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84 results for “Hox genes”
RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia
<p>Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis. </p> <p>To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.</p>
Cellular dataset for: The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo
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The cDNA sequence data of hox genes in Daphnia similoides sinensis
<p><span><span><span><span><span><span><span><span><span><span><span>Hox genes are important regulatory factors of transcription in metazoans, and are involved in the growth and development of organisms. In this study, the effects of <i><span>Microcystis aeruginosa </span></i>on Hox gene expression in the mothers and offspring of <i><span>Daphnia similoides sinensis</span></i> were investigated using a mixed diet of <i><span>M. aeruginosa</span></i> and <i><span>Scenedesmus obliquus</span></i><i> </i>in two clones. The 14 Hox genes sequence were identified in D<i><span>. similoides sinensisare </span></i>through the previous transcriptome data (Zhang et al., 2016. DOI: 10.1038/srep34241).</span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 3 in Phylogeny of pentatomomorphan bugs (Hemiptera-Heteroptera: Pentatomomorpha) based on six Hox gene fragments
FIGURE 3. Phylogeny of Pentatomomorpha based on six Hox gene fragments. The clades with morphological synapomorphies are illustrated by red lines. The support for each node is comprised of four values. The two numbers above each internode are the Bayesian posterior probability (BPP) while the two below are the bootstrap support (BS) of 100 replicates with maximum likelihood (ML) methods. Each number forward of the comma corresponds to the data matrix of amino acid (aa) sequences while each number behind corresponds to the data matrix of the first and second positions in the triplet codon of nucleotide (nt12) sequences. A dash stands for no support value for that node. The blue and green circles represent synapomorphy variants in C-terminal DFD 21 and 60, respectively. The lengths of the bugs are illustrated in proportion to their body sizes.
FIGURE 1 in Phylogeny of pentatomomorphan bugs (Hemiptera-Heteroptera: Pentatomomorpha) based on six Hox gene fragments
FIGURE 1. Summary of phylogenetic results of previous studies based on morphological characteristics, 18S rDNAs and mitochondrial genomes.
The cDNA sequence data of hox genes in Daphnia similoides sinensis
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Data from: Evolution of the snake body form reveals homoplasy in amniote Hox gene function
Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains9, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior–posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes.
Data from: Evolution of the snake body form reveals homoplasy in amniote Hox gene function
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Data from: Hox genes mediate the escalation of sexually antagonistic traits in water striders
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HOX gene complement and expression in the planarian Schmidtea mediterranea
GEO Series GSE78937. Schmidtea mediterranea. 6 samples. Type: Expression profiling by high throughput sequencing.
Rapid clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation: ChIP-chip
GEO Series GSE19447. Mus musculus. 27 samples. Type: Genome binding/occupancy profiling by genome tiling array.
RNA-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci
GEO Series GSE54952. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos - 5/6 somites embryonic stage
GEO Series GSE17658. Mus musculus. 4 samples. Type: Expression profiling by array.
Loss of Hoxa5 function affects Hox gene expression in different biological contexts
GEO Series GSE269950. Mus musculus. 57 samples. Type: Expression profiling by high throughput sequencing.
The Hox gene Abd-B controls stem cell niche function in the Drosophila testis
GEO Series GSE53709. Drosophila melanogaster. 4 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [H2AK119ub CUT&RUN]
GEO Series GSE183739. Mus musculus; Drosophila melanogaster. 28 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis.
CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia
GEO Series GSE113191. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos -13 somites embryonic stage
GEO Series GSE17660. Mus musculus. 2 samples. Type: Expression profiling by array.
C. elegans cnd-1/NeuroD1 functions with the Hox gene ceh-13/labial to control multiple genes required for nervous system development and function
GEO Series GSE125051. Caenorhabditis elegans. 6 samples. Type: Expression profiling by high throughput sequencing.
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [H3K27me3 CUT&RUN]
GEO Series GSE183737. Mus musculus. 31 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis.
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Allen Brain Atlas
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