scholarly journals Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

2017 ◽  
Vol 114 (10) ◽  
pp. E1913-E1922 ◽  
Author(s):  
Sabrina M. Schiemann ◽  
José M. Martín-Durán ◽  
Aina Børve ◽  
Bruno C. Vellutini ◽  
Yale J. Passamaneck ◽  
...  
Keyword(s):  
Hox Genes ◽  
Notch Pathway ◽  
Gene Clusters ◽  
Molecular Evidence ◽  
Expression Data ◽  
Specific Expression ◽  
Real Time Quantitative Pcr ◽  
Morphological Novelties ◽  
Animal Genomes

Temporal collinearity is often considered the main force preserving Hox gene clusters in animal genomes. Studies that combine genomic and gene expression data are scarce, however, particularly in invertebrates like the Lophotrochozoa. As a result, the temporal collinearity hypothesis is currently built on poorly supported foundations. Here we characterize the complement, cluster, and expression of Hox genes in two brachiopod species,Terebratalia transversaandNovocrania anomala.T. transversahas a split cluster with 10 genes (lab,pb,Hox3,Dfd,Scr,Lox5,Antp,Lox4,Post2, andPost1), whereasN. anomalahas 9 genes (apparently missingPost1). Our in situ hybridization, real-time quantitative PCR, and stage-specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; onlypb(inT. transversa),Hox3(in both brachiopods), andDfd(in both brachiopods) show staggered mesodermal expression. Thus, our findings support the idea that temporal collinearity might contribute to keeping Hox genes clustered. Remarkably, expression of the Hox genes in both brachiopod species demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of Hox genes, together withArx,Zic, and Notch pathway components in chaetae and shell fields in brachiopods, mollusks, and annelids provide molecular evidence supporting the conservation of the molecular basis for these lophotrochozoan hallmarks.

scholarly journals Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

2016 ◽  
Author(s):  
Sabrina M. Schiemann ◽  
José M. Martín-Durán ◽  
Aina Børve ◽  
Bruno C. Vellutini ◽  
Yale J. Passamaneck ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Molecular Basis ◽  
Hox Genes ◽  
Expression Data ◽  
Specific Expression ◽  
Spatial Expression ◽  
Morphological Novelties ◽  
Hox Clusters

AbstractTemporal collinearity is often regarded as the force preserving Hox clusters in vertebrate genomes. Studies that combine genomic and gene expression data in invertebrates would allow generalizing this observation across all animals, but are scarce, particularly within Lophotrochozoa (e.g., snails and segmented worms). Here, we use two brachiopod species –Terebratalia transversa, Novocrania anomala– to characterize the complement, cluster and expression of their Hox genes. T. transversa has an ordered, split cluster with ten genes (lab, pb, Hox3, dfd, scr, lox5, antp, lox4, post2, post1), while N. anomala has nine (missing post1). Our in situ hybridization, qPCR and stage specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; only pb (in T. transversa), Hox3 and dfd (in both brachiopods) show staggered mesodermal expression. The spatial expression of the Hox genes in both brachiopod species correlates with their morphology and demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of a subset of Hox genes, Arx and Zic orthologs in chaetae and shell-fields between brachiopods, mollusks, and annelids supports the deep conservation of the molecular basis forming these lophotrochozoan hallmarks. Our findings challenge that collinearity alone preserves lophotrochozoan Hox clusters, indicating that additional genomic traits need to be considered in understanding Hox evolution.

An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution

Development ◽  
1992 ◽  
Vol 116 (3) ◽  
pp. 653-661 ◽  
Author(s):  
P.W. Holland ◽  
L.Z. Holland ◽  
N.A. Williams ◽  
N.D. Holland
Keyword(s):  
Nerve Cord ◽  
Hox Genes ◽  
Homeobox Gene ◽  
Specific Expression ◽  
Vertebrate Brain ◽  
Close Phylogenetic Relationship ◽  
Mammalian Homologue ◽  
Dorsal Nerve ◽  
The Relationship

The embryology of amphioxus has much in common with vertebrate embryology, reflecting a close phylogenetic relationship between the two groups. Amphioxus embryology is simpler in several key respects, however, including a lack of pronounced craniofacial morphogenesis. To gain an insight into the molecular changes that accompanied the evolution of vertebrate embryology, and into the relationship between the amphioxus and vertebrate body plans, we have undertaken the first molecular level investigation of amphioxus embryonic development. We report the cloning, complete DNA sequence determination, sequence analysis and expression analysis of an amphioxus homeobox gene, AmphiHox3, evolutionarily homologous to the third-most 3′ paralogous group of mammalian Hox genes. Sequence comparison to a mammalian homologue, mouse Hox-2.7 (HoxB3), reveals several stretches of amino acid conservation within the deduced protein sequences. Whole mount in situ hybridization reveals localized expression of AmphiHox3 in the posterior mesoderm (but not in the somites), and region-specific expression in the dorsal nerve cord, of amphioxus neurulae, later embryos and larvae. The anterior limit to expression in the nerve cord is at the level of the four/five somite boundary at the neurula stage, and stabilises to just anterior to the first nerve cord pigment spot to form. Comparison to the anterior expression boundary of mouse Hox-2.7 (HoxB3) and related genes suggests that the vertebrate brain is homologous to an extensive region of the amphioxus nerve cord that contains the cerebral vesicle (a region at the extreme rostral tip) and extends posterior to somite four.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Neuroendocrine prostate cancer has distinctive, non-prostatic HOX code that is represented by the loss of HOXB13 expression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Siyuan Cheng ◽  
Shu Yang ◽  
Yingli Shi ◽  
Runhua Shi ◽  
Yunshin Yeh ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Hox Genes ◽  
Human Cancer ◽  
Specific Expression ◽  
Hox Gene ◽  
Human Cancer Cell Lines ◽  
All Trans Retinoic Acid ◽  
Neuroendocrine Prostate Cancer ◽  
Hox Code ◽  
Specific Expression Pattern

AbstractHOX gene-encoded homeobox proteins control body patterning during embryonic development; the specific expression pattern of HOX genes may correspond to tissue identity. In this study, using RNAseq data of 1019 human cancer cell lines that originated from 24 different anatomic sites, we established HOX codes for various types of tissues. We applied these HOX codes to the transcriptomic profiles of prostate cancer (PCa) samples and found that the majority of prostate adenocarcinoma (AdPCa) samples sustained a prostate-specific HOX code whereas the majority of neuroendocrine prostate cancer (NEPCa) samples did not, which reflects the anaplastic nature of NEPCa. Also, our analysis showed that the NEPCa samples did not correlate well with the HOX codes of any other tissue types, indicating that NEPCa tumors lose their prostate identities but do not gain new tissue identities. Additionally, using immunohistochemical staining, we evaluated the prostatic expression of HOXB13, the most prominently changed HOX gene in NEPCa. We found that HOXB13 was expressed in both benign prostatic tissues and AdPCa but its expression was reduced or lost in NEPCa. Furthermore, we treated PCa cells with all trans retinoic acid (ATRA) and found that the reduced HOXB13 expression can be reverted. This suggests that ATRA is a potential therapeutic agent for the treatment of NEPCa tumors by reversing them to a more treatable AdPCa.

scholarly journals A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data: Fig. 1.

2015 ◽  
Vol 31 (19) ◽  
pp. 3228-3230
Author(s):  
José M. Juanes ◽  
Ana Miguel ◽  
Lucas J. Morales ◽  
José E. Pérez-Ortín ◽  
Vicente Arnau
Keyword(s):  
Web Application ◽  
Differentially Expressed ◽  
Expression Data ◽  
Specific Expression

scholarly journals Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 517 ◽  
Author(s):  
Daniel García-Souto ◽  
Sandra Alonso-Rubido ◽  
Diana Costa ◽  
José Eirín-López ◽  
Emilio Rolán-Álvarez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromosome Numbers ◽  
Gene Clusters ◽  
Chromosomal Mapping ◽  
Closely Related Species ◽  
Submetacentric Chromosome ◽  
The Family ◽  
Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

Early response of gene clusters is associated with mouse lung resistance or sensitivity to cigarette smoke

2009 ◽  
Vol 296 (3) ◽  
pp. L418-L429 ◽  
Author(s):  
Eleonora Cavarra ◽  
Paolo Fardin ◽  
Silvia Fineschi ◽  
Annamaria Ricciardi ◽  
Giovanna De Cunto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cigarette Smoke ◽  
Gene Clusters ◽  
Early Response ◽  
Cigarette Smoke Exposure ◽  
Mouse Lung ◽  
Individual Response ◽  
Molecular Signaling ◽  
Gene Expression Response ◽  
Real Time Quantitative Pcr

We have investigated the effects of cigarette smoke exposure in three different strains of mice. DBA/2 and C57BL/6J are susceptible to smoke and develop different lung changes in response to chronic exposure, whereas ICR mice are resistant to smoke and do not develop emphysema. The present study was carried out to determine early changes in the gene expression profile of mice exposed to cigarette smoke with either a susceptible or resistant phenotype. The three strains of mice were exposed to smoke from three cigarettes per day, 5 days/wk, for 4 wk. Microarray analysis was carried out on total RNA extracted from the lung using the Affymetrix platform. Cigarette smoke modulates several clusters of genes (i.e., proemphysematous, acute phase response, and cell adhesion) in smoke-sensitive DBA/2 or C57BL/6J strains, but the same genes are not altered by smoke in ICR resistant mice. Only a few genes were commonly modulated by smoke in the three strains of mice. This pattern of gene expression suggests that the response to smoke is strain-dependent and may involve different molecular signaling pathways. Real-time quantitative PCR was used to verify the pattern of modulation of selected genes and their potential biological relevance. We conclude that gene expression response to smoke is highly dependent on the mouse genetic background. We speculate that the definition of gene clusters associated, to various degrees, with mouse susceptibility or resistance to smoke may be instrumental in defining the molecular basis of the individual response to smoke-induced lung injury in humans.

scholarly journals Localization of type 1 17beta-hydroxysteroid dehydrogenase mRNA and protein in syncytiotrophoblasts and invasive cytotrophoblasts in the human term villi

2000 ◽  
Vol 165 (2) ◽  
pp. 217-222 ◽  
Author(s):  
M Bonenfant ◽  
PR Provost ◽  
R Drolet ◽  
Y Tremblay
Keyword(s):  
In Situ Hybridization ◽  
Hydroxysteroid Dehydrogenase ◽  
Binding Activity ◽  
Placental Lactogen ◽  
Specific Expression ◽  
P450 Aromatase ◽  
Chain Cleavage ◽  
Extravillous Cytotrophoblasts

The 17beta-hydroxysteroid dehydrogenases (17beta-HSDs) play a key role in the synthesis of sex steroids. The hallmark of this family of enzymes is the interconversion, through their oxydoreductive reactivity at position C17, of 17-keto- and 17beta-hydroxy-steroids. Because this reaction essentially transforms steroids having low binding activity for the steroid receptor to their more potent 17beta-hydroxysteroids isoforms, it is crucial to the control of the physiological activities of both estrogens and androgens. The human placenta produces large amounts of progesterone and estrogens throughout pregnancy. The placental type 1 17beta-HSD enzyme (E17beta-HSD) catalyzes the reduction of the low activity estrogen, estrone, into the potent estrogen, estradiol. We studied the cell-specific expression of type 1 17beta-HSD in human term placental villous tissue by combining in situ hybridization to localize type 1 17beta-HSD mRNA with immunohistochemistry using an antibody against human placental lactogen, a trophoblast marker. Immunolocalization of E17beta-HSD was also performed. To ascertain whether other steroidogenic enzymes are present in the same cell type, cytochrome P450 cholesterol side-chain cleavage (P450scc), P450 aromatase, and type 1 3beta-hydroxysteroid dehydrogenase (3beta-HSD) were also localized by immunostaining. Our results showed that the syncytium is the major steroidogenic unit of the fetal term villi. In fact, type 1 17beta-HSD mRNA and protein, as well as P450scc, P450 aromatase, and 3beta-HSD immunoreactivities were found in these cells. In addition, our results revealed undoubtedly that extravillous cytotrophoblasts (CTBs), e.g. those from which cell columns of anchoring villous originate, also express the type 1 17beta-HSD gene. However, CTBs lying beneath the syncytial layer, e.g. those from which syncytiotrophoblasts develop, contained barely detectable amounts of type 1 17beta-HSD mRNA as determined by in situ hybridization. These findings, along with those from other laboratories confirm the primordial role of the syncytium in the synthesis of steroids during pregnancy. In addition, our results indicate for the first time that CTBs differentiating along the invasive pathway contain type 1 17beta-HSD mRNA.

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