that one can build pan-mammalian clocks that measure age in all mammalian species. To address this, we generated data using 11,754 methylation arrays, each profiling up to 36 thousand cytosines in highly-conserved stretches of DNA, from 59 tissue-types derived from 185 mammalian species. From these methylation profiles, we constructed three age predictors, each with a single mathematical formula, termed universal pan-mammalian clocks that are accurate in estimating the age (r>0.96) of any mammalian tissue. Deviations between epigenetic age and chronological age relate to mortality risk in humans, mutations that affect the somatotropic axis in mice, and caloric restriction. We characterized specific cytosines, whose methylation levels change with age across most mammalian species. These cytosines are greatly enriched in polycomb repressive complex 2-binding sites, are located in regions that gradually lose chromatin accessibility with age and are proximal to genes that play a role in mammalian development, cancer, human obesity, and human longevity. Collectively, these results support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new compelling evidence.

13: Lineage recording reveals dynamics of cerebral organoid regionalization
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Posted 20 Jun 2020

Lineage recording reveals dynamics of cerebral organoid regionalization
7,282 downloads bioRxiv developmental biology

Zhisong He, Tobias Gerber, Ashley Maynard, Akanksha Jain, Rebecca Petri, Malgorzata Santel, Kevin Ly, Leila Sidow, Fátima Sanchís-Calleja, Stephan Riesenberg, J. Gray Camp, Barbara Treutlein

Diverse regions develop within cerebral organoids generated from human induced pluripotent stem cells (iPSCs), however it has been a challenge to understand the lineage dynamics associated with brain regionalization. Here we establish an inducible lineage recording system that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze lineage relationships during cerebral organoid development. We infer fate-mapped whole organoid phylogenies over a scarring time course, and reconstruct progenitor-neuron lineage trees within microdissected cerebral organoid regions. We observe increased fate restriction over time, and find that iPSC clones used to initiate organoids tend to accumulate in distinct brain regions. We use lineage-coupled spatial transcriptomics to resolve lineage locations as well as confirm clonal enrichment in distinctly patterned brain regions. Using long term 4-D light sheet microscopy to temporally track nuclei in developing cerebral organoids, we link brain region clone enrichment to positions in the neuroectoderm, followed by local proliferation with limited migration during neuroepithelial formation. Our data sheds light on how lineages are established during brain organoid regionalization, and our techniques can be adapted in any iPSC-derived cell culture system to dissect lineage alterations during perturbation or in patient-specific models of disease. ### Competing Interest Statement The authors have declared no competing interest.

14: Combined single-cell and spatial transcriptomics reveals the molecular, cellular and spatial bone marrow niche organization
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Posted 30 Jul 2019

Combined single-cell and spatial transcriptomics reveals the molecular, cellular and spatial bone marrow niche organization
7,046 downloads bioRxiv developmental biology

Chiara Baccin, Jude Al-Sabah, Lars Velten, Patrick M. Helbling, Florian Grünschläger, Pablo Hernández-Malmierca, Cesar Nombela-Arrieta, Lars M. Steinmetz, Andreas Trumpp, Simon Haas

The bone marrow (BM) constitutes the primary site for life-long blood production and skeletal regeneration. However, its cellular composition and the spatial organization into distinct niches remains controversial. Here, we combine single-cell and spatially resolved transcriptomics to systematically map the molecular and cellular composition of the endosteal, sinusoidal, and arteriolar BM niches. This allowed us to transcriptionally profile all major BM resident cell types, determine their localization, and clarify the cellular and spatial sources of key growth factors and cytokines. Our data demonstrate that previously unrecognized Cxcl12-abundant reticular (CAR) cell subsets (i.e. Adipo- and Osteo- CAR cells) differentially localize to sinusoidal or arteriolar surfaces, locally act as professional cytokine secreting cells, and thereby establish distinct peri-vascular micro-niches. Importantly, we also demonstrate that the 3-dimensional organization of the BM can be accurately inferred from single-cell gene expression data using the newly developed RNA-Magnet algorithm. Together, our study reveals the cellular and spatial organization of BM niches, and offers a novel strategy to dissect the complex organization of whole organs in a systematic manner.

15: A spatially resolved single cell atlas of human gastrulation
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Posted 21 Jul 2020

A spatially resolved single cell atlas of human gastrulation
6,936 downloads bioRxiv developmental biology

Richard C.V. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas

Gastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro. ### Competing Interest Statement The authors have declared no competing interest.

16: Dynamic stem cell states: naive to primed pluripotency in rodents and humans
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Posted 06 Nov 2015

Dynamic stem cell states: naive to primed pluripotency in rodents and humans
6,865 downloads bioRxiv developmental biology

Leehee Weinberger, Muneef Ayyash, Noa Novershtern, Jacob H. Hanna

The molecular mechanisms and signalling pathways that regulate the in vitro preservation of distinct pluripotent stem cell configurations, and their induction in somatic cells via direct reprogramming approaches, continue to constitute a highly exciting area of research. In this review, we provide an integrative synthesis on recent discoveries related to isolating unique naive and primed pluripotent stem cell states with altered functional and molecular characteristics, and from different species. We overview pathways underlying pluripotent state transitions and interconversion in vitro and in vivo. We conclude by highlighting unresolved key questions, future directions and potential novel applications of such dynamic pluripotent cell states.

17: Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification
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Posted 13 Jan 2019

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification
6,642 downloads bioRxiv developmental biology

Ricard Argelaguet, Hisham Mohammed, Stephen J Clark, L Carine Stapel, Christel Krueger, Chantriolnt-Andreas Kapourani, Yunlong Xiang, Courtney Hanna, Sebastien Smallwood, Ximena Ibarra-Soria, Florian Buettner, Guido Sanguinetti, Felix Krueger, Wei Xie, Peter Rugg-Gunn, Gavin Kelsey, Wendy Dean, Jennifer Nichols, Oliver Stegle, John Marioni, Wolf Reik

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.

18: High-Resolution, Large Imaging Volume, and Multi-View Single Objective Light-Sheet Microscopy
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Posted 24 Sep 2020

High-Resolution, Large Imaging Volume, and Multi-View Single Objective Light-Sheet Microscopy
5,895 downloads bioRxiv developmental biology

Bin Yang, Merlin Lange, Alfred Millett-Sikking, Ahmet Can Solak, Shruthi VijayKumar, Wanpeng Wang, Hirofumi Kobayashi, Matthew McCarroll, Lachlan Whitehead, Reto Paul Fiolka, Tom B. Kornberg, Andrew York, Loic Alain Royer

Recent developments in Oblique Plane Microscopy (OPM) have shown that it can achieve high spatio-temporal resolution. Here we describe a single objective light-sheet microscope based on oblique plane illumination that achieves: (i) large field of view and high-resolution imaging via a custom remote focusing objective; (ii) fast volumetric imaging by means of light-sheet stabilised stage scanning - a novel scanning modality that extends the imaging volume without compromising imaging speed nor quality; (iii) multi-view imaging by alternating the orientation of light-sheet illumination and detection to improve the image quality on large samples; (iv) simpler design and ergonomics by remote placement of coverslips to allow inverted imaging, enabling imaging across scales in a high-throughput format. Overall, we achieved a resolution of 450nm laterally and 2m axially and a field of view of 3000m x 800m x 300m. We demonstrate the speed, field of view, resolution and versatility of our novel instrument by imaging various systems, including zebrafish whole brain activity, Drosophila egg chamber development, and zebrafish development - up to nine embryos simultaneously.

19: Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust
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Posted 19 Mar 2018

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust
5,581 downloads bioRxiv developmental biology

Harry M.T. Choi, Maayan Schwarzkopf, Mark E. Fornace, Aneesh Acharya, Georgios Artavanis, Johannes Stegmaier, Alexandre Cunha, Niles A. Pierce

In situ hybridization based on the mechanism of hybridization chain reaction (HCR) has addressed multi-decade challenges to imaging mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution, and versatility. Here, with third-generation in situ HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind non-specifically within the sample they will not generate amplified background. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of higher signal-to-background with the convenience of using unoptimized probe sets for new targets and organisms. In situ HCR v3.0 enables multiplexed quantitative mRNA imaging with subcellular resolution in the anatomical context of whole-mount vertebrate embryos, multiplexed quantitative mRNA flow cytometry for high-throughput single-cell expression profiling, and multiplexed quantitative single-molecule mRNA imaging in thick autofluorescent samples.

20: Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos
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Posted 05 Jun 2020

Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos
5,386 downloads bioRxiv developmental biology

Gregorio Alanis-Lobato, Jasmin Zohren, Afshan McCarthy, Norah M. E. Fogarty, Nada Kubikova, Emily Hardman, Maria Greco, Dagan Wells, James Turner, Kathy Niakan

CRISPR-Cas9 genome editing is a promising technique for clinical applications, such as the correction of disease-associated alleles in somatic cells. The use of this approach has also been discussed in the context of heritable editing of the human germline. However, studies assessing gene correction in early human embryos report low efficiency of mutation repair, high rates of mosaicism and the possibility of unintended editing outcomes that may have pathologic consequences. We developed computational pipelines to assess single-cell genomics and transcriptomics datasets from OCT4 (POU5F1) CRISPR-Cas9-targeted and control human preimplantation embryos. This allowed us to evaluate on-target mutations that would be missed by more conventional genotyping techniques. We observed loss-of-heterozygosity in edited cells that spanned regions beyond the POU5F1 on-target locus, as well as segmental loss and gain of chromosome 6, on which the POU5F1 gene is located. Unintended genome editing outcomes were present in approximately 16% of the human embryo cells analysed and spanned 4 to 20kb. Our observations are consistent with recent findings indicating complexity at on-target sites following CRISPR-Cas9 genome editing. Our work underscores the importance of further basic research to assess the safety of genome editing techniques in human embryos, which will inform debates about the potential clinical use of this technology. ### Competing Interest Statement The authors have declared no competing interest.

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