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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq]

ABSTRACT: We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

ORGANISM(S): Mus musculus

PROVIDER: GSE136415 | GEO | 2019/09/17

REPOSITORIES: GEO

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [RNA-seq]

Project description:We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

2019-09-17 | GSE136437 | GEO

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2019-12-14 | GSE142030 | GEO

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs (ChIP-chip)

Project description:During limb development, Hoxd genes are transcribed in two waves: Early on, when the arm and forearm are specified and subsequently, when digits form. While the latter phase is controlled by enhancers centromeric to the HoxD cluster, we show here that the early phase requires enhancers located in the opposite telomeric gene desert. The transition between the two types of regulations involves a functional switch between two distinct topological domains, as reflected by a subset of genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently shift to establish new contacts on the opposite side. This transition between two regulatory landscapes generates an intermediate area of low Hox dose developing into the wrist, the transition between our arms and our hands. This intriguing correspondence between genomic and morphological boundaries illustrates the mechanism underlying collinear Hox gene regulation in our developing appendages. Chromatin ImmoPrecipitation on chip (Tiling array): Distribution of H3K4me3 and H3K27me3 in early limb buds at E9.5, E10.5 and proximal late limbs E12.5. Distribution of H3K27me3 in del(8-13) and del(8-13)/del(attP-TpSB3) E10.5 limb buds. Distribution of H3K27me3 in WT and homozygote del(Nsi-Atf2) (Montavon et al., 2011) forelimb autopods.

2013-06-07 | E-GEOD-45454 | biostudies-arrayexpress

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Project description:The lateral plate mesoderm (LPM) is a transient tissue that produces a diverse range of differentiated structures, including the limbs. However, the molecular mechanisms that drive early LPM specification and development are poorly understood. In this study, we utilize single-cell transcriptomics to define the cell-fate decisions directing LPM specification, subdivision, and early initiation of the forelimb mesenchyme in chicken embryos. We establish a transcriptional atlas and global cell-cell signalling interactions in progenitor, transitional and mature cell types throughout the developing forelimb field.

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cis-regulatory logic of Shh expression reveals common history of unpaired and paired fins

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The minor spliceosome is required for limb growth but not patterning

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RING1B binding in the 11 dpc embryonic tissues

Project description:We report the distribution of RING1B (one of Polycomb group factors) within the genome of mouse embryonic tissues. We prepared the chromatin from 11 dpc embryonic forebrain, midbrain, and forelimb buds and made chromatin precipitation with antibody against RING1B (mouse monoclonal antibody). High-throughput sequencing applied for the ChIP analysis revealed the differential distribution of RING1B protein among embryonic tissues. ChIP analysis of mouse 11 dpc embryonic forebrain, midbrain and forelimb buds against anti-RING1B antibody.

2014-01-14 | E-GEOD-48464 | biostudies-arrayexpress

John Cobb 2006

Project description:The goal of the experiment was to identify genes downstream of the SHOX2 transcription factor during mouse forelimb development. Triplicate Samples were isolated from Shox2 mutants and wildtype/heterozygote limbs at E10.5 and E11.5.

2011-09-23 | E-MTAB-411 | biostudies-arrayexpress

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Project description:Wild type and Dicer null embryonic mouse limbs were analaysed using Affymetrix arrays to identify gene expression changes. Genes that were up-regulated in Dicer-null limbs were canidates for being miRNA targets. Potential miRNA target genes were validated using qRTPCR. Mice carrying a heterozygous Dicer floxed allele and the prxcre driver allele were crossed to homozygous Dicer Floxed mice. Embryos were harvested from pregent moms and genotyped to determine heterozygous, Wild type and mutant limb buds. These limb buds were used to prepare RNA for array analysis.

2011-01-31 | E-GEOD-13807 | biostudies-arrayexpress

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