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Flexibility And Constraint In Preimplantation Gene Regulation In Mouse, Colin C. Conine, Marina Krykbaeva, Lina Song, Robert C. Brewster, Nir Friedman, Oliver J. Rando 2020 University of Massachusetts Medical School

Flexibility And Constraint In Preimplantation Gene Regulation In Mouse, Colin C. Conine, Marina Krykbaeva, Lina Song, Robert C. Brewster, Nir Friedman, Oliver J. Rando

University of Massachusetts Medical School Faculty Publications

Although many features of embryonic development exhibit remarkable stability in the face of environmental perturbations, it is also clear that some aspects of early embryogenesis can be modulated by non-genetic influences during and after fertilization. Among potential perturbations experienced during reproduction, understanding the consequences of differing ex vivo fertilization methods at a molecular level is imperative for comprehending both the basic biology of early development and the potential consequences of assisted reproduction. Here, we set out to explore stable and flexible aspects of preimplantation gene expression using single-embryo RNA-sequencing of mouse embryos fertilized by natural mating, in vitro fertilization, or ...


Regulation Of Zebrafish Melanocyte Development By Ligand-Dependent Bmp Signaling, Alec Gramann, Arvind M. Venkatesan, Melissa Guerin, Craig J. Ceol 2019 University of Massachusetts Medical School

Regulation Of Zebrafish Melanocyte Development By Ligand-Dependent Bmp Signaling, Alec Gramann, Arvind M. Venkatesan, Melissa Guerin, Craig J. Ceol

Open Access Articles

Preventing terminal differentiation is important in the development and progression of many cancers including melanoma. Recent identification of the BMP ligand GDF6 as a novel melanoma oncogene showed GDF6-activated BMP signaling suppresses differentiation of melanoma cells. Previous studies have identified roles for GDF6 orthologs during early embryonic and neural crest development, but have not identified direct regulation of melanocyte development by GDF6. Here, we investigate the BMP ligand gdf6a, a zebrafish ortholog of human GDF6, during the development of melanocytes from the neural crest. We establish that the loss of gdf6a or inhibition of BMP signaling during neural crest development ...


The Genome-Wide Multi-Layered Architecture Of Chromosome Pairing In Early Drosophila Embryos, Jelena Erceg, Jumana AlHaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. McCole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, C-Ting Wu 2019 Harvard Medical School

The Genome-Wide Multi-Layered Architecture Of Chromosome Pairing In Early Drosophila Embryos, Jelena Erceg, Jumana Alhaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. Mccole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, C-Ting Wu

Program in Systems Biology Publications

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a ...


Integrins Have Cell-Type-Specific Roles In The Development Of Motor Neuron Connectivity, Devyn Oliver, Emily Norman, Heather Bates, Rachel Avard, Monika Rettler, Claire Y. Benard, Michael M. Francis, Michele L. Lemons 2019 University of Massachusetts Medical School

Integrins Have Cell-Type-Specific Roles In The Development Of Motor Neuron Connectivity, Devyn Oliver, Emily Norman, Heather Bates, Rachel Avard, Monika Rettler, Claire Y. Benard, Michael M. Francis, Michele L. Lemons

Open Access Articles

Formation of the nervous system requires a complex series of events including proper extension and guidance of neuronal axons and dendrites. Here we investigate the requirement for integrins, a class of transmembrane cell adhesion receptors, in regulating these processes across classes of C. elegans motor neurons. We show alpha integrin/ina-1 is expressed by both GABAergic and cholinergic motor neurons. Despite this, our analysis of hypomorphic ina-1(gm144) mutants indicates preferential involvement of alpha integrin/ina-1 in GABAergic commissural development, without obvious involvement in cholinergic commissural development. The defects in GABAergic commissures of ina-1(gm144) mutants included both premature termination ...


Pax9 Is Required For Cardiovascular Development And Interacts With Tbx1 In The Pharyngeal Endoderm To Control 4(Th) Pharyngeal Arch Artery Morphogenesis, Helen M. Phillips, Rene Maehr, Simon D. Bamforth 2019 Newcastle University

Pax9 Is Required For Cardiovascular Development And Interacts With Tbx1 In The Pharyngeal Endoderm To Control 4(Th) Pharyngeal Arch Artery Morphogenesis, Helen M. Phillips, Rene Maehr, Simon D. Bamforth

Open Access Articles

Developmental defects affecting the heart and aortic arch arteries are a significant phenotype observed in 22q11 deletion syndrome patients and are caused by a microdeletion on chromosome 22q11. TBX1, one of the deleted genes, is expressed throughout the pharyngeal arches and is considered a key gene, when mutated, for the arch artery defects. Pax9 is expressed in the pharyngeal endoderm and is downregulated in Tbx1 mutant mice. We show here that Pax9 deficient mice are born with complex cardiovascular malformations affecting the outflow tract and aortic arch arteries with failure of the 3(rd) and 4(th) pharyngeal arch arteries ...


Distinct Features Of Nucleolus-Associated Domains In Mouse Embryonic Stem Cells, Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman 2019 University of Massachusetts Medical School

Distinct Features Of Nucleolus-Associated Domains In Mouse Embryonic Stem Cells, Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman

University of Massachusetts Medical School Faculty Publications

Background Heterochromatin in eukaryotic interphase cells frequently localizes to the nucleolar periphery (nucleolus-associated domains, NADs) and the nuclear lamina (lamina-associated domains, LADs). Gene expression in somatic cell NADs is generally low, but NADs have not been characterized in mammalian stem cells.

Results Here, we generated the first genome-wide map of NADs in mouse embryonic stem cells (mESCs) via deep sequencing of chromatin associated with biochemically-purified nucleoli. As we had observed in mouse embryonic fibroblasts (MEFs), the large Type I subset of NADs overlaps with constitutive LADs and is enriched for features of constitutive heterochromatin, including late replication timing and low ...


Two Contrasting Classes Of Nucleolus-Associated Domains In Mouse Fibroblast Heterochromatin, Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Herve Pages, Haibo Liu, Lihua Julie Zhu, Paul D. Kaufman 2019 University of Massachusetts Medical School

Two Contrasting Classes Of Nucleolus-Associated Domains In Mouse Fibroblast Heterochromatin, Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Herve Pages, Haibo Liu, Lihua Julie Zhu, Paul D. Kaufman

Program in Molecular Medicine Publications

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, owing to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery and the ...


Tale And Nf-Y Co-Occupancy Marks Enhancers Of Developmental Control Genes During Zygotic Genome Activation In Zebrafish, William J. Stanney III, Franck Ladam, Ian J. Donaldson, Teagan J. Parsons, Rene Maehr, Nicoletta Bobola, Charles G. Sagerstrom 2019 University of Massachusetts Medical School

Tale And Nf-Y Co-Occupancy Marks Enhancers Of Developmental Control Genes During Zygotic Genome Activation In Zebrafish, William J. Stanney Iii, Franck Ladam, Ian J. Donaldson, Teagan J. Parsons, Rene Maehr, Nicoletta Bobola, Charles G. Sagerstrom

University of Massachusetts Medical School Faculty Publications

Animal embryogenesis is initiated by maternal factors, but zygotic genome activation (ZGA) shifts control to the embryo at early blastula stages. ZGA is thought to be mediated by specialized maternally deposited transcription factors (TFs), but here we demonstrate that NF-Y and TALE – TFs with known later roles in embryogenesis – co-occupy unique genomic elements at zebrafish ZGA. We show that these elements are selectively associated with early-expressed genes involved in transcriptional regulation and possess enhancer activity in vivo. In contrast, we find that elements individually occupied by either NF-Y or TALE are associated with genes acting later in development – such that ...


Rapid Irreversible Transcriptional Reprogramming In Human Stem Cells Accompanied By Discordance Between Replication Timing And Chromatin Compartment, Vishnu Dileep, Rachel Patton McCord, Job Dekker, David M. Gilbert 2019 Florida State University

Rapid Irreversible Transcriptional Reprogramming In Human Stem Cells Accompanied By Discordance Between Replication Timing And Chromatin Compartment, Vishnu Dileep, Rachel Patton Mccord, Job Dekker, David M. Gilbert

Open Access Articles

The temporal order of DNA replication is regulated during development and is highly correlated with gene expression, histone modifications and 3D genome architecture. We tracked changes in replication timing, gene expression, and chromatin conformation capture (Hi-C) A/B compartments over the first two cell cycles during differentiation of human embryonic stem cells to definitive endoderm. Remarkably, transcriptional programs were irreversibly reprogrammed within the first cell cycle and were largely but not universally coordinated with replication timing changes. Moreover, changes in A/B compartment and several histone modifications that normally correlate strongly with replication timing showed weak correlation during the early ...


Enhanced Cas12a Editing In Mammalian Cells And Zebrafish, Pengpeng Liu, Kevin Luk, Masahiro Shin, Feston Idrizi, Samantha F. Kwok, Benjamin P. Roscoe, Esther Mintzer, Sneha Suresh, Kyle Morrison, Josias B. Frazao, Mehmet Fatih Bolukbasi, Karthikeyan Ponnienselvan, Jeremy Luban, Lihua Julie Zhu, Nathan D. Lawson, Scot A. Wolfe 2019 University of Massachusetts Medical School

Enhanced Cas12a Editing In Mammalian Cells And Zebrafish, Pengpeng Liu, Kevin Luk, Masahiro Shin, Feston Idrizi, Samantha F. Kwok, Benjamin P. Roscoe, Esther Mintzer, Sneha Suresh, Kyle Morrison, Josias B. Frazao, Mehmet Fatih Bolukbasi, Karthikeyan Ponnienselvan, Jeremy Luban, Lihua Julie Zhu, Nathan D. Lawson, Scot A. Wolfe

Open Access Articles

Type V CRISPR-Cas12a systems provide an alternate nuclease platform to Cas9, with potential advantages for specific genome editing applications. Here we describe improvements to the Cas12a system that facilitate efficient targeted mutagenesis in mammalian cells and zebrafish embryos. We show that engineered variants of Cas12a with two different nuclear localization sequences (NLS) on the C terminus provide increased editing efficiency in mammalian cells. Additionally, we find that pre-crRNAs comprising a full-length direct repeat (full-DR-crRNA) sequence with specific stem-loop G-C base substitutions exhibit increased editing efficiencies compared with the standard mature crRNA framework. Finally, we demonstrate in zebrafish embryos that the ...


Defects In Fetal Mouth Movement And Pharyngeal Patterning Underlie Cleft Palate Caused By Retinoid Deficiency., Regina Friedl 2019 University of Louisville

Defects In Fetal Mouth Movement And Pharyngeal Patterning Underlie Cleft Palate Caused By Retinoid Deficiency., Regina Friedl

Electronic Theses and Dissertations

Cleft palate is a common birth defect. Etiologic mechanisms of palate cleft include defects in palate morphogenesis, mandibular growth, or spontaneous fetal mouth movement. Cleft palate linked to deficient fetal mouth movement has been demonstrated directly only in a single experimental model of loss of neurotransmission. Here, using retinoid deficient mouse embryos, we demonstrate directly for the first time that deficient fetal mouth movement and cleft palate occurs as a result of mis-patterned development of pharyngeal peripheral nerves and cartilages. Retinoid deficient embryos were generated by inactivation of retinol dehydrogenase 10 (Rdh10), which is critical for production of Retinoic Acid ...


Ouabain Enhances Cell-Cell Adhesion Mediated By Beta1 Subunits Of The Na(+),K(+)-Atpase In Cho Fibroblasts, Claudia Andrea Vilchis-Nestor, Maria Luisa Roldan, Angelina Leonardi, Juan G. Navea, Teresita Padilla-Benavides, Liora Shoshani 2019 University of Massachusetts Medical School

Ouabain Enhances Cell-Cell Adhesion Mediated By Beta1 Subunits Of The Na(+),K(+)-Atpase In Cho Fibroblasts, Claudia Andrea Vilchis-Nestor, Maria Luisa Roldan, Angelina Leonardi, Juan G. Navea, Teresita Padilla-Benavides, Liora Shoshani

Open Access Articles

Adhesion is a crucial characteristic of epithelial cells to form barriers to pathogens and toxic substances from the environment. Epithelial cells attach to each other using intercellular junctions on the lateral membrane, including tight and adherent junctions, as well as the Na(+),K(+)-ATPase. Our group has shown that non-adherent chinese hamster ovary (CHO) cells transfected with the canine beta1 subunit become adhesive, and those homotypic interactions amongst beta1 subunits of the Na(+),K(+)-ATPase occur between neighboring epithelial cells. Ouabain, a cardiotonic steroid, binds to the alpha subunit of the Na(+),K(+)-ATPase, inhibits the pump activity and induces ...


Single-Cell Rna-Sequencing-Based Crispri Screening Resolves Molecular Drivers Of Early Human Endoderm Development, Ryan M. Genga, Eric M. Kernfeld, Krishna M. Parsi, Teagan J. Parsons, Michael J. Ziller, Rene Maehr 2019 University of Massachusetts Medical School

Single-Cell Rna-Sequencing-Based Crispri Screening Resolves Molecular Drivers Of Early Human Endoderm Development, Ryan M. Genga, Eric M. Kernfeld, Krishna M. Parsi, Teagan J. Parsons, Michael J. Ziller, Rene Maehr

Open Access Articles

Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. However, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human embryonic stem cells (ESCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of ESCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following ...


Arterial Distribution Of The Human Aorta: An Examination Of The Evolutionary, Developmental, And Physiological Bases Of Asymmetry., Brandon Oddo, Cooker Storm 2019 Pepperdine University

Arterial Distribution Of The Human Aorta: An Examination Of The Evolutionary, Developmental, And Physiological Bases Of Asymmetry., Brandon Oddo, Cooker Storm

Seaver College Research And Scholarly Achievement Symposium

The study of anatomy contends that “form follows function”; a disciplinary theme purporting that anatomical structures (i.e., cells, tissues, and organs) have a shape that serves its proper function. With this in mind, it is unclear why human arterial distribution off the aortic arch is asymmetrical, while the corresponding venous anatomy is symmetrical. We investigated the evolutionary, developmental, and physiological bases for the asymmetry of aortic arch branches in humans. First, we investigated the cardiovascular anatomy of ancestral species to determine if, and at what level, anatomical divergence (from aortic symmetry to asymmetry) occurs. Second, we examined the formation ...


Entosis Controls A Developmental Cell Clearance In C. Elegans, Yongchan Lee, Jens C. Hamann, Mark Pellegrino, Joanne Durgan, Marie-Charlotte Domart, Lucy M. Collinson, Cole M. Haynes, Oliver Florey, Michael Overholtzer 2019 Sloan Kettering Institute for Cancer Research

Entosis Controls A Developmental Cell Clearance In C. Elegans, Yongchan Lee, Jens C. Hamann, Mark Pellegrino, Joanne Durgan, Marie-Charlotte Domart, Lucy M. Collinson, Cole M. Haynes, Oliver Florey, Michael Overholtzer

Open Access Articles

Metazoan cell death mechanisms are diverse and include numerous non-apoptotic programs. One program called entosis involves the invasion of live cells into their neighbors and is known to occur in cancers. Here, we identify a developmental function for entosis: to clear the male-specific linker cell in C. elegans. The linker cell leads migration to shape the gonad and is removed to facilitate fusion of the gonad to the cloaca. We find that the linker cell is cleared in a manner involving cell-cell adhesions and cell-autonomous control of uptake through linker cell actin. Linker cell entosis generates a lobe structure that ...


Complement Targets Newborn Retinal Ganglion Cells For Phagocytic Elimination By Microglia, Sarah R. Anderson, Jianmin Zhang, Michael R. Steele, Cesar O. Romero, Amanda G. Kautzman, Dorothy P. Schafer, Monica L. Vetter 2019 University of Utah

Complement Targets Newborn Retinal Ganglion Cells For Phagocytic Elimination By Microglia, Sarah R. Anderson, Jianmin Zhang, Michael R. Steele, Cesar O. Romero, Amanda G. Kautzman, Dorothy P. Schafer, Monica L. Vetter

Neurobiology Publications

Microglia play important roles in shaping the developing CNS, and at early stages they have been proposed to regulate progenitor proliferation, differentiation, and neuronal survival. However, these studies reveal contradictory outcomes, highlighting the complexity of these cell-cell interactions. Here, we investigate microglia function during embryonic mouse retina development, where only microglia, progenitors, and neurons are present. In both sexes, we determine that microglia primarily interact with retinal neurons and find that depletion of microglia via conditional KO of the Csf1 receptor results in increased density of retinal ganglion cells (RGCs). Pharmacological inhibition of microglia also results in an increase in ...


Receptor Interacting Protein Kinase 3 (Rip3) Regulates Ipscs Generation Through Modulating Cell Cycle Progression Genes, Ahmad Al-Moujahed, Bo Tian, Nikolaos E. Efstathiou, Eleni K. Konstantinou, Mien Hoang, Haijiang Lin, Joan W. Miller, Demetrios G. Vavvas 2019 Harvard Medical School

Receptor Interacting Protein Kinase 3 (Rip3) Regulates Ipscs Generation Through Modulating Cell Cycle Progression Genes, Ahmad Al-Moujahed, Bo Tian, Nikolaos E. Efstathiou, Eleni K. Konstantinou, Mien Hoang, Haijiang Lin, Joan W. Miller, Demetrios G. Vavvas

Open Access Articles

The molecular mechanisms involved in induced pluripotent stem cells (iPSCs) generation are poorly understood. The cell death machinery of apoptosis-inducing caspases have been shown to facilitate the process of iPSCs reprogramming. However, the effect of other cell death processes, such as programmed necrosis (necroptosis), on iPSCs induction has not been studied. In this study, we investigated the role of receptor-interacting protein kinase 3 (RIP3), an essential regulator of necroptosis, in reprogramming mouse embryonic fibroblast cells (MEFs) into iPSCs. RIP3 was found to be upregulated in iPSCs compared to MEFs. Deletion of RIP3 dramatically suppressed the reprogramming of iPSCs (~82%). RNA-seq ...


Spag17 Deficiency Impairs Neuronal Cell Differentiation In Developing Brain, Olivia J. Choi 2019 Virginia Commonwealth University

Spag17 Deficiency Impairs Neuronal Cell Differentiation In Developing Brain, Olivia J. Choi

Theses and Dissertations

The development of the nervous system is a multi-level, time-sensitive process that relies heavily on cell differentiation. However, the molecular mechanisms that control brain development remain poorly understood. We generated a knockout (KO) mouse for the cilia associated gene Spag17. These animals develop hydrocephalus and enlarged ventricles consistent with the role of Spag17 in the motility of ependymal cilia. However, other phenotypes that cannot be explained by this role were also present. Recently, a mutation in Spag17 has been associated with brain malformations and severe intellectual disability in humans. Therefore, we hypothesized that Spag17 plays a crucial role in nervous ...


Factors Affecting The Survival And Implantation Of Human Blastocysts Following Vitrification, Hamish Barblett 2019 Edith Cowan University

Factors Affecting The Survival And Implantation Of Human Blastocysts Following Vitrification, Hamish Barblett

Theses: Doctorates and Masters

The increased cell numbers, presence of the blastocoel and rapid cell re-organisation have required the development of specific survival criteria post warm to effectively select the most viable blastocyst for transfer. Pre-freeze blastocyst expansion and post warm re-expansion have been shown to contribute significantly to the chances of an implantation and subsequent live birth. The aim of this study was to explore factors that influence the outcome of blastocyst transfers after vitrification and warming, and hopefully improve outcomes by further applying improvements in future cycles. Variables from 8 years of vitrified/warmed blastocysts were retrospectively compiled and analysed to determine ...


Two Contrasting Classes Of Nucleolus-Associated Domains In Mouse Fibroblast Heterochromatin, Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Hervé Pagès, Haibo Liu, Lihua Julie Zhu, Paul D. Kaufman 2018 University of Massachusetts Medical School

Two Contrasting Classes Of Nucleolus-Associated Domains In Mouse Fibroblast Heterochromatin, Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Hervé Pagès, Haibo Liu, Lihua Julie Zhu, Paul D. Kaufman

University of Massachusetts Medical School Faculty Publications

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus Associated Domains (NADs) and Lamina Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, due to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery ...


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