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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse rhombomere 4 at E10.5 from knockins of Hoxb1 gene expressing Hox-A1 protein

ABSTRACT: This study analyzed mRNA profiles in rhombomere 4 of E10.5 mouse knock-in embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus. The Hox-A1 protein was found to be detectably less efficacious than Hox-B1 in promoting neurogenesis in the basal plate of rhombomere 4 and its transcriptional profile shared several similarities with the Hoxb1 mutant. Experiment Overall Design: GFP-positive cells were FACS-sorted from dissected hindbrains of entire litters of E10.5 mouse embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus, either one tagged with IRES-tauGFP. Three independent biological replicates of each genotype were analyzed. Total RNA was isolated, amplified and hybridized to Affymetrix Mouse Genome 430 2.0 Arrays.

ORGANISM(S): Mus musculus

SUBMITTER: Petr Tvrdik

PROVIDER: E-GEOD-5124 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Reversal of Hox1 gene subfunctionalization in the mouse.

Tvrdik Petr P Capecchi Mario R MR

Developmental cell 20060801 2

In vertebrates, paralogous Hox genes play diverse biological roles. We examined the interchangeability of Hoxa1 and Hoxb1 in mouse development by swapping their protein-coding regions. Remarkably, the mice expressing the Hox-B1 protein from the Hoxa1 locus, and vice versa, are essentially normal. We noted, nonetheless, a specific facial nerve hypomorphism in hemizygous Hoxb1(A1/-) mice and decreased viability in homozygous Hoxa1(B1/B1) embryos. Further, we established a mouse line in which we ha ...[more]

PMID: 16890163

Similar Datasets

Hoxb1 gene expressing Hox-A1 protein: Altered transcriptional profile in rhombomere 4 at E10.5

Project description:This study analyzed mRNA profiles in rhombomere 4 of E10.5 mouse knock-in embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus. The Hox-A1 protein was found to be detectably less efficacious than Hox-B1 in promoting neurogenesis in the basal plate of rhombomere 4 and its transcriptional profile shared several similarities with the Hoxb1 mutant. Keywords: gene swap, knock-in, hindbrain development, rhombomere 4

2006-08-28 | GSE5124 | GEO

Mus musculus

Project description:Hoxb1 gene expressing Hox-A1 protein: Altered transcriptional profile in rhombomere 4 at E10.5

| PRJNA96623 | ENA

Hoxb1 mutant mRNA levels in rhombomere 4 at E10.5

Project description:Hoxb1 is required for proper specification of rhombomere 4 and the facial motor neurons. This study analyzed gene expression in the corresponding hindbrain segment of E10.5 mutant embryos. Several genetic pathways were found altered, including transcription factors such as Phox2b, Gata3, Nkx2-2 and Nkx6-1. Keywords: hindbrain development, rhombomere 4, Hoxb1

2006-08-28 | GSE5126 | GEO

The role of Hoxb1 in NMPs and neural progenitors

Project description:We found that, whereas Hoxb1 does not affect NMP specification per se, it promotes NMP survival through the upregulation of Fgf8 and other components of Fgf signaling as well as the repression of components of the apoptotic pathway. Additionally, it upregulates the expression of some, primarily anterior, Hox genes suggesting that it plays an active role in the early steps of AP specification. In hindbrain neural progenitors Hoxb1 synergizes with shh to repress the expression of dorsal markers, regulate the expression of ventral markers and direct the specification of facial branchiomotorneuron (FBM) - like progenitors. Additionally, Hoxb1 and shh synergize in regulating the expression of diverse signals and signaling molecules in neural progenitors, including the Ret tyrosine kinase receptor. Hoxb1 synergizes with GDNF to strengthen Ret expression and further promote the generation of facial branchiomotorneuron (FBM) – like progenitors

2022-05-09 | GSE174021 | GEO

Mus musculus

Project description:Hoxb1 mutant mRNA levels in rhombomere 4 at E10.5

| PRJNA96627 | ENA

Muscle Developmental Defects in Heterogeneous Nuclear Ribonucleoprotein A1 Knockout Mice

Project description:Transcriptome analysis of total RNA samples from heart tissue of knockout mice Alternative splicing is the main mechanism to increase protein diversity from an mRNA. Heterogeneous ribonucleoprotein (hnRNP) family members are vital regulators of alternative splicing. The hnRNP A1 is the most well-known protein in this family, but its role in embryonic development is not well understood. We generated hnRNP A1 knockout mice to study the function of hnRNP A1 in vivo. The hnRNP A1-depleted mice showed embryonic lethality because of muscle developmental defects. In a previous study, cellular hnRNP A2/B1 was reported to be capable of compensating for the expression of hnRNP A1. However, this phenomenon did not occur in the hnRNP A1 heterozygous mice in vivo. We demonstrated that hnRNP A1 regulated muscle-related genes expression and alternative splicing. In summary, our data demonstrated that hnRNP A1 plays a critical role in embryonic muscle development. Understanding the effects of hnRNP A1 in vivo may help to define the function of hnRNP A1 in alternative splicing.

2016-12-05 | GSE79076 | GEO

Transcriptome profiling of hnRNP A2/B1 and A1 depleted cells

Project description:We used NEBNext UltraÂ DirectionalÂ RNA Library Prep Kits to prepare RNA-seq libraries of total RNA from hnRNP A2/B1 and A1 depleted A549 cells. Pro-seq libraries were prepared from A549 cells using Illumina adapters hnRNP A2/B1 and A1 depleted A549 cells were generated by lentiviral infections of shRNA constructs. RNAs were isolated using Trizol.

2016-05-17 | E-GEOD-76151 | biostudies-arrayexpress

Expression profiling of whole E10.5 embryos expressing 5 copies of Mir483 at the endogenous locus

Project description:In this study we generated mice with over-expression of microRNA Mir483, by insertion of four extra-copies at the endogenous locus. Whole transcriptome analysis was performed by RNA-seq in in total lysates of E10.5 embryos (mutants with five copies - 5C - and wild-type controls).

2024-02-26 | GSE256306 | GEO

Hox Abdominal-B Genes in the Developing Kidney

Project description:The Hox complex consists of 39 genes arranged in 4 clusters of flanking genes and 13 paralogous groups in mammals. To assess the functional redundancy of Hox abdominal-B genes during renal development, we used a modified recombineering strategy to simultaneous introduce frameshift mutations into the Hox9, Hox10, and Hox11 flanking genes of the HoxA, HoxC, and HoxD paralogous groups. We performed RNA seq on whole kidneys at E18.5 in triplicates for representative genotypes including: wild type; Hoxa9,10,11-/- HoxC9,10,11+/-, Hoxa9,10,11+/- HoxC9,10,11-/-, Hoxa9,10,11-/- HoxC9,10,11-/-. Our results suggest that the loss of Hox function results in a partial metanephric to mesonephric transformation, with tubules co-expressing markers of both proximal tubules and collecting ducts, as well as markers of mesonephric-derived epididymis tubules.

2018-04-25 | GSE90816 | GEO

Selective compartmentalization in condensin-depleted mitotic chromosomes [ChIP-seq]

Project description:During mitosis, condensin activity is thought to disrupt interphase chromatin structures. Here, we utilize condensin-deficient mitotic chromosomes as a unique architectural platform to further investigate genome folding principles. Upon condensin loss, compartments progressively emerge in mitotic chromosomes. Euchromatin diverges into two different compartments A1 and A2, the former of which shows strong homotypic interactions while the latter exhibit reduced self-aggregation. Constitutive heterochromatin (B1) displays reduced level of compartmentalization and the normally inert facultative heterochromatin (B2) participates to compartmentalize the genome. Dynamically, A1 compartment is established remarkably fast with similarly efficient separation from B1 while reformation of B1 is delayed, implying that A1 self-attraction is the engine to compartmentalizalize the condensin-depleted mitotic chromosomes. Notified by the mitotic compartmentalization of B1 which lacks HP1 binding, we sought to explore the role of HP1 proteins in genome folding and demonstrat that HP1& are dispensible for chromatin structural restoration during cell divison. Our observations unveil delicate patterns and novel principles of genome compartmentalization that are otherwise hidden in interphase cells.

2023-11-22 | GSE228160 | GEO

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