scholarly journals An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

2017 ◽  
Vol 27 (5) ◽  
pp. 885-896 ◽  
Author(s):  
Bernardo J. Clavijo ◽  
Luca Venturini ◽  
Christian Schudoma ◽  
Gonzalo Garcia Accinelli ◽  
Gemy Kaithakottil ◽  
...  
Keyword(s):  
Wheat Genome ◽  
Chromosomal Translocations ◽  
Allohexaploid Wheat

scholarly journals Methylation, Transcription, and Rearrangements of Transposable Elements in Synthetic Allopolyploids

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Beery Yaakov ◽  
Khalil Kashkush
Keyword(s):  
Transposable Elements ◽  
Transcriptional Activation ◽  
Genome Structure ◽  
Biological Significance ◽  
Wheat Genome ◽  
Wheat Species ◽  
Noncoding Sequences ◽  
Genomic Stress ◽  
Underlying Mechanisms ◽  
Allohexaploid Wheat

Transposable elements (TEs) constitute over 90% of the wheat genome. It was suggested that “genomic stress” such as hybridity or polyploidy might activate transposons. Intensive investigations of various polyploid systems revealed that allopolyploidization event is associated with widespread changes in genome structure, methylation, and expression involving low- and high-copy, coding and noncoding sequences. Massive demethylation and transcriptional activation of TEs were also observed in newly formed allopolyploids. Massive proliferation, however, was reported for very limited number of TE families in various polyploidy systems. The aim of this review is to summarize the accumulated data on genetic and epigenetic dynamics of TEs, particularly in synthetic allotetraploid and allohexaploid wheat species. In addition, the underlying mechanisms and the potential biological significance of TE dynamics following allopolyploidization are discussed.

scholarly journals The Pros and Cons of Rye Chromatin Introgression into Wheat Genome

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 456
Author(s):  
Kinga Moskal ◽  
Sylwia Kowalik ◽  
Wiesław Podyma ◽  
Bogusław Łapiński ◽  
Maja Boczkowska
Keyword(s):  
Agronomic Traits ◽  
Wheat Breeding ◽  
Wheat Genome ◽  
Chromosomal Translocations ◽  
Biotic And Abiotic Stresses ◽  
Substitution Lines ◽  
Cereal Species ◽  
Pros And Cons ◽  
Improvement Programs ◽  
End Use

Rye is one of the most commonly used sources of elite genes in wheat improvement programs. Due to the high collinearity of the genomes of both cereal species, it is possible to obtain interspecific chromosomal translocations and substitution lines. Rye chromatin is used to transfer numerous genes for resistance to biotic and abiotic stresses into the wheat genome. Introgression has also resulted in improved agronomic traits. However, despite the numerous advantages, the transfer of large fragments or whole chromosomes has been quite often accompanied by a decrease in end-use quality. This paper presents an overview of the benefits and drawbacks of using rye as a source of variability in wheat breeding.

Selective Destruction of Tumor Cells through Specific Inhibition of Products Resulting from Chromosomal Translocations

2001 ◽  
Vol 1 (2) ◽  
pp. 109-119 ◽  
Author(s):  
A. Rodriguez-Garcia ◽  
M. Sanchez-Martin ◽  
J. Perez-Losada ◽  
P. Perez-Mancera ◽  
A. Sagrera-Aparisi ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Chromosomal Translocations ◽  
Specific Inhibition ◽  
Selective Destruction

scholarly journals Metabolic Effects of Recurrent Genetic Aberrations in Multiple Myeloma

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 396
Author(s):  
Timon A. Bloedjes ◽  
Guus de Wilde ◽  
Jeroen E. J. Guikema
Keyword(s):  
Multiple Myeloma ◽  
Cell Metabolism ◽  
Chromosomal Rearrangements ◽  
Chromosomal Translocations ◽  
Metabolic Effects ◽  
Aberrant Expression ◽  
Metabolic Functions ◽  
Complex Chromosomal Rearrangements ◽  
Cancer Cell Metabolism ◽  
The Many

Oncogene activation and malignant transformation exerts energetic, biosynthetic and redox demands on cancer cells due to increased proliferation, cell growth and tumor microenvironment adaptation. As such, altered metabolism is a hallmark of cancer, which is characterized by the reprogramming of multiple metabolic pathways. Multiple myeloma (MM) is a genetically heterogeneous disease that arises from terminally differentiated B cells. MM is characterized by reciprocal chromosomal translocations that often involve the immunoglobulin loci and a restricted set of partner loci, and complex chromosomal rearrangements that are associated with disease progression. Recurrent chromosomal aberrations in MM result in the aberrant expression of MYC, cyclin D1, FGFR3/MMSET and MAF/MAFB. In recent years, the intricate mechanisms that drive cancer cell metabolism and the many metabolic functions of the aforementioned MM-associated oncogenes have been investigated. Here, we discuss the metabolic consequences of recurrent chromosomal translocations in MM and provide a framework for the identification of metabolic changes that characterize MM cells.

scholarly journals Toward a Personalized Therapy in Soft-Tissue Sarcomas: State of the Art and Future Directions

Cancers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2359
Author(s):  
Liliana Montella ◽  
Lucia Altucci ◽  
Federica Sarno ◽  
Carlo Buonerba ◽  
Stefano De Simone ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Soft Tissue Sarcomas ◽  
Chromosomal Translocations ◽  
Intrinsic Variability ◽  
Poor Survival ◽  
Genomic Alterations ◽  
Future Directions ◽  
Oncogenic Mutations ◽  
Targeted Treatments ◽  
Innovative Therapies

Soft-tissue sarcomas are rare tumors characterized by pathogenetic, morphological, and clinical intrinsic variability. Median survival of patients with advanced tumors are usually chemo- and radio-resistant, and standard treatments yield low response rates and poor survival results. The identification of defined genomic alterations in sarcoma could represent the premise for targeted treatments. Summarizing, soft-tissue sarcomas can be differentiated into histotypes with reciprocal chromosomal translocations, with defined oncogenic mutations and complex karyotypes. If the latter are improbably approached with targeted treatments, many suggest that innovative therapies interfering with the identified fusion oncoproteins and altered pathways could be potentially resolutive. In most cases, the characteristic genetic signature is discouragingly defined as “undruggable”, which poses a challenge for the development of novel pharmacological approaches. In this review, a summary of genomic alterations recognized in most common soft-tissue sarcoma is reported together with current and future therapeutic opportunities.

scholarly journals Typing FGFR2 translocation determines the response to targeted therapy of intrahepatic cholangiocarcinomas

2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Xiaohong Pu ◽  
Qing Ye ◽  
Jing Cai ◽  
Xin Yang ◽  
Yao Fu ◽  
...  
Keyword(s):  
Targeted Therapy ◽  
Bile Duct ◽  
Kinase Inhibitors ◽  
Fibroblast Growth Factor Receptor ◽  
Growth Factor Receptor ◽  
Chromosomal Translocations ◽  
Small Bile Duct ◽  
Druggable Targets ◽  
Inhibitor Treatment ◽  
Specific Inhibitors

AbstractChromosomal translocations involving fibroblast growth factor receptor 2 (FGFR2) gene at the breakpoints are common genetic lesions in intrahepatic cholangiocarcinoma (ICC) and the resultant fusion protein products have emerged as promising druggable targets. However, predicting the sensitivity of FGFR2 fusions to FGFR kinase inhibitors is crucial to the prognosis of the ICC-targeted therapy. Here, we report identification of nine FGFR2 translocations out of 173 (5.2%) ICC tumors. Although clinicopathologically these FGFR2 translocation bearing ICC tumors are indistinguishable from the rest of the cohort, they are invariably of the mass-forming type originated from the small bile duct. We show that the protein products of FGFR2 fusions can be classified into three subtypes based on the breaking positions of the fusion partners: the classical fusions that retain the tyrosine kinase (TK) and the Immunoglobulin (Ig)-like domains (n = 6); the sub-classical fusions that retain only the TK domain without the Ig-like domain (n = 1); and the non-classical fusions that lack both the TK and Ig-like domains (n = 2). We demonstrate that cholangiocarcinoma cells engineered to express the classical and sub-classical fusions show sensitivity to FGFR-specific kinase inhibitors as evident by the suppression of MAPK/ERK and AKT/PI3K activities following the inhibitor treatment. Furthermore, the kinase-deficient mutant of the sub-classical fusion also lost its sensitivity to the FGFR-specific inhibitors. Taken together, our study suggests that it is essential to determine the breakpoint and type of FGFR2 fusions in the small bile duct subtype of ICC for the targeted treatment.

scholarly journals A Microsatellite Map of Wheat

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2007-2023 ◽  
Author(s):  
Marion S Röder ◽  
Victor Korzun ◽  
Katja Wendehake ◽  
Jens Plaschke ◽  
Marie-Hélène Tixier ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Population ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
D Genome ◽  
B Genome ◽  
Microsatellite Map ◽  
A Genome ◽  
Polymorphic Microsatellite ◽  
Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

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