scholarly journals Chimeric Genes Revealed in the Polyploidy Fish Hybrids of Carassius cuvieri (Female) × Megalobrama amblycephala (Male)

2016 ◽  
Author(s):  
Fangzhou Hu ◽  
Chang Wu ◽  
Yunfan Zhou ◽  
Shi Wang ◽  
Jun Xiao ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Orthologous Gene ◽  
Megalobrama Amblycephala ◽  
K Channel ◽  
The Novel ◽  
Distant Hybridization ◽  
Chimeric Genes ◽  
Hybrid Fish ◽  
Fish Hybrids ◽  
Phenotypic Novelty

AbstractThe genomes of newly formed natural or artificial polyploids may experience rapid gene loss and genome restructuring. In this study, we obtained tetraploid hybrids (4n=148, 4nJB) and triploid hybrids (3n=124, 3nJB) derived from the hybridization of two different subfamily species Carassius cuvieri (♀, 2n = 100, JCC) and Megalobrama amblycephala (♂, 2n = 48, BSB). Some significant morphological and physiological differences were detected in the polyploidy hybrids compared with their parents. To reveal the molecular traits of the polyploids, we compared the liver transcriptomes of 4nJB, 3nJB and their parents. The results indicated high proportion chimeric genes (31 > %) and mutated orthologous genes (17 > %) both in 4nJB and 3nJB. We classified 10 gene patterns within three categories in 4nJB and 3nJB orthologous gene, and characterized 30 randomly chosen genes using genomic DNA to confirm the chimera or mutant. Moreover, we mapped chimeric genes involved pathways and discussed that the phenotypic novelty of the hybrids may relate to some chimeric genes. For example, we found there is an intragenic insertion in the K+ channel kcnk5b, which may be related to the novel presence of the barbels in 4nJB. Our results indicated that the genomes of newly formed polyploids experienced rapid restructuring post-polyploidization, which may results in the phenotypic and phenotypic changes among the polyploidy hybrid offspring. The formation of the 4nJB and 3nJB provided new insights into the genotypic and phenotypic diversity of hybrid fish resulting from distant hybridization between subfamilies.

scholarly journals Emerging crosstalk between two signaling pathways coordinates K+ and Na+ homeostasis in the halophyte Hordeum brevisubulatum

2020 ◽  
Vol 71 (14) ◽  
pp. 4345-4358
Author(s):  
Haiwen Zhang ◽  
Hao Feng ◽  
Junwen Zhang ◽  
Rongchao Ge ◽  
Liyuan Zhang ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Regulatory Mechanisms ◽  
K Channel ◽  
Interacting Proteins ◽  
The Novel ◽  
Voltage Gated ◽  
Primary Core ◽  
High Salt Stress ◽  
Hordeum Brevisubulatum

Abstract K+/Na+ homeostasis is the primary core response for plant to tolerate salinity. Halophytes have evolved novel regulatory mechanisms to maintain a suitable K+/Na+ ratio during long-term adaptation. The wild halophyte Hordeum brevisubulatum can adopt efficient strategies to achieve synergistic levels of K+ and Na+ under high salt stress. However, little is known about its molecular mechanism. Our previous study indicated that HbCIPK2 contributed to prevention of Na+ accumulation and K+ reduction. Here, we further identified the HbCIPK2-interacting proteins including upstream Ca2+ sensors, HbCBL1, HbCBL4, and HbCBL10, and downstream phosphorylated targets, the voltage-gated K+ channel HbVGKC1 and SOS1-like transporter HbSOS1L. HbCBL1 combined with HbCIPK2 could activate HbVGKC1 to absorb K+, while the HbCBL4/10–HbCIPK2 complex modulated HbSOS1L to exclude Na+. This discovery suggested that crosstalk between the sodium response and the potassium uptake signaling pathways indeed exists for HbCIPK2 as the signal hub, and paved the way for understanding the novel mechanism of K+/Na+ homeostasis which has evolved in the halophytic grass.

scholarly journals CTCF, a novel fusion partner of ETO2 in a post-transplant relapsed acute myeloid leukemia patient

2020 ◽  
Author(s):  
Jiao Li ◽  
Zhen Shen ◽  
zheng wang ◽  
Yi Xu ◽  
Zhao Zeng ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Critical Role ◽  
Fusion Partner ◽  
The Novel ◽  
Rna Seq ◽  
Rt Pcr ◽  
Chimeric Genes ◽  
Post Transplant ◽  
Acute Myeloid

Abstract Background ETO2 is a nuclear co-repressor, which plays a critical role in the regulation of the cell cycle, self-renewal capacity, and differentiation of hematopoietic progenitor cells. Methods We identified novel fusion transcripts involving ETO2 and CTCF by RNA-seq in a post-transplant relapsed case. Results The CTCF-ETO2 and ETO2-CTCF chimeric genes were validated by RT-PCR and Sanger sequencing. In addition, both transcripts apparently promoted cell proliferation which is beneficial to tumorigenesis. Conclusion The novel fusions may have prognostic value and pathogenic mechanisms in acute myeloid leukemia.

scholarly journals Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

2016 ◽  
Author(s):  
Lihai Ye ◽  
Xiaojun Tang ◽  
Yiyi Chen ◽  
Li Ren ◽  
Fangzhou Hu ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Artificial Chromosome ◽  
Strand Break ◽  
Bacterial Artificial Chromosomes ◽  
Distant Hybridization ◽  
Artificial Chromosomes ◽  
Hybrid Fish ◽  
The Relationship ◽  
Allotetraploid Hybrid

AbstractThe formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species and therefore it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs are benefit from the intervention of recombinases. In addition, TRs and TEs are linked not only with the recombinations, but also with the insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents which reduces the genomic shock effects and favors the evolutionary and adaptive capacity of the allotetraploidization. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.

Molecular Cloning and Expression of the Novel Splice Variants of K+ Channel-Interacting Protein 2

2001 ◽  
Vol 282 (1) ◽  
pp. 96-102 ◽  
Author(s):  
Susumu Ohya ◽  
Yuichi Morohashi ◽  
Katsuhiko Muraki ◽  
Taisuke Tomita ◽  
Minoru Watanabe ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Splice Variants ◽  
Cloning And Expression ◽  
K Channel ◽  
The Novel ◽  
Interacting Protein

Functional properties of a brain-specific NH2-terminally spliced modulator of Kv4 channels

2003 ◽  
Vol 285 (1) ◽  
pp. C161-C170 ◽  
Author(s):  
Linda M. Boland ◽  
Min Jiang ◽  
So Yeong Lee ◽  
Scott C. Fahrenkrug ◽  
Mark T. Harnett ◽  
...  
Keyword(s):  
Terminal Region ◽  
K Channel ◽  
The Novel ◽  
Splice Form ◽  
Interacting Protein ◽  
Current Decay ◽  
Amino Terminal ◽  
Human Genes ◽  
Kv4 Channels ◽  
Inactivation Gating

Kv4/K channel-interacting protein (KChIP) potassium channels are a major class of rapidly inactivating K channels in brain and heart. Considering the importance of alternative splicing to the quantitative features of KChIP gating modulation, a previously uncharacterized splice form of KChIP1 was functionally characterized. The KChIP1b splice variant differs from the previously characterized KChIP1a splice form by the inclusion of a novel amino-terminal region that is encoded by an alternative exon that is conserved in mouse, rat, and human genes. The expression of KChIP1b mRNA was high in brain but undetectable in heart or liver by RT-PCR. In cerebellar tissue, KChIP1b and KChIP1a transcripts were expressed at nearly equal levels. Coexpression of KChIP1b or KChIP1a with Kv4.2 channels in oocytes slowed K current decay and destabilized open-inactivated channel gating. Like other KChIP subunits, KChIP1b increased Kv4.2 current amplitude and KChIP1b also shifted Kv4.2 conductance-voltage curves by —10 mV. The development of Kv4.2 channel inactivation accessed from closed gating states was faster with KChIP1b coexpression. Deletion of the novel amino-terminal region in KChIP1b selectively altered the subunit's modulation of Kv4.2 closed inactivation gating. The role of the KChIP1b NH2-terminal region was further confirmed by direct comparison of the properties of the NH2-terminal deletion mutant and the KChIP1a subunit, which is encoded by a transcript that lacks the novel exon. The features of KChIP1b modulation of Kv4 channels are likely to be conserved in mammals and demonstrate a role for the KChIP1 NH2-terminal region in the regulation of closed inactivation gating.

Safety of the novel atrial-selective K+-channel blocker AVE0118 in experimental heart failure

2008 ◽  
Vol 379 (3) ◽  
pp. 225-232 ◽  
Author(s):  
H.-J. Schneider ◽  
O. Husser ◽  
M. Rihm ◽  
S. Fredersdorf ◽  
C. Birner ◽  
...  
Keyword(s):  
Heart Failure ◽  
Channel Blocker ◽  
K Channel ◽  
The Novel ◽  
Experimental Heart Failure

scholarly journals Potential role of chimeric genes in pathway-related gene co-expression modules

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Piaopiao Li ◽  
Yingxia Li ◽  
Lei Ma
Keyword(s):  
T Cells ◽  
Gene Fusion ◽  
Epigenetic Modification ◽  
Protein Localization ◽  
Binding Activity ◽  
The Novel ◽  
Chimeric Genes ◽  
Novel Proteins ◽  
Cell Growth And Differentiation ◽  
Underlying Mechanisms

Abstract Background Gene fusion has epigenetic modification functions. The novel proteins encoded by gene fusion products play a role in cancer development. Therefore, a better understanding of the novel protein products may provide insights into the pathogenesis of tumors. However, the characteristics of chimeric genes are rarely studied. Here, we used weighted co-expression network analysis to investigate the biological roles and underlying mechanisms of chimeric genes. Methods Download the pig transcriptome data, we screened chimeric genes and parental genes from 688 sequences and 153 samples, predict their domains, and analyze their associations. We constructed a co-expression network of chimeric genes in pigs and conducted Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the generated modules using DAVID to identify key networks and modules related to chimeric genes. Results Our findings showed that most of the protein domains of chimeric genes were derived from fused pre-genes. Chimeric genes were enriched in modules involved in the negative regulation of cell proliferation and protein localization to centrosomes. In addition, the chimeric genes were related to the growth factor-β superfamily, which regulates cell growth and differentiation. Furthermore, in helper T cells, chimeric genes regulate the specific recognition of T cell receptors, implying that chimeric genes play a key role in the regulation pathway of T cells. Chimeric genes can produce new domains, and some chimeric genes are a key role involved in pathway-related function. Conclusions Most chimeric genes show binding activity. Domains of chimeric genes are derived from several combinations of parent genes. Chimeric genes play a key role in the regulation of several cellular pathways. Our findings may provide new directions to explore the roles of chimeric genes in tumors.

scholarly journals Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (♀) × Culter alburnus (♂)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wuhui Li ◽  
Shi Wang ◽  
Jie Hu ◽  
Chenchen Tang ◽  
Chang Wu ◽  
...  
Keyword(s):  
Differential Expression ◽  
Megalobrama Amblycephala ◽  
Genetic Breeding ◽  
Dietary Adaptation ◽  
Homoeologous Genes ◽  
Hybrid Fish ◽  
Culter Alburnus ◽  
Mechanistic Basis ◽  
Fish Genetic Breeding ◽  
Asymmetric Expression

Abstract Background Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish. Results Differential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet. Conclusions Our results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application.

scholarly journals Rapid genomic DNA variation in newly hybridized carp lineages derived from Cyprinus carpio (♀) × Megalobrama amblycephala (♂)

2019 ◽  
Author(s):  
Kaikun Luo ◽  
Shi Wang ◽  
Yeqing Fu ◽  
Pei Zhou ◽  
Xuexue Huang ◽  
...  
Keyword(s):  
Common Carp ◽  
Genomic Dna ◽  
First Generation ◽  
Second Generation ◽  
Hox Genes ◽  
Gene Clusters ◽  
Megalobrama Amblycephala ◽  
Distant Hybridization ◽  
Hox Gene ◽  
Blunt Snout Bream

Abstract Background: Distant hybridization can generate changes in phenotypes and genotypes that lead to the formation of new hybrid lineages with genetic variation. In this study, based on the establishment of two bisexual fertile carp lineages, including the improved diploid common carp (IDC) lineage and the improved diploid scattered mirror carp (IDMC) lineage, from the interspecific hybridization of common carp (Cyprinus carpio, 2n = 100) (♀) × blunt snout bream (Megalobrama amblycephala, 2n = 48) (♂), provided a good platform to investigate the relationship of genetic and variation between the parents and their hybrid progenies. Result: In this study, we investigated the genetic variation of 12 Hox genes in the two types of carp lineages derived from common carp (♀) × blunt snout bream (♂). Hox gene clusters were abundant in the first generation of IDC, but most were not stably inherited in the second generation. In contrast, we did not find obvious mutations in Hox genes in the first generation of IDMC, and almost all the Hox gene clusters were stably inherited from the first generation to the second generation of IDMC. Interestingly, we found obvious recombinant clusters of Hox genes in both carp lineages, and partially recombinant clusters of Hox genes were stably inherited from the first generation to the second generation in both types of carp lineages. On the other hand, some Hox genes were gradually becoming pseudogenes, and some genes were completely pseudogenised in IDC or IDMC. Conclusions: Our results provided important evidence that distant hybridization produces rapid genomic DNA changes that may or may not be stably inherited, providing novel insights into the function of hybridization in the establishment of improved lineages used as new fish resources for aquaculture.

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