scholarly journals Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine

2017 ◽  
Vol 175 (2) ◽  
pp. 786-801 ◽  
Author(s):  
Pablo Carbonell-Bejerano ◽  
Carolina Royo ◽  
Rafael Torres-Pérez ◽  
Jérôme Grimplet ◽  
Lucie Fernandez ◽  
...  
Keyword(s):  
Genome Rearrangements

scholarly journals Mitochondrial Genome Rearrangements in Glomus Species Triggered by Homologous Recombination between Distinct mtDNA Haplotypes

2013 ◽  
Vol 5 (9) ◽  
pp. 1628-1643 ◽  
Author(s):  
Denis Beaudet ◽  
Yves Terrat ◽  
Sébastien Halary ◽  
Ivan Enrique de la Providencia ◽  
Mohamed Hijri
Keyword(s):  
Homologous Recombination ◽  
Mitochondrial Genome ◽  
Genome Rearrangements ◽  
Mtdna Haplotypes ◽  
Glomus Species

scholarly journals Vector and Helper Genome Rearrangements Occur During Production of Helper-Dependent Adenoviral Vectors

2013 ◽  
Vol 24 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Miwon Ahn ◽  
Aisha Gamble ◽  
Scott R. Witting ◽  
Jack Magrisso ◽  
Sneha Surendran ◽  
...  
Keyword(s):  
Genome Rearrangements ◽  
Adenoviral Vectors

scholarly journals Human rDNA Copy Number Is Unstable in Metastatic Breast Cancers

2019 ◽  
Author(s):  
Virginia Valori ◽  
Katalin Tus ◽  
Christina Laukaitis ◽  
David T. Harris ◽  
Lauren LeBeau ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Instability ◽  
Gene Clusters ◽  
Genome Rearrangements ◽  
Epigenetic Silencing ◽  
Healthy Tissue ◽  
Gene Promoters ◽  
Number Variation

AbstractEpigenetic silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of epigenetic silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their etiology. We find support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumors and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation – both losses and gains of copies – compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed etiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.Authors’ StatementOne of the common hallmarks of cancer is genome instability, including hypermutation and changes to chromosome structure. Using tumor tissues obtained from women with invasive ductal carcinoma, we find that a sensitive area of the genome – the ribosomal DNA gene repeat cluster – shows hypervariability in copy number. The patterns we observe as not consistent with an adaptive loss leading to increased tumor growth, but rather we conclude that copy number variation at repeat DNA is a general consequence of reduced heterochromatin function in cancer progression.

scholarly journals PaReBrick: PArallel REarrangements and BReaks identification toolkit

2021 ◽  
Author(s):  
Alexey Zabelkin ◽  
Yulia Yakovleva ◽  
Olga Bochkareva ◽  
Nikita Alexeev
Keyword(s):  
Antigenic Variation ◽  
Phenotypic Diversity ◽  
Genome Rearrangements ◽  
Supplementary Information ◽  
High Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Phyletic Pattern ◽  
Bacterial Populations ◽  
Different Strains

Abstract Motivation High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results Here we define the term “parallel rearrangements” as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. Availability PaReBrick is written in Python and is available on GitHub https://github.com/ctlab/parallelrearrangements Supplementary information Supplementary data are available at Bioinformatics online.

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