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.

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

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kaikun Luo ◽  
Shi Wang ◽  
Yeqing Fu ◽  
Pei Zhou ◽  
Xuexue Huang ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Common Carp ◽  
Cyprinus Carpio ◽  
Genomic Dna ◽  
First Generation ◽  
Second Generation ◽  
Gene Clusters ◽  
Megalobrama Amblycephala ◽  
Distant Hybridization ◽  
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, 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 genetic relationship 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 improved 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 improved carp lineages, and partially recombinant clusters of Hox genes were stably inherited from the first generation to the second generation in both types of improved 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.

Hox gene clusters in blunt snout bream, Megalobrama amblycephala and comparison with those of zebrafish, fugu and medaka genomes

Gene ◽  
2007 ◽  
Vol 400 (1-2) ◽  
pp. 60-70 ◽  
Author(s):  
Shu-Ming Zou ◽  
Xia-Yun Jiang ◽  
Zhu-Zi He ◽  
Jian Yuan ◽  
Xiang-Nan Yuan ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Megalobrama Amblycephala ◽  
Hox Gene ◽  
Blunt Snout Bream

The CALM/AF10 Fusion: Molecular Analysis of the Fusion Transcripts in 13 Cases of AML and ALL; Gene Expression Profiling Reveals HOX Gene Deregulation.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2895-2895 ◽  
Author(s):  
Alexandre Krause ◽  
Alexander Kohlmann ◽  
Torsten Haferlach ◽  
Claudia Schoch ◽  
Susanne Schnittger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fusion Protein ◽  
Hox Genes ◽  
Lymphoblastic Leukemia ◽  
Critical Role ◽  
Gene Clusters ◽  
Dominant Negative ◽  
Nucleotide Position ◽  
Gamma Delta ◽  
Hox Gene

Abstract The t(10;11)(p13;q14) is a recurring translocation associated with the CALM/AF10 fusion gene which is found in undifferentiated leukemia, acute myeloid leukemia, acute lymphoblastic leukemia and malignant lymphoma with poor prognosis. The CALM/AF10 fusion protein was reported to be the most common fusion protein in T-ALL with TCR gamma delta rearrangement. We have analyzed samples from 9 patients with different types of leukemia: case 1 (AML M2), case 2 (AML M0), case 3 (Pre T-ALL), case 4 (Acute Undifferentiated Leukemia), case 5 (PreT-ALL), case 6 and 7 (ProT-ALL), case 8 (T-ALL), case 9 (AML), with a t(10;11) translocation suggesting a CALM/AF10-rearrangement. The samples were analyzed for the presence of the CALM/AF10 and AF10/CALM mRNA by RT-PCR and sequence analysis. All these patients were found positive for the CALM/AF10 fusion. In addition, we analyzed a series of twenty-nine patients with T-ALL with gamma delta rearrangement. Among these patients, four were positive for CALM/AF10 transcripts, indicating a high incidence of CALM/AF10 fusions in this group of leukemia. We found three different breakpoints in CALM at nucleotide 1926, 2091 and a new exon, with 106 bases inserted after nt 2064 of CALM in patient 4. In AF10 four breakpoints were identified: at nucleotide position 424, 589, 883 and 979. In seven patients it was also possible to amplify the reciprocal AF10/CALM fusion transcript (case 1, 3, 4, 8, 9, 10 and 11). There was no correlation between disease phenotype and breakpoint location. The patients were 5 to 46 years old (median 25). Ten CALM/AF10 positive patients were further analyzed using oligonucleotide microarrays representing 33,000 different genes (U133 set, Affymetrix). Analysis of microarray gene expression signatures of these patients revealed high expression levels of the homeobox gene MEIS1 and the HOXA cluster genes HOXA1, HOXA4, HOXA5, HOXA7, HOXA9, and HOXA10. The overexpression of HOX genes seen in these CALM/AF10 positive leukemias is reminiscent of the pattern seen in leukemias with rearrangements of the MLL gene, and complex aberrant karyotypes suggesting a common effector pathway (i.e. HOX gene deregulation) for these diverse leukemias. It is known that alhambra, the Drosophila homologue of AF10 can act on polycomb group responsive elements, which play a critical role in the regulation of the HOX gene clusters. It is thus conceivable that the CALM/AF10 fusion proteins acts in a dominant negative fashion on wild type AF10 function relieving the repression that is presumably normally exerted by AF10 on the expression of HOX genes.

scholarly journals Hox Gene Collinearity May Be Related to Noether Theory on Symmetry and Its Linked Conserved Quantity

J ◽  
2020 ◽  
Vol 3 (2) ◽  
pp. 151-161
Author(s):  
Spyros Papageorgiou
Keyword(s):  
Hox Genes ◽  
Fundamental Property ◽  
Gene Clusters ◽  
Strand Break ◽  
Early Embryo ◽  
Conserved Quantity ◽  
Biophysical Model ◽  
Self Similarity ◽  
Hox Gene ◽  
Hox Clusters

Hox Gene Collinearity (HGC) is a fundamental property that controls the development of many animal species, including vertebrates. In the Hox gene clusters, the genes are located in a sequential order Hox1, Hox2, Hox3, etc., along the 3’ to 5’ direction of the cluster in the chromosome. During Hox cluster activation, the Hox genes are expressed sequentially in the ontogenetic units D1, D2, D3, etc., along the anterior–posterior axis (A-P) of the early embryo. This collinearity, first observed by E.B. Lewis, is surprising because the spatial collinearity of these structures (Hox clusters and embryos) correlates entities that differ by about four orders of magnitude. Biomolecular mechanisms alone cannot explain such correlations. Long-range physical interactions, such as diffusion or electric attractions, should be involved. A biophysical model (BM) was formulated, which, in alignment with the biomolecular processes, successfully describes the existing vertebrate genetic engineering data. One hundred years ago, Emmy Noether made a fundamental discovery in mathematics and physics. She proved, rigorously, that a physical system obeying a symmetry law (e.g., rotations or self-similarity) is followed by a conserved physical quantity. It is argued here that HGC obeys a ‘primitive’ self-similarity symmetry. In this case, the associated primitive conserved quantity is the irreversibly increasing ‘ratchet’-like Hoxgene ordering where some genes may be missing. The genes of a vertebrate Hox clusterare located along a finite straight line. The same order follows the ontogenetic unitsof the vertebrate embryo. Therefore, HGC is a manifestation of a primitive Noether Theory (NT). NT may be applied to other than the vertebrate case, for instance, to animals with a circular topological symmetry. For example, the observed abnormal Hox gene ordering of the echinoderm Hox clusters may be reproduced by a double-strand break of the circular Hox gene ordering and its subsequent incorporation in the flanking chromosome.

scholarly journals HOX Gene Aberrant Expression in Skin Melanoma: A Review

2012 ◽  
Vol 2012 ◽  
pp. 1-4 ◽  
Author(s):  
Gérald E. Piérard ◽  
Claudine Piérard-Franchimont
Keyword(s):  
Protein Interactions ◽  
Hox Genes ◽  
Tumour Progression ◽  
Gene Clusters ◽  
Skin Melanoma ◽  
Protein Protein Interactions ◽  
Cell Nuclei ◽  
Aberrant Expression ◽  
Hox Gene ◽  
Hox Protein

The homeobox family and its subset of HOX gene products represent a family of transcription factors directing DNA-protein and protein-protein interactions. In the embryo, they are central regulators in cell differentiation during morphogenesis. A series of genes of the four HOX gene clusters A, B, C, and D were reported to show aberrant expressions in oncogenesis, particularly in cutaneous malignant melanoma (CMM). They are involved in cell proliferation and progression in the CMM metastatic path. We present relevant peer-reviewed literature findings about the aberrant expression of HOX genes in CMM. The number of CMM cell nuclei exhibiting aberrant HOX protein expression appears correlated with tumour progression.

scholarly journals Hox Gene Collinearity May Be Related to Noether’s Theory on Symmetry and Its Linked Conserved Quantities

2019 ◽  
Author(s):  
Spyros Papageorgiou
Keyword(s):  
Hox Genes ◽  
Fundamental Property ◽  
Gene Clusters ◽  
Early Embryo ◽  
Biophysical Model ◽  
Self Similarity ◽  
Hox Gene ◽  
Hox Cluster ◽  
Straight Line ◽  
Physical Interactions

Hox Gene Collinearity (HGC) is a fundamental property that determines the development of many animal clades including Vertebrates. In the Hox gene clusters the genes are located in a sequence Hox1, Hox2, Hox3,… along the 3’ to 5’ direction of the cluster in the chromosome. During Hox cluster activation the Hox genes are expressed sequentially in the ontogenetic units D1, D2, D3,… along the anterior (A)- Posterior (P) axis of the early embryo. This collinearity, first observed by E.B. Lewis, is surprising because the spatial extent of these structures (Hox clusters and embryos) differ by about 4 orders of magnitude. Biomolecular mechanisms alone cannot explain this correlation. Long range physical interactions like diffusion or electric attractions should be involved. A biophysical model (BM) has been  formulated which cooperates with the biomolecular processes and describes the data successfully. Hundred years ago E. Noether made a fundamental discovery in Mathematics and Physics. She proved rigorously that a physical system obeying a symmetry law (e.g.rotations or self similarity) is linked to a conserved physical quantity. It is argued here that HGC obeys a ‘primitive’ self similarity symmetry of the genes of a Hox cluster along a finite straight line. In the case of Vertebrates, the associated partially conserved quantity is the ever increasing ‘ratchet’- like gene ordering where some Hox genes are missing. Another application of Noether’s Theory is performed to rotationally symmetric embryos like the sea urchin.

scholarly journals Role of HOX Genes in Stem Cell Differentiation and Cancer

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Seema Bhatlekar ◽  
Jeremy Z. Fields ◽  
Bruce M. Boman
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Hox Genes ◽  
Stem Cell Differentiation ◽  
Gene Clusters ◽  
Bilateral Symmetry ◽  
The Cancer Genome Atlas ◽  
Cancer Development ◽  
Hox Gene

HOX genes encode an evolutionarily conserved set of transcription factors that control how the phenotype of an organism becomes organized during development based on its genetic makeup. For example, in bilaterian-type animals, HOX genes are organized in gene clusters that encode anatomic segment identity, that is, whether the embryo will form with bilateral symmetry with a head (anterior), tail (posterior), back (dorsal), and belly (ventral). Although HOX genes are known to regulate stem cell (SC) differentiation and HOX genes are dysregulated in cancer, the mechanisms by which dysregulation of HOX genes in SCs causes cancer development is not fully understood. Therefore, the purpose of this manuscript was (i) to review the role of HOX genes in SC differentiation, particularly in embryonic, adult tissue-specific, and induced pluripotent SC, and (ii) to investigate how dysregulated HOX genes in SCs are responsible for the development of colorectal cancer (CRC) and acute myeloid leukemia (AML). We analyzed HOX gene expression in CRC and AML using information from The Cancer Genome Atlas study. Finally, we reviewed the literature on HOX genes and related therapeutics that might help us understand ways to develop SC-specific therapies that target aberrant HOX gene expression that contributes to cancer development.

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