Evx1 is required to regulate appropriate anterior-posterior patterning during murine gastrulation
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE75737 | GEO | 2016/05/26
SECONDARY ACCESSION(S): PRJNA305244
REPOSITORIES: GEO
Similar Datasets
Project description:We generated loss of function mESC clones by CRISPR-Cas9 to test whether Evx1as has a function beyond that of Evx1. Evx1/Evx1asΔ2.6kb (Del#3) mESCs were differentiated to D4 in serum and compared directly to Evx1Δfs mESCs
2016-05-26 | GSE75735 | GEO
Project description:Thousands of sense-antisense mRNA-lncRNA gene pairs occur in the mammalian genome. While there is usually little doubt about the function of the coding transcript, the function of the lncRNA partner is mostly untested. Here we examine the function of the homeotic Evx1-Evx1as gene locus. Expression is tightly co-regulated in posterior mesoderm of mouse embryos and in embryoid bodies. Expression of both genes is enhanced by BMP4 and WNT3A, and reduced by Activin. We generated a suite of deletions in the locus by CRISPR-Cas9 editing. We show EVX1 is a critical downstream effector of BMP4 and WNT3A with respect to patterning of posterior mesoderm. The lncRNA, Evx1as arises from alternative promoters and is difficult to fully abrogate by gene editing or siRNA approaches. Nevertheless, we were able to generate a large 2.6 kb deletion encompassing the shared promoter with Evx1 and multiple additional exons of Evx1as. This led to an identical dorsal-ventral patterning defect to that generated by micro-deletion in the DNA-binding domain of EVX1. Thus, Evx1as has no function independent of EVX1, and is therefore unlikely to act in trans. We predict many antisense lncRNAs have no specific trans function, possibly only regulating the linked coding genes in cis.
| S-EPMC4880930 | biostudies-literature
Project description:Single-cell technology was used to investigate dynamic transcriptional changes in the blastula and gastrula of Drosophila embryos. Cells from embryo of stages 5 to 9 were isolated and subjected to library construction. Mesoderm cells were labeled with mCD8-GFP utilizing the GAL/UAS system. PCA identified 12 unique cell clusters that represent the blastoderm, mesoderm, endoderm and ectoderm anlage, primordia, and a sampling of differentiating cell types. In the cellular blastoderm, we found that the major wave of zygotic gene activation consists of two steps, which is supported by sub-clustering analysis. Trajectory analysis of stage 6-8 mesoderm cells suggested that transcription factors, previously linked to ectodermal segment polarity, also control mesoderm segmentation, patterning and differentiation. With the cells originating from the posterior ventral region of the blastoderm, trajectory analysis identified a group of cells that are multipotent progenitors giving rise to visceral muscles, Malpighian tubules as well as a new cell type. In summary, this single-cell study of gastrulation demonstrates early patterning involves trunk- versus pole-centered programs, the mesoderm is segmentally patterned, and a new cell type arises from the caudal mesoderm.
2023-10-18 | GSE222660 | GEO
Project description:The anterior-posterior (AP) axis is the most ancient of the embryonic axes and exists in most metazoans. Different animals use a wide variety of mechanisms to create this axis in the early embryo. In this study, we focus on three animals, including two insects (Drosophila and Tribolium) and a vertebrate (zebrafish) to examine different strategies used to form the AP axis. While Drosophila forms the entire axis within a syncytial blastoderm using transcription factors as morphogens, zebrafish uses signaling factors in a cellularized embryo, progressively forming the AP axis over the course of a day. Tribolium uses an intermediate strategy that has commonalities with both Drosophila and zebrafish. We discuss the specific molecular mechanisms used to create the AP axis and identify conserved features.
| S-EPMC5560123 | biostudies-other
Project description:Background: V0v spinal interneurons are highly-conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and scRNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild-type siblings. Results: Our data reveal two molecularly-distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly-distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
2023-08-09 | GSE240239 | GEO
Project description:Background: V0v spinal interneurons are highly-conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and scRNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild-type siblings. Results: Our data reveal two molecularly-distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly-distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
2023-08-09 | GSE240238 | GEO
Project description:How did the complex structure of the telencephalon evolve? Existing explanations are based on phenomena and lack a first-principles account. The Darwinian dynamics and endogenous network theory-established decades ago-provides a mathematical and theoretical framework and a general constitutive structure for theory-experiment coupling for answering this question from a first-principles perspective. By revisiting a gene network that explains the anterior-posterior patterning of the vertebrate telencephalon, we found that upon increasing the cooperative effect within this network, fixed points gradually evolve, accompanied by the occurrence of two bifurcations. The dynamic behavior of this network is informed by the knowledge obtained from experiments on telencephalic evolution. Our work provides a quantitative explanation for how telencephalon anterior-posterior patterning evolved from the pre-vertebrate chordate to the vertebrate and provides a series of verifiable predictions from a first-principles perspective.
| S-EPMC11353805 | biostudies-literature
Project description:Growth and differentiation factor 11 (GDF11) is a transforming growth factor ? family member that has been identified as the central player of anterior-posterior (A-P) axial skeletal patterning. Mice homozygous for Gdf11 deletion exhibit severe anterior homeotic transformations of the vertebrae and craniofacial defects. During early embryogenesis, Gdf11 is expressed predominantly in the primitive streak and tail bud regions, where new mesodermal cells arise. On the basis of this expression pattern of Gdf11 and the phenotype of Gdf11 mutant mice, it has been suggested that GDF11 acts to specify positional identity along the A-P axis either by local changes in levels of signaling as development proceeds or by acting as a morphogen. To further investigate the mechanism of action of GDF11 in the vertebral specification, we used a Cdx2-Cre transgene to generate mosaic mice in which Gdf11 expression is removed in posterior regions including the tail bud, but not in anterior regions. The skeletal analysis revealed that these mosaic mice display patterning defects limited to posterior regions where Gdf11 expression is deficient, whereas displaying normal skeletal phenotype in anterior regions where Gdf11 is normally expressed. Specifically, the mosaic mice exhibited seven true ribs, a pattern observed in wild-type (wt) mice (vs. 10 true ribs in Gdf11-/- mice), in the anterior axis and nine lumbar vertebrae, a pattern observed in Gdf11 null mice (vs. six lumbar vertebrae in wt mice), in the posterior axis. Our findings suggest that GDF11, rather than globally acting as a morphogen secreted from the tail bud, locally regulates axial vertebral patterning.
| S-EPMC6772169 | biostudies-literature
Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.
2016-03-24 | E-GEOD-70419 | biostudies-arrayexpress
Project description:Gastrulation of the Drosophila embryo is one of the most intensively studied morphogenetic processes in animal development [1-4]. Particular efforts have focused on the formation of the ventral furrow, whereby ∼1,000 presumptive mesoderm cells exhibit coordinated apical constrictions that mediate invagination [5, 6]. Apical constriction depends on a Rho GTPase signaling pathway (T48/Fog) that is deployed by the developmental regulatory genes twist and snail [7-10]. It is thought that coordinate mesoderm constriction depends on high levels of myosin along the ventral midline, although the basis for this localization is uncertain. Here, we employ newly developed quantitative imaging methods to visualize the transcriptional dynamics of two key components of the Rho signaling pathway in living embryos, T48 and Fog. Both genes display dorsoventral (DV) gradients of expression due to differential timing of transcription activation. Transcription begins as a narrow stripe of two or three cells along the ventral midline, followed by progressive expansions into more lateral regions. Quantitative image analyses suggest that these temporal gradients produce differential spatial accumulations of t48 and fog mRNAs along the DV axis, similar to the distribution of myosin activity. We therefore propose that the transcriptional dynamics of t48 and fog expression foreshadow the coordinated invagination of the mesoderm at the onset of gastrulation.
| S-EPMC5471612 | biostudies-literature