scholarly journals Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

2019 ◽  
Author(s):  
Svein Ole Mikalsen ◽  
Marni Tausen ◽  
Sunnvør í Kongsstovu
Keyword(s):  
Gene Family ◽  
Protein Gene ◽  
Atlantic Cod ◽  
Divergence Times ◽  
High Quality ◽  
Connexin Gene ◽  
Family Pattern ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Connexin Genes

Abstract Background: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

scholarly journals Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

2020 ◽  
Author(s):  
Svein Ole Mikalsen ◽  
Marni Tausen ◽  
Sunnvør í Kongsstovu
Keyword(s):  
Gene Family ◽  
Protein Gene ◽  
Atlantic Cod ◽  
Divergence Times ◽  
High Quality ◽  
Connexin Gene ◽  
Family Pattern ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Connexin Genes

Abstract Background: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P , but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like ). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

scholarly journals Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

2020 ◽  
Author(s):  
Svein Ole Mikalsen ◽  
Marni Tausen ◽  
Sunnvør í Kongsstovu
Keyword(s):  
Gene Family ◽  
Protein Gene ◽  
Atlantic Cod ◽  
Divergence Times ◽  
High Quality ◽  
Connexin Gene ◽  
Family Pattern ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Connexin Genes

Abstract Background: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

scholarly journals Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

2020 ◽  
Author(s):  
Svein Ole Mikalsen ◽  
Marni Tausen ◽  
Sunnvør í Kongsstovu
Keyword(s):  
Gene Family ◽  
Atlantic Cod ◽  
Divergence Times ◽  
Atlantic Herring ◽  
High Quality ◽  
Connexin Gene ◽  
Family Pattern ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Connexin Genes

Abstract Background: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence).Results: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently.Conclusions: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

Gap-junction protein gene suppresses tumorigenicity

1993 ◽  
Vol 14 (5) ◽  
pp. 1073-1075 ◽  
Author(s):  
Birgit Rose ◽  
Parmender P. Mehta ◽  
Werner R. Loewenstein
Keyword(s):  
Gap Junction ◽  
Protein Gene ◽  
Junction Protein ◽  
Gap Junction Protein

Differential Regulation of Gap Junction Protein (Connexin) Genes during Cardiomyocytic Differentiation of Mouse Embryonic Stem Cellsin Vitro

1996 ◽  
Vol 229 (2) ◽  
pp. 318-326 ◽  
Author(s):  
Yumiko Oyamada ◽  
Kiyoshi Komatsu ◽  
Hisakazu Kimura ◽  
Michio Mori ◽  
Masahito Oyamada
Keyword(s):  
Gap Junction ◽  
Embryonic Stem ◽  
Differential Regulation ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Connexin Genes

1264Genetic investigation of gap junction protein, alpha 5 of in Russian families with sick sinus syndrome

EP Europace ◽  
2020 ◽  
Vol 22 (Supplement_1) ◽  
Author(s):  
A Chernova ◽  
S Nikulina ◽  
V Maksimov
Keyword(s):  
Gap Junction ◽  
Germ Line ◽  
Vital Role ◽  
Cardiac Conduction ◽  
Control Group ◽  
Av Node ◽  
Connexin Gene ◽  
Junction Protein ◽  
A Cell ◽  
Gap Junction Protein

Abstract Background Connexin 40 (Cx40) is a gap-junction protein expressed in the heart where it mediates the coordinated electrical activation of the atria and ventricular conduction tissues, facilitates cell-to-cell adhesion, and provides pathways for direct intercellular communication. Recent studies have shown that Cx40 null mice have cardiac conduction abnormalities with a very high incidence of cardiac malformations in heterozygous (18%) and homozygous (33%) animals, indicating that Cx40 plays a vital role in cardiomorphogenesis.The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.  Methods This first study of SSS in a Russian population comprises the clinical and genetic investigation of 30 Russian families, including 67 members. The involvement of the Cx40 genes was investigated. The control group consisted of 615 patients without clinical ECG manifestations of cardiac diseases. All the examinees have undergone ECG, echocardioscopy, electrophysiological examination of the heart.  Results We conclude that polymorphism 44AG has mutation-specific effects on Cx40-related SSS.  Conclusions Mutation Cx40 impairs gap junction formation at cell-cell interfaces. This is the first demonstration of a germ line mutation in a connexin gene that emphasizes the importance of Cx40 in normal propagation in the specialized conduction system.  This study provides further evidence of the genetic heterogeneity of SSS.

Abstract 3290: G674A Polymorphism of the Connexin 40.1 Gene and Atrial Fibrillation in Patients With Dilated Cardiomyopahty

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Akiyoshi Ogimoto ◽  
Hideki Okayama ◽  
Tomoaki Ohtsuka ◽  
Jun Suzuki ◽  
Akira Kurata ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Significant Risk ◽  
Significant Risk Factor ◽  
Atrial Myocytes ◽  
Odds Ratios ◽  
Junction Protein ◽  
Significant Difference ◽  
Gap Junction Protein ◽  
Connexin Genes ◽  
Allele Model

Background: Atrial fibrillation (AF) is the most common type of cardiac arrhythmia and a leading cause of cardiovascular morbidity. The cardiac gap-junction protein connexin is expressed in atrial myocytes and mediates the coordinated electrical activation of the atria. Some polymorphisms in connexin genes were reported to be significantly associated with AF. We hypothesized that polymorphism (G674A) in the connexin 40.1 gene may be associated with AF in patients with dilated cardiomyopathy (DCM). Methods and Results: We genotyped this polymorphism (G674A, rs595652 ) in 83 patients with DCM by using the TaqMan chemical method. Patients were classified into AF group (n=21) if they had AF, and sinus rhythm (SR) group (n=62) if they had SR. Distribution of the connexin 40.1 genotypes (G/G, G/A, and A/A) among the total patients with DCM was 27.7%, 54.2%, and 18.1%, respectively. Allele frequency for the A allele was 0.52 in the AF group and 0.43 in the SR group. In a dominant G allele model (G/G and G/A genotypes vs A/A genotype), there was a significant difference in genotypes between the AF group and the SR group (p=0.035). This table shows odds ratios for atrial fibrillation in patients with DCM determined by logistic regression analysis. The odds of AF in DCM patients with the A/A genotype was 3.38-fold. In addition, age and left atrial dimension were also risk factors. Conclusion: The A/A genotype in the connexin 40.1 gene is a significant risk factor for AF in patients with DCM. Odds Ratios* for Atrial Fibrillation

Regulation of Gap Junction Protein (Connexin) Genes and Function in Differentiating ES Cells

2003 ◽  
pp. 63-69
Author(s):  
Masahito Oyamada ◽  
Yumiko Oyamada ◽  
Tomoyuki Kaneko ◽  
Tetsuro Takamatsu
Keyword(s):  
Gap Junction ◽  
Es Cells ◽  
Junction Protein ◽  
Gap Junction Protein ◽  
Connexin Genes ◽  
And Function
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