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Transcriptional trajectories highlight the transition from anterior-posterior to proximal-distal patterning in the early limb bud [scRNA-seq]

ABSTRACT: Transcriptional trajectories highlight the transition from anterior-posterior to proximal-distal patterning in the early limb bud [scRNA-seq]

PROVIDER: PRJNA666650 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12748008_1.fastq.gz	Fastqsanger.gz
	SRR12748008_2.fastq.gz	Fastqsanger.gz
	SRR12748009_1.fastq.gz	Fastqsanger.gz
	SRR12748009_2.fastq.gz	Fastqsanger.gz
	SRR12748010_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcriptional trajectories highlight the transition from anterior-posterior to proximal-distal patterning in the early limb bud [scRNA-seq]

Project description:Limb patterning relies in a large part on the function of the Hox family of developmental genes. While the differential expression of Hox genes shifts from the anterior-posterior (A-P) to the proximal-distal (P-D) axis around embryonic day 11 (E11), whether this shift coincides with a more global change of P-D versus A-P patterning program remains unclear. By performing and analyzing the transcriptome of the developing limb bud from E10.5 to E12.5, at single cell resolution, we have uncovered transcriptional trajectories which revealed a general switch from A-P to P-D genetic program between E10.5 and E11.5. Interestingly, the transcriptional trajectories at E10.5 all end with cells expressing either proximal or distal markers suggesting a progressive acquisition of P-D identity. Moreover, we observed that distally expressed Hox genes, namely Hoxa13 and Hoxd13, act as a key determinant for P-D patterning as their transcriptional control results in their distal restricted expression, which in turn restricts Hoxa11 in the proximal limb bud domain, in progenitor cells of the zeugopod. Finally, we identified three categories of genes expressed in the distal limb mesenchyme characterized by distinct temporal expression dynamics. As anticipated from previous results, HOX13 binding was observed within or in the neighborhood of several of these genes consistent with previous evidence suggesting that the transition from the early/proximal to the late/distal transcriptome of the limb mesenchyme largely relies on HOX13 function.

2020-12-15 | GSE158820 | GEO

Early limb bud transcriptome analysis between anterior and posterior domain

Project description:Shh signal mediated by Gli family of transcription factors regulates digit growth and patterning in early limb development. Shh expression in the posterior margin of the limb bud defines the zone of polarizing activity. However, much less is know about downstream targets that mediate Shh signal functions. In this dataset, we include the expression data obtained from dissected anterior and posterior halves of mouse limb bud respectively. These data are used to obtain 889 transcripts that were upregulated 1.3 fold or more in the posterior limb bud, and 1189 transcripts that were enriched in the anterior limb bud at 1.3 fold or more. Two samples were analyzed. We generate pairwise comparisons between anterior and posterior limb tissues. Genes with a fold-change ≥1.3 were selected.

2013-01-06 | E-GEOD-41691 | biostudies-arrayexpress

Early limb bud transcriptome analysis between anterior and posterior domain

2013-01-06 | GSE41691 | GEO

PRDM15 loss-of-function causes brain malformations through defective embryonic anterior-posterior patterning

Project description:PRDM15 loss-of-function causes brain malformations through defective embryonic anterior-posterior patterning

| PRJNA517443 | ENA

Transcriptional Trajectories in Mouse Limb Buds Reveal the Transition from Anterior-Posterior to Proximal-Distal Patterning at Early Limb Bud Stage.

Project description:Limb patterning relies in large part on the function of the Hox family of developmental genes. While the differential expression of Hox genes shifts from the anterior-posterior (A-P) to the proximal-distal (P-D) axis around embryonic day 11 (E11), whether this shift coincides with a more global change of A-P to P-D patterning program remains unclear. By performing and analyzing the transcriptome of the developing limb bud from E10.5 to E12.5, at single-cell resolution, we have uncovered transcriptional trajectories that revealed a general switch from A-P to P-D genetic program between E10.5 and E11.5. Interestingly, all the transcriptional trajectories at E10.5 end with cells expressing either proximal or distal markers suggesting a progressive acquisition of P-D identity. Moreover, we identified three categories of genes expressed in the distal limb mesenchyme characterized by distinct temporal expression dynamics. Among these are Hoxa13 and Hoxd13 (Hox13 hereafter), which start to be expressed around E10.5, and importantly the binding of the HOX13 factors was observed within or in the neighborhood of several of the distal limb genes. Our data are consistent with previous evidence suggesting that the transition from the early/proximal to the late/distal transcriptome of the limb mesenchyme largely relies on HOX13 function. Based on these results and the evidence that HOX13 factors restrict Hoxa11 expression to the proximal limb, in progenitor cells of the zeugopod, we propose that HOX13 act as a key determinant of P-D patterning.

| S-EPMC7768367 | biostudies-literature

Single-cell transcriptomics illuminates anterior-posterior patterning of the mesoderm in Drosophila embryos at gastrulation

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

Molecular characterization of chick anterior and posterior half-scleorotomes by RNA-sequencing.

Project description:During amniote peripheral nervous system development, segmentation ensures the correct patterning of the spinal nerves relative to vertebral column. Along the antero-posterior (rostro-caudal) axis, each somite-derived half-sclerotome has intrinsic molecular properties that govern this segmentation process. Posterior half-sclerotomes express repellent molecules to restrict axon growth and neural crest migration to anterior half-sclerotomes. Here, we report an RNA-sequencing-based molecular characterization of anterior and posterior half-sclerotomes, using the chick embryo as a model organism.

2020-09-12 | GSE103748 | GEO

Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis and retinoic acid

Project description:Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis and retinoic acid

| PRJNA610053 | ENA

Single-cell transcriptomics illuminates anterior-posterior patterning of the mesoderm in Drosophila embryos at gastrulation

Project description:Single-cell transcriptomics illuminates anterior-posterior patterning of the mesoderm in Drosophila embryos at gastrulation

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Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis and retinoic acid

Project description:Vertebrate axial skeletal patterning is controlled by coordinated collinear expression of Hox genes and axial level-dependent activity of Hox protein combinations. Transcription factors of the Meis family act as cofactors of Hox proteins and profusely bind to Hox complex DNA, however their roles in mammalian axial patterning have not been established. Similarly, retinoic acid (RA) is known to regulate axial skeletal element identity through the transcriptional activity of its receptors, however whether this role is related to Meis/Hox regulation or functions in axial patterning remains unknown. Here we study the role of Meis factors in axial skeleton formation and its relationship to the RA pathway by characterizing Meis1, Meis2 and Raldh2 mutant mice. We report that Meis and Raldh2 regulate each other in a positive feedback regulatory loop that controls axial skeletal identity. Meis elimination produces homeotic transformations similar to those found in Raldh2 and anterior-Hox mutants and disrupts the expression of Hox target genes without changing the transcriptional profiles of Hox complexes. We propose that Meis regulates vertebrate axial skeleton patterning by exclusively affecting Hox protein function, and that alterations in RA levels can produce homeotic transformations without altering Hox transcription through regulating Meis expression.

2020-12-22 | GSE146301 | GEO

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