scholarly journals Centromere scission drives chromosome shuffling and reproductive isolation

2019 ◽  
Author(s):  
Vikas Yadav ◽  
Sheng Sun ◽  
Marco A. Coelho ◽  
Joseph Heitman
Keyword(s):  
Reproductive Isolation ◽  
Sexual Reproduction ◽  
Large Scale ◽  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Chromosome Translocation ◽  
Dna Double Strand Breaks ◽  
Chromosome Translocations ◽  
Genomic Studies ◽  
Eukaryotic Organisms

AbstractA fundamental characteristic of eukaryotic organisms is the generation of genetic variation via sexual reproduction. Conversely, significant large-scale genome structure variations could hamper sexual reproduction, causing reproductive isolation and promote speciation. The underlying processes behind large-scale genome rearrangements are not well understood and include chromosome translocations involving centromeres. Recent genomic studies in the Cryptococcus species complex revealed that chromosome translocations generated via centromere recombination have reshaped the genomes of different species. In this study, multiple DNA double-strand breaks (DSBs) were generated via the CRISPR/Cas9 system at centromere-specific retrotransposons in the human fungal pathogen Cryptococcus neoformans. The resulting DSBs were repaired in a complex manner, leading to the formation of multiple inter-chromosomal rearrangements and new telomeres, similar to chromothripsis-like events. The newly generated strains harboring chromosome translocations exhibited normal vegetative growth but failed to undergo successful sexual reproduction with the parental wild-type strain. One of these strains failed to produce any spores, while another produced ∼3% viable progeny. The germinated progeny exhibited aneuploidy for multiple chromosomes and showed improved fertility with both parents. All chromosome translocation events were accompanied without any detectable change in gene sequences and thus, suggest that chromosomal translocations alone may play an underappreciated role in the onset of reproductive isolation and speciation.

scholarly journals Centromere scission drives chromosome shuffling and reproductive isolation

2020 ◽  
Vol 117 (14) ◽  
pp. 7917-7928 ◽  
Author(s):  
Vikas Yadav ◽  
Sheng Sun ◽  
Marco A. Coelho ◽  
Joseph Heitman
Keyword(s):  
Reproductive Isolation ◽  
Sexual Reproduction ◽  
Large Scale ◽  
Genome Structure ◽  
Chromosome Translocation ◽  
Dna Double Strand Breaks ◽  
Chromosome Translocations ◽  
Human Fungal Pathogen ◽  
Genomic Studies ◽  
Eukaryotic Organisms

A fundamental characteristic of eukaryotic organisms is the generation of genetic variation via sexual reproduction. Conversely, significant large-scale genome structure variations could hamper sexual reproduction, causing reproductive isolation and promoting speciation. The underlying processes behind large-scale genome rearrangements are not well understood and include chromosome translocations involving centromeres. Recent genomic studies in theCryptococcusspecies complex revealed that chromosome translocations generated via centromere recombination have reshaped the genomes of different species. In this study, multiple DNA double-strand breaks (DSBs) were generated via the CRISPR/Cas9 system at centromere-specific retrotransposons in the human fungal pathogenCryptococcus neoformans. The resulting DSBs were repaired in a complex manner, leading to the formation of multiple interchromosomal rearrangements and new telomeres, similar to chromothripsis-like events. The newly generated strains harboring chromosome translocations exhibited normal vegetative growth but failed to undergo successful sexual reproduction with the parental wild-type strain. One of these strains failed to produce any spores, while another produced ∼3% viable progeny. The germinated progeny exhibited aneuploidy for multiple chromosomes and showed improved fertility with both parents. All chromosome translocation events were accompanied without any detectable change in gene sequences and thus suggest that chromosomal translocations alone may play an underappreciated role in the onset of reproductive isolation and speciation.

scholarly journals TCL1 oncogene activation in preleukemic T cells from a case of ataxia- telangiectasia

Blood ◽  
1995 ◽  
Vol 86 (6) ◽  
pp. 2358-2364 ◽  
Author(s):  
MG Narducci ◽  
L Virgilio ◽  
M Isobe ◽  
A Stoppacciaro ◽  
R Elli ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Ataxia Telangiectasia ◽  
Chromosomal Rearrangements ◽  
Chromosome Translocation ◽  
Peripheral Blood Lymphocytes ◽  
Genomic Locus ◽  
Chromosome Translocations ◽  
Inverted Duplication ◽  
Immunodeficiency Syndrome

The TCL1 oncogene on human chromosome 14q32.1 is involved in chromosome translocations [t(14;14)(q11;q32.1) and t(7;14)(q35;q32.1)] and inversions [inv14(q11;q32.1)] with TCR alpha/beta loci in T-cell leukemias, such as T-prolymphocytic (T-PLL). It is also involved in T- acute and -chronic leukemias arising in cases of ataxia-telangiectasia (AT), an immunodeficiency syndrome. Similar chromosomal rearrangements occur also in the clonally expanded T cells in AT patients before the appearance of the overt leukemia. We have analyzed the expression of TCL1 mRNA and protein in peripheral blood lymphocytes (PBLs) from four AT cases and from healthy controls. We found that the TCL1 gene was overexpressed in the PBLs of an AT patient with a large clonal T-cell population exhibiting the t(14;14) translocation but not in the lymphocytes of the other cases. Fluorescence in situ hybridization of the TCL1 genomic locus to lymphocyte metaphases from the AT patient with the T-cell clonal expansion showed that the breakpoint of the t(14;14) translocation lies within the TCL1 locus and is accompanied by an inverted duplication of the distal part of chromosome 14. These data indicate that TCL1 is activated in preleukemic clonal cells as a consequence of chromosome translocation involving sequences from the TCR locus at 14q11. Deregulation of TCL1 is the first event in the initiation of malignancy in these types of leukemias and represents a potential tool for clinical evaluation.

scholarly journals Identification of genes bordering breakpoints of the pericentric inversions on 2B, 4B, and 5A in bread wheat (Triticum aestivum L.)

Genome ◽  
2015 ◽  
Vol 58 (8) ◽  
pp. 385-390 ◽  
Author(s):  
Jian Ma ◽  
Shang Gao ◽  
Jiri Stiller ◽  
Qian-Tao Jiang ◽  
Xiu-Jin Lan ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Chromosomal Rearrangements ◽  
Crop Improvement ◽  
Triticum Aestivum L ◽  
Chromosome Translocation ◽  
Detailed Knowledge ◽  
Chromosome Engineering ◽  
Chromosome Translocations ◽  
Pericentric Inversions ◽  
Close Relatives

Chromosome translocation is an important driving force in shaping genomes during evolution. Detailed knowledge of chromosome translocations in a given species and its close relatives should increase the efficiency and precision of chromosome engineering in crop improvement. To identify genes flanking the breakpoints of translocations and inversions as a step toward identifying breakpoints in bread wheat, we systematically analysed genes in the Brachypodium genome against wheat survey sequences and bin-mapped ESTs (expressed sequence tags) derived from the hexaploid wheat genotype ‘Chinese Spring’. In addition to those well-known translocations between group 4, 5, and 7 chromosomes, this analysis identified genes flanking the three pericentric inversions on chromosomes 2B, 4B, and 5A. However, numerous chromosomal rearrangements reported in early studies could not be confirmed. The genes flanking the breakpoints reported in this study are valuable for isolating these breakpoints.

scholarly journals Inconclusive evidence of sexual reproduction of invasive Halophila stipulacea: a new field guide to encourage investigation of flower and fruit production throughout its invasive range

2020 ◽  
Vol 63 (6) ◽  
pp. 537-540
Author(s):  
Fee O.H. Smulders ◽  
Kelcie L. Chiquillo ◽  
Demian A. Willette ◽  
Paul H. Barber ◽  
Marjolijn J.A. Christianen
Keyword(s):  
Sexual Reproduction ◽  
Clonal Growth ◽  
Large Scale ◽  
Fruit Production ◽  
Morphological Evidence ◽  
Invasive Range ◽  
Reproductive Structures ◽  
Halophila Stipulacea ◽  
The Caribbean ◽  
Low Rate

AbstractThe dioecious seagrass species Halophila stipulacea reproduces mainly through fast clonal growth, underlying its invasive behavior. Here, we provide morphological evidence to show that the first findings of fruits in the Caribbean were misidentified. Consequently, H. stipulacea reproduction is likely still only asexual in the Caribbean. Therefore, we introduce an identification key of H. stipulacea reproductive structures to encourage careful identification and quantification throughout its invasive range. Until large-scale seed production in invaded habitats is reported, the apparent low rate of sexual reproduction needs to be considered in current studies investigating the invasion capacity of this species.

scholarly journals The Role of RNA in DNA Breaks, Repair and Chromosomal Rearrangements

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 550
Author(s):  
Matvey Mikhailovich Murashko ◽  
Ekaterina Mikhailovna Stasevich ◽  
Anton Markovich Schwartz ◽  
Dmitriy Vladimirovich Kuprash ◽  
Aksinya Nicolaevna Uvarova ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Gene Mutations ◽  
Nonhomologous End Joining ◽  
Published Data ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
End Joining ◽  
Homology Directed Repair ◽  
Chromosome Aberration Frequency

Incorrect reparation of DNA double-strand breaks (DSB) leading to chromosomal rearrangements is one of oncogenesis’s primary causes. Recently published data elucidate the key role of various types of RNA in DSB formation, recognition and repair. With growing interest in RNA biology, increasing RNAs are classified as crucial at the different stages of the main pathways of DSB repair in eukaryotic cells: nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. In this review, we discuss recent evidence demonstrating the role of various RNAs in DSB formation and repair. We also consider how RNA may mediate certain chromosomal rearrangements in a sequence-specific manner.

scholarly journals Unusual Large-Scale Chromosomal Rearrangements in Mycobacterium tuberculosis Beijing B0/W148 Cluster Isolates

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e84971 ◽  
Author(s):  
Egor A. Shitikov ◽  
Julia A. Bespyatykh ◽  
Dmitry S. Ischenko ◽  
Dmitry G. Alexeev ◽  
Irina Y. Karpova ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Large Scale ◽  
Chromosomal Rearrangements

scholarly journals Evidence for Replicative Repair of DNA Double-Strand Breaks Leading to Oncogenic Translocation and Gene Amplification

2002 ◽  
Vol 196 (4) ◽  
pp. 469-480 ◽  
Author(s):  
Michael J. Difilippantonio ◽  
Simone Petersen ◽  
Hua Tang Chen ◽  
Roger Johnson ◽  
Maria Jasin ◽  
...  
Keyword(s):  
Dna Repair ◽  
Dna Cleavage ◽  
Chromosomal Rearrangements ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Telomere Capture ◽  
Culture Models ◽  
Recombination Activating Gene ◽  
Dna Repair Protein ◽  
Break Induced Replication

Nonreciprocal translocations and gene amplifications are commonly found in human tumors. Although little is known about the mechanisms leading to such aberrations, tissue culture models predict that they can arise from DNA breakage, followed by cycles of chromatid fusion, asymmetric mitotic breakage, and replication. Mice deficient in both a nonhomologous end joining (NHEJ) DNA repair protein and the p53 tumor suppressor develop lymphomas at an early age harboring amplification of an IgH/c-myc fusion. Here we report that these chromosomal rearrangements are initiated by a recombination activating gene (RAG)-induced DNA cleavage. Subsequent DNA repair events juxtaposing IgH and c-myc are mediated by a break-induced replication pathway. Cycles of breakage-fusion-bridge result in amplification of IgH/c-myc while chromosome stabilization occurs through telomere capture. Thus, mice deficient in NHEJ provide excellent models to study the etiology of unbalanced translocations and amplification events during tumorigenesis.

scholarly journals Gene Expression Imputation with Generative Adversarial Imputation Nets

2020 ◽  
Author(s):  
Ramon Viñas ◽  
Tiago Azevedo ◽  
Eric R. Gamazon ◽  
Pietro Liò
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Biological Significance ◽  
Predictive Performance ◽  
Cost Effective ◽  
Rna Seq ◽  
Comprehensive Collection ◽  
Genomic Studies ◽  
Biological Discovery ◽  
Cancer Types

AbstractA question of fundamental biological significance is to what extent the expression of a subset of genes can be used to recover the full transcriptome, with important implications for biological discovery and clinical application. To address this challenge, we present GAIN-GTEx, a method for gene expression imputation based on Generative Adversarial Imputation Networks. In order to increase the applicability of our approach, we leverage data from GTEx v8, a reference resource that has generated a comprehensive collection of transcriptomes from a diverse set of human tissues. We compare our model to several standard and state-of-the-art imputation methods and show that GAIN-GTEx is significantly superior in terms of predictive performance and runtime. Furthermore, our results indicate strong generalisation on RNA-Seq data from 3 cancer types across varying levels of missingness. Our work can facilitate a cost-effective integration of large-scale RNA biorepositories into genomic studies of disease, with high applicability across diverse tissue types.

scholarly journals RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair

2021 ◽  
Author(s):  
Takaaki Yasuhara ◽  
Reona Kato ◽  
Motohiro Yamauchi ◽  
Yuki Uchihara ◽  
Lee Zou ◽  
...  
Keyword(s):  
Active Regions ◽  
Strand Break ◽  
Double Strand Breaks ◽  
Critical Component ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Dsb Repair ◽  
Strand Breaks ◽  
Chromosome Translocations ◽  
Dna Double Strand Break

AbstractR-loops, consisting of ssDNA and DNA-RNA hybrids, are potentially vulnerable unless they are appropriately processed. Recent evidence suggests that R-loops can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. Yet, how the vulnerability of R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops and chromosome translocations and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end-joining dependent on BRCA1, Polθ, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.

scholarly journals The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket Laupala

2017 ◽  
Author(s):  
Thomas Blankers ◽  
Kevin P. Oh ◽  
Aureliano Bombarely ◽  
Kerry L. Shaw
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Evolutionary Genetics ◽  
Rate Variation ◽  
Linkage Maps ◽  
Recombination Rates ◽  
Behavioral Isolation ◽  
Genomic Architecture ◽  
Suppressed Recombination

ABSTRACTPhenotypic evolution and speciation depend on recombination in many ways. Within populations, recombination can promote adaptation by bringing together favorable mutations and decoupling beneficial and deleterious alleles. As populations diverge, cross-over can give rise to maladapted recombinants and impede or reverse diversification. Suppressed recombination due to genomic rearrangements, modifier alleles, and intrinsic chromosomal properties may offer a shield against maladaptive gene flow eroding co-adapted gene complexes. Both theoretical and empirical results support this relationship. However, little is known about this relationship in the context of behavioral isolation, where co-evolving signals and preferences are the major hybridization barrier. Here we examine the genomic architecture of recently diverged, sexually isolated Hawaiian swordtail crickets (Laupala). We assemble a de novo genome and generate three dense linkage maps from interspecies crosses. In line with expectations based on the species’ recent divergence and successful interbreeding in the lab, the linkage maps are highly collinear and show no evidence for large-scale chromosomal rearrangements. The maps were then used to anchor the assembly to pseudomolecules and estimate recombination rates across the genome. We tested the hypothesis that loci involved in behavioral isolation (song and preference divergence) are in regions of low interspecific recombination. Contrary to our expectations, a genomic region where a male song QTL co-localizes with a female preference QTL was not associated with particularly low recombination rates. This study provides important novel genomic resources for an emerging evolutionary genetics model system and suggests that trait-preference co-evolution is not necessarily facilitated by locally suppressed recombination.

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