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Analysis of gene expression in the distal forelimbs in 2.4Mb inversion adjacent to the HoxD cluster

ABSTRACT: E12.5 mouse distal forelimb embryonic transcriptome

ORGANISM(S): Mus musculus

PROVIDER: GSE98232 | GEO | 2017/07/12

SECONDARY ACCESSION(S): PRJNA384355

REPOSITORIES: GEO

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Mus musculus

Project description:E12.5 distal forelimb embryonnic transcriptome

| PRJNA293664 | ENA

Genome-wide maps of chromatin state in E12.5 mouse forelimbs

Project description:The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile. Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimnb tissues using the Illumina HiSeq 2000.

2015-02-20 | E-GEOD-49010 | biostudies-arrayexpress

Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster [RNA-seq]

Project description:RNA-seq analysis of the effect of CRISPR/Cas9-induced CTCF binding sites deletions on gene expression. We studied E12.5 distal or proximal forelimbs of wildtype and mutant alleles.

2021-10-05 | GSE181385 | GEO

Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster [cHi-C]

Project description:We used Capture Hi-C enriching the Hoxd locus and its flanking TADs to study the effects of CRISPR/Cas9-induced CTCF binding sites deletions on chromatin architecture. We analysed wildtype and homozygous mutant E9.5 trunks and E12.5 distal and proximal forelimbs.

2021-10-05 | GSE181386 | GEO

E12.5 distal forelimb embryonnic transcriptome

Project description:Analysis of gene expression in the distal forelimbs RNA-Seq polyA on transcripts extracted from the dissection of three pairs of embryonnic forelimbs at E12.5

2015-10-26 | E-GEOD-72285 | biostudies-arrayexpress

Variant PRC1 competes with retinoic acid-related signals to repress Meis2 in distal forelimb bud

Project description:Suppression of Meis genes in the distal limb bud is required for Proximal-Distal (PD) specification of the forelimb. Polycomb group (PcG) factors play a role in downregulation of retinoic acid (RA)-related signals in the distal forelimb bud, causing Meis repression. It is, however, not known if downregulation of RA-related signals and PcG-mediated proximal genes repression are functionally linked. Here, we reveal that PcG factors and RA-related signals antagonize each other to polarize Meis2 expression along the PD axis. With mathematical modeling and simulation, we propose that PcG factors are required to adjust the threshold for RA-related signaling to regulate Meis2 expression. Finally, we show that a variant Polycomb repressive complex 1 (PRC1), incorporating PCGF3 and PCGF5, represses Meis2 expression in the distal limb bud. Taken together, we reveal a previously unknown link between PcG proteins and downregulation of RA-related signals to mediate the phase transition of Meis2 transcriptional status during forelimb patterning.

2018-09-07 | GSE105206 | GEO

RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (mRNA)

Project description:Polycomb group (PcG) proteins play a pivotal role in silencing of development-related genes and contribute to maintain various stem and precursor cells and regulate their differentiation. However, it is not well understood how PcG factors regulate dynamic and complex morphogenetic processes particularly in mammals. In this study, we focused on proximal-distal (PD) patterning of forelimb bud to elucidate how PcG factors contribute to regulation of morphogenetic processes that depends on developmental signals. Depletion of RING1 proteins, which are common components of both canonical and variant Polycomb repressive complex-1 (PRC1), led to dramatic deficiencies in forelimb formation. By using Ring1-deficient forelimb buds, we revealed the early defects in distal specification, which is due to the functional coupling of RING1 and retinoic acid (RA) signaling. RING1 activity is shown to antagonize with RA signals at Meis2 and likely Meis1, which are superior suppressors of distal formation program, in the prospective distal region of outgrowing forelimb bud. This study exhibits a first example showing how PcG factors interplay with developmental signals to mediate compartmentalization of elongating anlagen by regulating the expression of developmental genes.

2015-12-28 | GSE70075 | GEO

RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-chip)

2015-12-28 | GSE70074 | GEO

RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-Seq)

2015-12-28 | GSE70076 | GEO

Transcription profiling of mouse forelimb autopods and genital buds from wild type and homozygous Del9 E12.5 embryos

Project description:Despite the importance of Hox genes in patterning the mouse embryo, few target genes of the Hox transcription factors have been identified. To search for HoxD targets we contrasted gene expression profiles in the presence and absence of the HoxD genes in two tissues where these genes are important in embryonic patterning-the genital bud and the distal domain of the limb. The Del9 mutant, in which all nine HoxD genes are absent, shows perturbed digit and genital morphogenesis. Therefore we used Affymetrix GeneChip arrays to compare gene expression in forelimb autopods and genital buds from wild type and homozygous Del9 E12.5 embryos.

2005-06-30 | E-MEXP-257 | biostudies-arrayexpress

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