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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse developing hindlimb bud to identify genes controlled by LMX1B

ABSTRACT: A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in e11.5 mouse proximal limb tissue lacking the Lmx1b gene. Because Lmx1b is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning. Experiment Overall Design: The proximal portion of e11.5 hindlimb buds (~500um) was used for RNA extraction. Each array was hybridized with pooled cRNAs from both hindlimb buds of three embryos (6 hindlimbs/sample).

ORGANISM(S): Mus musculus

SUBMITTER: dayana krawchuk

PROVIDER: E-GEOD-10516 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of genes controlled by LMX1B in the developing mouse hindlimb bud

Project description:A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in e11.5 mouse proximal limb tissue lacking the Lmx1b gene. Because Lmx1b is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning. Keywords: Genetic allele comparison

2008-02-15 | GSE10516 | GEO

Identification of genes controlled by LMX1B in the developing limb, embryonic day (E) 13.5

Project description:A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in E13.5 mouse limb tissue lacking the Lmx1b gene. Because LMX1B is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning. The forelimb or hindlimb of wild-type controls or Lmx1b loss-of-function mutants was used for RNA extraction. Each array was hybridized with cDNAs of an individual limb.

2010-07-30 | E-GEOD-21446 | biostudies-arrayexpress

Identification of genes controlled by LMX1B in the developing limb, embryonic day (E) 13.5

2010-07-06 | GSE21446 | GEO

Differenetial Gene Expression in Limbs of Wild Type and Lmx1b KO mice during limb dorsalization (e11.5, e12.5 & e13.5)

Project description:Lmx1b regulates dorsalization of limb fates, but the mechanism of this regulation has not been characterized. To identify candidate genes regulated by Lmx1b we compared the limbs from Lmx1b KO mice to wild type mice during limb dorsalization (e11.5-13.5). Differentially expressed genes that we common to all three stages examined were considered to be likely candidates for Lmx1b regulation and further evaluated. At 11.5 and 12.5 dpc, embryos were harvested and the limb buds with the limb girdles were isolated. Embryos at 13.5dpc were also harvested and their distal limb buds (zeugopods and autopods) were isolated. Embryos were genotyped to confirm Lmx1b homozygosity (-/- or +/+). RNA from embryonic forelimbs and hindlimbs of wild type (WT) and Lmx1b KO mice was harvested using the Rneasy Kit (Qiagen). RNA was pooled to decrease genetic variability, i.e., six limbs at 11.5 dpc, three limbs at 12.5 dpc and six limbs at 13.5 dpc. Duplicate samples were generated using different embryos for each stage and then hybridized to the Affymetrix GeneChip® Mouse Genome 430 2.0 Array (UCI, Irvine, CA).

2012-05-21 | E-GEOD-34732 | biostudies-arrayexpress

Lmx1b ChIP-seq dataset in embryonic day 12.5 (e12.5) wild type mouse limb buds

Project description:Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct downstream gene targets in the limb have been confirmed. To determine direct targets of Lmx1b during limb dorsalization (E12.5), we performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Nearly 84% (n=617) of the Lmx1b-bound genomic fragments or intervals (LBIs) identified by two Lmx1b-ChIP-seqs overlap with chromatin regulatory marks indicative of potential cis-regulatory modules (PCRMs). In addition, 73 LBIs mapped to known cis-regulatory modules (CRMs) active during limb development. We compared Lmx1b-bound PCRMs to genes differentially expressed by Lmx1b at E12.5 and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontology analysis of these associated genes suggests that Lmx1b mediates dorsalization through the regulation of extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of 2 PCRMs associated to Lmx1b-regulated genes, demonstrating activity and overlap with the associated gene during limb development. This is the first report to describe the genome-wide distribution of Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization.

2017-05-06 | GSE84064 | GEO

Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity

Project description:Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of ΔLARM1/2 mutants that lack limb-specific Lmx1b enhancers, fail to regenerate. To separate the nail’s effect from the lack of DV polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration and the nail requirement is supported. Transcriptomic comparison between wild-type and non-regenerative ΔLARM1/2 mutant blastemas reveals differential up-regulation of vascularization and connective tissue functional signatures in wild-type versus upregulation of inflammation in the mutant. These results, together with the finding of Lmx1b expression in the postnatal dorsal dermis underneath the nail and uniformly in the regenerative blastema opens the possibility of additional Lmx1b roles in the progression of digit tip regeneration, in addition to the indirect effect of mediating the formation of the nail.

2022-12-02 | GSE202223 | GEO

Differenetial Gene Expression in Limbs of Wild Type and Lmx1b KO mice during limb dorsalization (e11.5, e12.5 & e13.5)

2012-05-22 | GSE34732 | GEO

Geminin is required for Hox gene regulation to pattern the developing limb

Project description:Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5’ Hox transcription factor expression is essential for proper limb bud patterning and development. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5’ Hox gene expression expanded into more proximal and anterior regions of embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior Shh signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the Hoxd13 target Shh, and the Shh target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of Gli3, a Shh pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.

2020-06-05 | GSE143211 | GEO

A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2 [single-cell RNA-seq]

Project description:During development cell fates are specified by tightly controlled gene expression programs. PBX TALE transcription factors control gene regulatory networks (GRN) that direct vertebrate tissue patterning and organ morphogenesis. How PBX1/2 proteins achieve context-specific functions, despite widespread embryonic Pbx expression, remains elusive. In mouse limbs, mesenchymal-specific loss of PBX1/2 or of the limb regulator HAND2 results in strikingly similar phenotypes, suggesting that PBX1/2- and HAND2-dependent programs converge to control limb development. To investigate this scenario using the murine hindlimb model, we combined tissue-specific and temporally controlled mutagenesis to multi-omics approaches on dissected hindlimb buds. This resulted in the reconstruction of a GRN that is collaboratively directed by PBX1/2-HAND2, demonstrating that Pbx1-Hand2 genetically interact in vivo during pentadactylous hindlimb patterning, with PBX1 concomitantly acting as an upstream regulator of Hand2. At organismal-level resolution the GRN is active within restricted subsets of posterior-proximal hindlimb mesenchymal cells, wherein Pbx1/2 and Hand2 are co-expressed with their target genes. Profiling the binding of Pbx1 and Hand2 genome-wide across multiple tissues revealed that HAND2 can act selectively on a subset of PBX-bound regions to impart limb patterning functionality. Our research elucidates mechanisms on the limb-specific activities of PBX1/2, while informing general principles by which promiscuous transcription factors cooperate with select cofactors to instruct distinct developmental programs.

2023-04-26 | GSE197858 | GEO

A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2 [bulk RNA-seq]

2023-04-26 | GSE197857 | GEO

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