SRY-related (Sox) genes in the genome of European Atlantic sturgeon (Acipenser sturio)

Genome ◽  
2005 ◽  
Vol 48 (2) ◽  
pp. 181-186 ◽  
Author(s):  
Anne Kathrin Hett ◽  
Arne Ludwig
Keyword(s):  
Sex Determination ◽  
Gene Evolution ◽  
High Mobility ◽  
Atlantic Sturgeon ◽  
Neighbor Joining ◽  
Degenerate Primers ◽  
Sox Proteins ◽  
Sox Gene ◽  
Dna Binding And Bending ◽  
Sox Genes

The Sox-gene family represents an ancient group of transcription factors involved in numerous developmental processes and sex determination in vertebrates. SOX proteins are characterized by a conserved high mobility group (HMG)-box domain, which is responsible for DNA binding and bending. We studied Sox genes in sturgeon, one of the most primitive groups of fishes characterized by a high chromosome number. Male and female genomes were screened for Sox genes using highly degenerate primers that amplified a broad range of HMG boxes. A total of 102 clones, representing 22 different sequences coding for 8 Sox genes, was detected and classified according to their orthologues. Sox2, Sox3, Sox4, Sox9, Sox11, Sox17, Sox19, and Sox21 were found in sturgeon; these genes represent Sox groups B, C, E, and F. In a phylogenetic analysis (neighbor-joining, maximum likelihood, maximum parsimony), these genes clustered with their mouse orthologues. In the case of Sox4, Sox17, and Sox21, we found evidence of gene duplication.Key words: Acipenseridae, gene evolution, sex determination, Sox genes.

scholarly journals Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers

2021 ◽  
Vol 11 (8) ◽  
pp. 823
Author(s):  
Jaekwon Seok ◽  
Minchan Gil ◽  
Ahmed Abdal Dayem ◽  
Subbroto Kumar Saha ◽  
Ssang-Goo Cho
Keyword(s):  
Gene Family ◽  
Cancer Progression ◽  
Prognostic Value ◽  
High Mobility ◽  
Functional Protein ◽  
Human Cancers ◽  
Kaplan Meier ◽  
Sox Proteins ◽  
Sox Gene ◽  
Sox Genes

The Sry-related HMG BOX (SOX) gene family encodes transcription factors containing highly conserved high-mobility group domains that bind to the minor groove in DNA. Although some SOX genes are known to be associated with tumorigenesis and cancer progression, their expression and prognostic value have not been systematically studied. We performed multi-omic analysis to investigate the expression of SOX genes in human cancers. Expression and phylogenetic tree analyses of the SOX gene family revealed that the expression of three closely related SOX members, SOX4, SOX11, and SOX12, was increased in multiple cancers. Expression, mutation, and alteration of the three SOX members were evaluated using the Oncomine and cBioPortal databases, and the correlation between these genes and clinical outcomes in various cancers was examined using the Kaplan–Meier, PrognoScan, and R2 database analyses. The genes commonly correlated with the three SOX members were categorized in key pathways related to the cell cycle, mitosis, immune system, and cancer progression in liver cancer and sarcoma. Additionally, functional protein partners with three SOX proteins and their probable signaling pathways were explored using the STRING database. This study suggests the prognostic value of the expression of three SOX genes and their associated pathways in various human cancers.

scholarly journals Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 314 ◽  
Author(s):  
Lan Jiang ◽  
De Bi ◽  
Hengwu Ding ◽  
Xuan Wu ◽  
Ran Zhu ◽  
...  
Keyword(s):  
Gene Family ◽  
High Mobility ◽  
Coturnix Japonica ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Biological Studies ◽  
Model Animal ◽  
Sox Gene ◽  
Sox Genes

Coturnix japonica (Japanese quail) has been extensively used as a model animal for biological studies. The Sox gene family, which was systematically characterized by a high-mobility group (HMG-box) in many animal species, encodes transcription factors that play central roles during multiple developmental processes. However, genome-wide investigations on the Sox gene family in birds are scarce. In the current study, we first performed a genome-wide study to explore the Sox gene family in galliform birds. Based on available genomic sequences retrieved from the NCBI database, we focused on the global identification of the Sox gene family in C. japonica and other species in Galliformes, and the evolutionary relationships of Sox genes. In our result, a total of 35 Sox genes in seven groups were identified in the C. japonica genome. Our results also revealed that dispersed gene duplications contributed the most to the expansion of the Sox gene family in Galliform birds. Evolutionary analyses indicated that Sox genes are an ancient gene family, and strong purifying selections played key roles in the evolution of CjSox genes of C. japonica. More interestingly, we observed that most Sox genes exhibited highly embryo-specific expression in both gonads. Our findings provided new insights into the molecular function and phylogeny of Sox gene family in birds.

scholarly journals Differential Expression of Members of SOX Family of Transcription Factors in Failing Human Hearts

2020 ◽  
Author(s):  
Chia-Feng Liu ◽  
Ying Ng ◽  
Varun Thachil ◽  
Michael Morley ◽  
Christine S Moravec ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differential Expression ◽  
Cardiac Fibrosis ◽  
Meta Analysis ◽  
High Mobility ◽  
Human Myocardium ◽  
Cardiac Tissues ◽  
Protein Levels ◽  
Sox Genes ◽  
Rna Levels

Abstract Background: The Sry-related high-mobility-group box (SOX) gene family, with 20 known transcription factors in humans, plays essential roles during development and in many disease processes. Several SOX proteins, e.g., SOX4, SOX11, and SOX9, are required for normal heart morphogenesis. SOX9 was shown to contribute to cardiac fibrosis in animal models. However, differential expression of other SOX transcription factors and their functional roles in the failing human myocardium have not been explored.Methods and Findings: All 20 SOX genes from RNA-seq data were extracted, and their RNA levels were compared to the NF, DCM, and hypertrophic cardiomyopathy (HCM) groups. The protein levels of the differential expressed SOX genes were confirmed by Western blot. Four SOX genes whose RNA levels were significantly upregulated in DCM or HCM compared to NF. However, only SOX4 and SOX8 proteins were markedly increased in the heart failure groups. Gene co-expression network analysis identified genes associated and respond similarly to perturbations with SOX4 in cardiac tissues. Using a meta-analysis combining epigenetics and genome-wide association data, we reported several genomic variants associated with HF phenotype linked to SOX4 or SOX8.Conclusions: Elevation of SOX8 and SOX4 are observed in the failing human myocardium. The molecular mechanism associated with them in HF warrants further investigation.

scholarly journals Further complexity of the human SOX gene family revealed by the combined use of highly degenerate primers and nested PCR

FEBS Letters ◽  
1998 ◽  
Vol 438 (3) ◽  
pp. 311-314 ◽  
Author(s):  
Frederic Cremazy ◽  
Stephan Soullier ◽  
Philippe Berta ◽  
Philippe Jay
Keyword(s):  
Gene Family ◽  
Nested Pcr ◽  
Degenerate Primers ◽  
Combined Use ◽  
Sox Gene

scholarly journals Duplication and divergence of Sox genes in spiders

2017 ◽  
Author(s):  
Christian L. B. Paese ◽  
Daniel J. Leite ◽  
Anna Schoenauer ◽  
Alistair P. McGregor ◽  
Steven Russell
Keyword(s):  
Limb Development ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Regulatory Mechanism ◽  
Recent Analysis ◽  
Parasteatoda Tepidariorum ◽  
Arthropod Species ◽  
Sox Gene ◽  
And Function ◽  
Sox Genes

AbstractBackgroundThe Sox family of transcription factors are present and conserved in the genomes of all metazoans examined to data and are known to play important developmental roles in vertebrates and insects. However, outside the commonly studied Drosophila model little is known about the extent or conservation of the Sox family in other arthropod species. Here we characterise the Sox family in two chelicerate species, the spiders Parasteatoda tepidariorum and Stegodyphus mimosarum, which have experienced a whole genome duplication (WGD) in their evolutionary history.ResultsWe find that virtually all of the duplicate Sox genes have been retained in these spiders after the WGD. Analysis of the expression of Sox genes in P. tepidariorum embryos indicates that it is likely that some of these genes have neofunctionalised after duplication. Our expression analysis also strengthens the view that an orthologue of vertebrate Group B1 genes, SoxNeuro, is implicated in the earliest events of CNS specification in both vertebrates and invertebrates. In addition, a gene in the Dichaete/Sox21b class is dynamically expressed in the spider segment addition zone, suggestive of an ancient regulatory mechanism controlling arthropod segmentation as recently suggested for flies and beetles. Together with the recent analysis of Sox gene expression in the embryos of other arthropods, our findings are also indicative of conserved functions for some of these genes, including a role for SoxC and SoxD genes in CNS development, SoxF in limb development and a tantalising suggestion that SoxE genes may be involved in gonadogenesis across the metazoa.ConclusionsOur study provides a new chelicerate perspective to understanding the evolution and function of Sox genes and how the retention of duplicates of such important tool-box genes after WGD has contributed to different aspects of spider embryogenesis. Future characterisation of the function of these genes in spiders will help us to better understand the evolution of the regulation of important developmental processes in arthropods and other metazoans including neurogenesis and segmentation.

scholarly journals Idiopathic Weight Reduction in Mice Deficient in the High-Mobility-Group Transcription Factor Sox8

2001 ◽  
Vol 21 (20) ◽  
pp. 6951-6959 ◽  
Author(s):  
Elisabeth Sock ◽  
Katy Schmidt ◽  
Irm Hermanns-Borgmeyer ◽  
Michael R. Bösl ◽  
Michael Wegner
Keyword(s):  
Nervous System ◽  
Neural Crest ◽  
Substantial Reduction ◽  
High Mobility ◽  
Developmental Defects ◽  
Mild Phenotype ◽  
Neural Crest Development ◽  
Sox Proteins ◽  
Male Sex ◽  
Deficient Mice

ABSTRACT Sox8, Sox9, and Sox10 constitute subgroup E within the Sox family of transcription factors. Many Sox proteins are essential regulators of development. Sox9, for instance, is required for chondrogenesis and male sex determination; Sox10 plays key roles in neural crest development and peripheral gliogenesis. The function of Sox8 has not been studied so far. Here, we generated mice deficient in this third member of subgroup E. In analogy to the case for the related Sox9 and Sox10, we expected severe developmental defects in these mice. Despite strong expression of Sox8 in many tissues, including neural crest, nervous system, muscle, cartilage, adrenal gland, kidney, and testis, homozygous mice developed normally in utero, were born at Mendelian frequencies, and were viable. A substantial reduction in weight was observed in these mice; however, this reduction was not attributable to significant structural deficits in any of the Sox8-expressing tissues. Because of frequent coexpression with either Sox9 or Sox10, the mild phenotype of Sox8-deficient mice might at least in part be due to functional redundancy between group E Sox proteins.

scholarly journals Sex Determination Directs Uniparental Mitochondrial Inheritance in Phycomyces

2013 ◽  
Vol 13 (2) ◽  
pp. 186-189 ◽  
Author(s):  
Viplendra P. S. Shakya ◽  
Alexander Idnurm
Keyword(s):  
Sex Determination ◽  
Mating Type ◽  
Sex Chromosome ◽  
High Mobility ◽  
Uniparental Inheritance ◽  
Phycomyces Blakesleeanus ◽  
Type Locus ◽  
Content Type ◽  
Mating Type Locus ◽  
Major Factors

ABSTRACTUniparental inheritance (UPI) of mitochondria is common among eukaryotes. The underlying molecular basis by which the sexes of the parents control this non-Mendelian pattern of inheritance is yet to be fully understood. Two major factors have complicated the understanding of the role of sex-specific genes in the UPI phenomenon: in many cases (i) fusion occurs between cells of unequal size or (ii) mating requires a large region of the genome or chromosome that includes genes unrelated to sex determination. The fungusPhycomyces blakesleeanusis a member of the Mucoromycotina and has a simple mating type locus encoding only one high-mobility group (HMG) domain protein, and mating occurs by fusion of isogamous cells, thus providing a model system without the limitations mentioned above. Analysis of more than 250 progeny from a series of genetic crosses between wild-type strains ofPhycomycesrevealed a correlation between the individual genes in the mating type locus and UPI of mitochondria. Inheritance is from the plus (+) sex type and is associated with degradation of the mtDNA from the minus (−) parent. These findings suggest that UPI can be directly controlled by genes that determine sex identity, independent of cell size or the complexity of the genetic composition of a sex chromosome.

Validity of an external sex determination method in Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus )

2018 ◽  
Vol 35 (1) ◽  
pp. 187-191
Author(s):  
Carolyn R. Wheeler ◽  
Ashleigh J. Novak ◽  
Gail S. Wippelhauser ◽  
James A. Sulikowski
Keyword(s):  
Sex Determination ◽  
Atlantic Sturgeon ◽  
Determination Method ◽  
Acipenser Oxyrinchus

scholarly journals Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors

2009 ◽  
Vol 185 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Cristina Gontan ◽  
Thomas Güttler ◽  
Erik Engelen ◽  
Jeroen Demmers ◽  
Maarten Fornerod ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nuclear Import ◽  
Nuclear Export ◽  
Embryonic Stem ◽  
High Mobility ◽  
Parallel Import ◽  
Sox Proteins ◽  
Bona Fide ◽  
Transport Receptor ◽  
Import Receptor

SRY and other Sox-type transcription factors are important developmental regulators with various implications in human disease. In this study, we identified Exp4 (exportin 4) as an interaction partner of Sox2 in mouse embryonic stem cells and neural progenitors. We show that, besides its established function in nuclear export, Exp4 acts as a bona fide nuclear import receptor for Sox2 and SRY. Thus, Exp4 is an example of a nuclear transport receptor carrying distinct cargoes into different directions. In contrast to a published study, we observed that the import activity of Imp-α (importin-a) isoforms toward Sox2 is negligible. Instead, we found that Imp9 and the Imp-β/7 heterodimer mediate nuclear import of Sox2 in parallel to Exp4. Import signals for the three pathways overlap and include conserved residues in the Sox2 high-mobility group (HMG) box domain that are also critical for DNA binding. This suggests that nuclear import of Sox proteins is facilitated by several parallel import pathways.

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