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.

scholarly journals Cloning of the Human Cytomegalovirus (HCMV) Genome as an Infectious Bacterial Artificial Chromosome in Escherichia coli: a New Approach for Construction of HCMV Mutants

1999 ◽  
Vol 73 (10) ◽  
pp. 8320-8329 ◽  
Author(s):  
Eva-Maria Borst ◽  
Gabriele Hahn ◽  
Ulrich H. Koszinowski ◽  
Martin Messerle
Keyword(s):  
Escherichia Coli ◽  
Human Cytomegalovirus ◽  
Human Fibroblasts ◽  
Artificial Chromosome ◽  
Bacterial Artificial Chromosomes ◽  
Reading Frame ◽  
E Coli ◽  
Artificial Chromosomes ◽  
Internal Repeat ◽  
The Stability

ABSTRACT We have recently introduced a novel procedure for the construction of herpesvirus mutants that is based on the cloning and mutagenesis of herpesvirus genomes as infectious bacterial artificial chromosomes (BACs) in Escherichia coli (M. Messerle, I. Crnković, W. Hammerschmidt, H. Ziegler, and U. H. Koszinowski, Proc. Natl. Acad. Sci. USA 94:14759–14763, 1997). Here we describe the application of this technique to the human cytomegalovirus (HCMV) strain AD169. Since it was not clear whether the terminal and internal repeat sequences of the HCMV genome would give rise to recombination, the stability of the cloned HCMV genome was examined during propagation inE. coli, during mutagenesis, and after transfection in permissive fibroblasts. Interestingly, the HCMV BACs were frozen in defined conformations in E. coli. The transfection of the HCMV BACs into human fibroblasts resulted in the reconstitution of infectious virus and isomerization of the reconstituted genomes. The power of the BAC mutagenesis procedure was exemplarily demonstrated by the disruption of the gpUL37 open reading frame. The transfection of the mutated BAC led to plaque formation, indicating that the gpUL37 gene product is dispensable for growth of HCMV in fibroblasts. The new procedure will considerably speed up the construction of HCMV mutants and facilitate genetic analysis of HCMV functions.

FISH of a maize sh2-selected sorghum BAC to chromosomes of Sorghum bicolor

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 475-478 ◽  
Author(s):  
Martha I. Gómez ◽  
M. Nurul Islam-Faridi ◽  
Sung-Sick Woo ◽  
Don Czeschin Jr. ◽  
Michael S. Zwick ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Sorghum Bicolor ◽  
Fluorescence In Situ Hybridization ◽  
Artificial Chromosome ◽  
Single Copy ◽  
Bacterial Artificial Chromosomes ◽  
Extra Copy ◽  
Artificial Chromosomes ◽  
Sorghum Plant

Fluorescence in situ hybridization (FISH) of a 205 kb Sorghum bicolor bacterial artificial chromosome (BAC) containing a sequence complementary to maize sh2 cDNA produced a large pair of FISH signals at one end of a midsize metacentric chromosome of S. bicolor. Three pairs of signals were observed in metaphase spreads of chromosomes of a sorghum plant containing an extra copy of one arm of the sorghum chromosome arbitrarily designated with the letter D. Therefore, the sequence cloned in this BAC must reside in the arm of chromosome D represented by this monotelosome. This demonstrates a novel procedure for physically mapping cloned genes or other single-copy sequences by FISH, sh2 in this case, by using BACs containing their complementary sequences. The results reported herein suggest homology, at least in part, between one arm of chromosome D in sorghum and the long arm of chromosome 3 in maize.Key words: sorghum, maize, shrunken locus, physical mapping, fluorescence in situ hybridization, bacterial artificial chromosomes.

scholarly journals Using Bacterial Artificial Chromosomes in Leukemia Research: The Experience at the University Cytogenetics Laboratory in Brest, France

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Etienne De Braekeleer ◽  
Nathalie Douet-Guilbert ◽  
Audrey Basinko ◽  
Frédéric Morel ◽  
Marie-Josée Le Bris ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Artificial Chromosome ◽  
Genome Project ◽  
Comparative Genomic ◽  
Cancer Genes ◽  
Bacterial Artificial Chromosomes ◽  
Artificial Chromosomes ◽  
Bac Clones ◽  
Dna Libraries ◽  
Conventional Cytogenetics

The development of the bacterial artificial chromosome (BAC) system was driven in part by the human genome project in order to construct genomic DNA libraries and physical maps for genomic sequencing. The availability of BAC clones has become a valuable tool for identifying cancer genes. We report here our experience in identifying genes located at breakpoints of chromosomal rearrangements and in defining the size and boundaries of deletions in hematological diseases. The methodology used in our laboratory consists of a three-step approach using conventional cytogenetics followed by FISH with commercial probes, then BAC clones. One limitation to the BAC system is that it can only accommodate inserts of up to 300 kb. As a consequence, analyzing the extent of deletions requires a large amount of material. Array comparative genomic hybridization (array-CGH) using a BAC/PAC system can be an alternative. However, this technique has limitations also, and it cannot be used to identify candidate genes at breakpoints of chromosomal rearrangements such as translocations, insertions, and inversions.

scholarly journals Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions

2010 ◽  
Vol 190 (5) ◽  
pp. 761-776 ◽  
Author(s):  
Paul Sinclair ◽  
Qian Bian ◽  
Matt Plutz ◽  
Edith Heard ◽  
Andrew S. Belmont
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Tandem Repeats ◽  
Es Cells ◽  
Embryonic Stem ◽  
Bacterial Artificial Chromosomes ◽  
Artificial Chromosomes ◽  
Lac Operator ◽  
Chromatin Folding ◽  
Chromosome Regions

Interphase chromatin compaction well above the 30-nm fiber is well documented, but the structural motifs underlying this level of chromatin folding remain unknown. Taking a reductionist approach, we analyzed in mouse embryonic stem (ES) cells and ES-derived fibroblasts and erythroblasts the folding of 10–160-megabase pair engineered chromosome regions consisting of tandem repeats of bacterial artificial chromosomes (BACs) containing ∼200 kilobases of mammalian genomic DNA tagged with lac operator (LacO) arrays. Unexpectedly, linear mitotic and interphase chromatid regions formed from noncontiguously folded DNA topologies. Particularly, in ES cells, these model chromosome regions self-organized with distant sequences segregating into functionally distinct, compact domains. Transcriptionally active and histone H3K27me3-modified regions positioned toward the engineered chromosome subterritory exterior, with LacO repeats and the BAC vector backbone localizing within an H3K9me3, HP1-enriched core. Differential compaction of Dhfr and α- and β-globin transgenes was superimposed on dramatic, lineage-specific reorganization of large-scale chromatin folding, demonstrating a surprising plasticity of large-scale chromatin organization.

Chimeras Linked to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

2017 ◽  
Vol 19 (4) ◽  
pp. 401-409 ◽  
Author(s):  
Lihai Ye ◽  
Ni Jiao ◽  
Xiaojun Tang ◽  
Yiyi Chen ◽  
Xiaolan Ye ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Tetraploid Hybrid ◽  
Hybrid Fish

scholarly journals An Overlapping Bacterial Artificial Chromosome System That Generates Vectorless Progeny for Channel Catfish Herpesvirus

2008 ◽  
Vol 82 (8) ◽  
pp. 3872-3881 ◽  
Author(s):  
Dusan Kunec ◽  
Larry A. Hanson ◽  
Sandra van Haren ◽  
I. F. Nieuwenhuizen ◽  
Shane C. Burgess
Keyword(s):  
Channel Catfish ◽  
Infectious Clone ◽  
Artificial Chromosome ◽  
Bacterial Artificial Chromosomes ◽  
Bac Clone ◽  
Artificial Chromosomes ◽  
Targeted Mutation ◽  
Infectious Clones ◽  
Viral Progeny ◽  
Herpesvirus 1

ABSTRACT Herpesviruses are important pathogens of humans and other animals. Herpesvirus infectious clones that can reconstitute phenotypically wild-type (wt) virus are extremely valuable tools for elucidating the roles of specific genes in virus pathophysiology as well as for making vaccines. Ictalurid herpesvirus 1 (channel catfish herpesvirus [CCV]) is economically very important and is the best characterized of the herpesviruses that occur primarily in bony fish and amphibians. Here, we describe the cloning of the hitherto recalcitrant CCV genome as three overlapping subgenomic bacterial artificial chromosomes (BACs). These clones allowed us to regenerate vectorless wt CCVs with a phenotype that is indistinguishable from that of the wt CCV from which the BACs were derived. To test the recombinogenic systems, we next used the overlapping BACs to construct a full-length CCV BAC by replacing the CCV ORF5 with the BAC cassette and cotransfecting CCO cells. The viral progeny that we used to transform Escherichia coli and the resulting BAC had only one of the 18-kb terminal repeated regions. Both systems suggest that one of the terminal repeat regions is lost during the replicative stage of the CCV life cycle. We also demonstrated the feasibility of introducing a targeted mutation into the CCV BAC infectious clone by constructing a CCV ORF12 deletion mutant and showed that ORF12 encodes a nonessential protein for virus replication. This is the first report of the generation of an infectious BAC clone of a member of the fish and amphibian herpesviruses and its use to generate recombinants.

scholarly journals Genetic Stability of Bacterial Artificial Chromosome-Derived Human Cytomegalovirus during CultureIn Vitro

2016 ◽  
Vol 90 (8) ◽  
pp. 3929-3943 ◽  
Author(s):  
Isa Murrell ◽  
Gavin S. Wilkie ◽  
Andrew J. Davison ◽  
Evelina Statkute ◽  
Ceri A. Fielding ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Human Cytomegalovirus ◽  
Artificial Chromosome ◽  
Cell Types ◽  
Clinical Strain ◽  
Minimal Risk ◽  
Bacterial Artificial Chromosomes ◽  
Wild Type ◽  
Artificial Chromosomes

ABSTRACTClinical human cytomegalovirus (HCMV) strains invariably mutate when propagatedin vitro. Mutations in gene RL13 are selected in all cell types, whereas in fibroblasts mutants in the UL128 locus (UL128L; genes UL128, UL130, and UL131A) are also selected. In addition, sporadic mutations are selected elsewhere in the genome in all cell types. We sought to investigate conditions under which HCMV can be propagated without incurring genetic defects. Bacterial artificial chromosomes (BACs) provide a stable, genetically defined source of viral genome. Viruses were generated from BACs containing the genomes of strains TR, TB40, FIX, and Merlin, as well as from Merlin-BAC recombinants containing variant nucleotides in UL128L from TB40-BAC4 or FIX-BAC. Propagation of viruses derived from TR-BAC, TB40-BAC4, and FIX-BAC in either fibroblast or epithelial cells was associated with the generation of defects around the prokaryotic vector, which is retained in the unique short (US) region of viruses. This was not observed for Merlin-BAC, from which the vector is excised in derived viruses; however, propagation in epithelial cells was consistently associated with mutations in the unique longb′ (UL/b′) region, all impacting on gene UL141. Viruses derived from Merlin-BAC in fibroblasts had mutations in UL128L, but mutations occurred less frequently with recombinants containing UL128L nucleotides from TB40-BAC4 or FIX-BAC. Viruses derived from a Merlin-BAC derivative in which RL13 and UL128L were either mutated or repressed were remarkably stable in fibroblasts. Thus, HCMV containing a wild-type gene complement can be generatedin vitroby deriving virus from a self-excising BAC in fibroblasts and repressing RL13 and UL128L.IMPORTANCEResearchers should aim to study viruses that accurately represent the causative agents of disease. This is problematic for HCMV because clinical strains mutate rapidly when propagatedin vitro, becoming less cell associated, altered in tropism, more susceptible to natural killer cells, and less pathogenic. Following isolation from clinical material, HCMV genomes can be stabilized by cloning into bacterial artificial chromosomes (BACs), and then virus is regenerated by DNA transfection. However, mutations can occur not only during isolation prior to BAC cloning but also when virus is regenerated. We have identified conditions under which BAC-derived viruses containing an intact, wild-type genome can be propagatedin vitrowith minimal risk of mutants being selected, enabling studies of viruses expressing the gene complement of a clinical strain. However, even under these optimized conditions, sporadic mutations can occur, highlighting the advisability of sequencing the HCMV stocks used in experiments.

scholarly journals Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa

2004 ◽  
Vol 34 (1) ◽  
pp. 85-93 ◽  
Author(s):  
Gerald A Tuskan ◽  
Lee E Gunter ◽  
Zamin K Yang ◽  
TongMing Yin ◽  
Mitchell M Sewell ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Populus Trichocarpa ◽  
Repeat Unit ◽  
Artificial Chromosome ◽  
Genetic Maps ◽  
Bacterial Artificial Chromosomes ◽  
Tetranucleotide Repeat ◽  
Artificial Chromosomes ◽  
High Utility ◽  
Populus Species

Microsatellites or simple sequence repeats (SSRs) are highly polymorphic, codominant markers that have great value for the construction of genetic maps, comparative mapping, population genetic surveys, and paternity analyses. Here, we report the development and testing of a set of SSR markers derived from shotgun sequencing from Populus trichocarpa Torr. & A. Gray, a nonenriched genomic DNA library, and bacterial artificial chromosomes. Approximately 23% of the 1536 genomic clones and 48% of the 768 bacterial artificial chromosome subclones contained an SSR. Of the sequences containing an SSR, 72.4% contained a dinucleotide, 19.5% a trinucleotide, and 8.1% a tetranucleotide repeat unit; 26.6% of the sequences contained multiple SSR motifs in a complex or compound repeat structures. A survey of the genome sequence database revealed very similar proportional distribution, indicating that our limited rapid, shallow sequencing effort is representative of genome-wide patterns. In total, 492 primer pairs were designed and these yielded 77 markers that were mapped in an F2 pedigree, including 26 that were sufficiently informative to be included in a Populus framework map. SSRs with GC-rich motifs mapped at a significantly higher frequency than expected, although AT-rich SSRs accounted for the majority of mapped markers due to their higher representation in the genome. SSR markers developed from P. trichocarpa showed high utility throughout the genus, with amplification rates in excess of 70% for all Populus species tested. Finally, at least 30% of the markers amplified in several willow species, suggesting that some of these SSRs will be transferable across genera.

scholarly journals Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Musaddeque Ahmed ◽  
Ping Liang
Keyword(s):  
Transposable Elements ◽  
Human Genome ◽  
Tandem Repeats ◽  
Sequence Similarity ◽  
Genomic Alteration ◽  
Repeat Elements ◽  
Significant Contributor ◽  
Repeat Units ◽  
Local Duplication ◽  
The Relationship

Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. In this study, we identified TRs that are derived from TEs either based on sequence similarity or overlapping genomic positions. We then analyzed the distribution of these TRs among TE families/subfamilies. Our study shows that at least 7,276 TRs or 23% of all minisatellites/satellites is derived from TEs, contributing ∼0.32% of the human genome. TRs seem to be generated more likely from younger/more active TEs, and once initiated they are expanded with time via local duplication of the repeat units. The currently postulated mechanisms for origin of TRs can explain only 6% of all TE-derived TRs, indicating the presence of one or more yet to be identified mechanisms for the initiation of such repeats. Our result suggests that TEs are contributing to genome expansion and alteration not only by transposition but also by generating tandem repeats.

scholarly journals Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

2021 ◽  
Vol 22 (4) ◽  
pp. 1614
Author(s):  
María Esther Rodríguez ◽  
Ismael Cross ◽  
Alberto Arias-Pérez ◽  
Silvia Portela-Bens ◽  
Manuel Alejandro Merlo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Fish Species ◽  
Gasterosteus Aculeatus ◽  
Sparus Aurata ◽  
Chromosomal Rearrangements ◽  
Scophthalmus Maximus ◽  
Cynoglossus Semilaevis ◽  
Solea Senegalensis ◽  
Reference Species ◽  
Artificial Chromosomes

Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.

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