Rapid genomic changes in newly synthesized amphiploids ofTriticumandAegilops. II. Changes in low-copy coding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 535-542 ◽  
Author(s):  
B Liu ◽  
J M Vega ◽  
M Feldman
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Gene Dosage ◽  
Restriction Enzymes ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Coding Sequences ◽  
Genomic Changes ◽  
Cdna Sequences ◽  
Specific Sequences

We recently reported that formation of allopolyploid wheat was accompanied by rapid nonrandom changes in low-copy noncoding DNA sequences. In this report we show that following allopolyploidization, changes also occurred in coding sequences. Genomic DNA of nine different newly synthesized amphiploids of different ploidy levels and their parental lines was digested with five restriction enzymes and probed with 43 coding sequences. The sequences, 19 genomic and 24 cDNA sequences, are group (homoeologous) specific and represent the proximal and distal regions of the short and long arms of the seven homoeologous groups of the Triticeae. We revealed three types of changes: disappearance of a parental hybridization fragment(s), appearance of a novel fragment(s), and simultaneous disappearance of a parental fragment(s) and appearance of a novel fragment(s). No elimination of sequences took place, since in every sequence studied the parental hybridization fragments were present in at least one of the enzyme digests. Variations in pattern among individual plants of the same amphiploid, as well as between several synthetic and natural amphiploids, indicated that at least some of the genomic changes occurred at random. Intergenomic recombination was not the cause of the observed changes. Evidence was obtained, however, that changes were also brought about by DNA methylation. Methylation may cause inactivation of genes or modify their expression levels in some of the newly synthesized amphiploid plants, leading to genetic diploidization and gene-dosage compensation and thus increasing variation among individuals.Key words: wheat, allopolyploidy, DNA methylation, genetic diploidization, genome evolution, group (homoeologous) specific sequences.

Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 272-277 ◽  
Author(s):  
B Liu ◽  
J M Vega ◽  
G Segal ◽  
S Abbo ◽  
M Rodova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
High Frequency ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Chromosome Differentiation ◽  
Genomic Changes ◽  
Parental Lines ◽  
Copy Dna ◽  
Homoeologous Chromosomes ◽  
Specific Sequences

We recently reported that allopolyploid formation in wheat was accompanied by rapid nonrandom elimination of specific low-copy, noncoding DNA sequences. These sequences occur in all diploid progenitors but are chromosome- or genome-specific at the polyploid level. To further investigate this phenomenon, we studied nine of these sequences, six chromosome-specific sequences and three genome-specific sequences, all isolated from common wheat. The various sequences were hybridized to DNA derived from nine newly synthesized amphiploids at different ploidy levels and to DNA from their parental lines. Although sequences homologous to the probes occur in all parental lines, a nonrandom loss of hybridization fragments was found at a high frequency in all amphiploids studied. In addition, a "loss/gain" of a hybridization fragment(s) was noticed in some of the amphiploids at lower frequency. Neither the type nor the frequency of changes was affected by intergenomic recombination or DNA methylation. It is suggested that rapid genomic changes culminated in a "programmed" pattern of elimination and (or) modification of specific low-copy DNA sequences following allopolyploidization. These events augmented the differentiation of homoeologous chromosomes, thus providing the physical basis for the diploid-like cytological behavior of polyploid wheat.Key words: wheat, allopolyploidy, genome evolution, chromosome- or genome-specific sequences, sequence elimination, homoeologous chromosome differentiation.

Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 272-277 ◽  
Author(s):  
B. Liu ◽  
J.M. Vega ◽  
G. Segal ◽  
S. Abbo ◽  
M. Rodova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Noncoding Dna ◽  
Genomic Changes

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2020 ◽  
Author(s):  
Richard V. Miller ◽  
Rafik Neme ◽  
Derek M. Clay ◽  
Jananan S. Pathmanathan ◽  
Michael W. Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

AbstractThe germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

scholarly journals Congruity of the Polymorphisms in the Expressed and Noncoding Parts of the Gli-B1 Locus in Common Wheat

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1510
Author(s):  
Yulia Popovych ◽  
Sabina Chebotar ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
Laura Pascual ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Evolutionary Significance ◽  
Sequence Length ◽  
Noncoding Dna ◽  
Important Region ◽  
Novel Variants ◽  
Specific Sequences

The previously defined pairs of primers GliB1.1 and GliB1.2 were found to produce three and four principal variants, respectively, of PCR sequence length for the γ-gliadin pseudogene in 46 Triticum aestivum L. cultivars from 15 countries carrying 19 known alleles at the Gli-B1 locus. A congruity was established between this polymorphism, allelic sets of the Gli-B1-produced gliadins (especially of the electrophoretic mobility in acid gels of the encoded γ-gliadin) and the presence in the wheat genotype of the Gli-B5b + Rg-1 allelic combination. Six different alleles at the Gli-B1 locus encoding an identical γ-gliadin produced a PCR sequence of about 400 bp (GliB1.1). Nine Gli-B1d-carrying genotypes from four countries produced an identical sequence of about 409 bp (GliB1.2), while three cultivars with Gli-B1h and four with Gli-B1b produced three and two specific sequences, respectively, of slightly different length. Allele Gli-B1j might be the result of recombination between coding and noncoding DNA sequences within the Gli-B1 locus. These observations imply that genetic diversity of the agriculturally important region of chromosome 1B marked by variants of the Gli-B1 locus is rather limited among common wheat cultivars of the 20th century, specifically to eight principal versions. These might have been incorporated into common wheat from diverged genotypes of diploid donor(s), and, due to the scarcity of recombination, subsequently maintained relatively intact. As well as its evolutionary significance, this information is of potential use in wheat breeding and we consider it likely that novel variants of the Gli-B1 locus will be found in hitherto unstudied germplasm.

Effects of 5-azacytidine on methylation and expression of specific DNA sequences in C3H 10T1/2 cells

1984 ◽  
Vol 4 (4) ◽  
pp. 634-641
Author(s):  
W L Hsiao ◽  
S Gattoni-Celli ◽  
P Kirschmeier ◽  
I B Weinstein
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Cell Lineage ◽  
Population Level ◽  
Restriction Enzymes ◽  
Detectable Level ◽  
Beta Globin ◽  
Mouse Embryo Fibroblasts ◽  
Per Se ◽  
Differential Digestion

The present study indicates that the transient exposure of C3H 10T1/2 mouse embryo fibroblasts to 5-azacytidine leads to extensive loss of methylation of the protooncogene c-mos and the beta-globin locus at the cell population level and in at least 40 isolated subclones. These changes persisted, even when the cells were serially passaged for many generations without further exposure to the drug. Even though the amount of demethylation, assessed through differential digestion by the restriction enzymes HpaII and MspI, was quite extensive, neither locus was transcribed at a detectable level. This nonselective analysis suggests, therefore, that loss of DNA methylation is not sufficient per se to induce the expression of certain loci. Presumably, the expression of these loci requires additional factors, some of which may be related to cell lineage and differentiation.

scholarly journals A Bead-Based Method for Multiplexed Identification and Quantitation of DNA Sequences Using Flow Cytometry

2000 ◽  
Vol 66 (10) ◽  
pp. 4258-4265 ◽  
Author(s):  
Alexander Spiro ◽  
Mary Lowe ◽  
Drew Brown
Keyword(s):  
Flow Cytometry ◽  
Dna Sequences ◽  
Intergenic Spacer ◽  
Polystyrene Spheres ◽  
Intergenic Spacer Region ◽  
Cdna Sequences ◽  
Capture Assay ◽  
Flow Cytometric ◽  
Target Sequences ◽  
Specific Sequences

ABSTRACT A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-μm diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and flow cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte. In this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation.

scholarly journals Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences

2019 ◽  
Author(s):  
Thomas D. Schneider ◽  
Vishnu Jejjala
Keyword(s):  
Information Theory ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sphere Packing ◽  
Restriction Enzymes ◽  
High Dimensional ◽  
Leech Lattice ◽  
Communications Systems ◽  
Single Protein ◽  
Specific Sequences

AbstractRestriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.

A prognostic method for the litter size in Berkshire pigs based on DNA methylation of IGFBP4 gene

2018 ◽  
Vol 98 (4) ◽  
pp. 845-851
Author(s):  
Seulgi Kwon ◽  
Sang Mi An ◽  
Go Eun Yu ◽  
Jung Hye Hwang ◽  
Da Hye Park ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Litter Size ◽  
Dna Sequences ◽  
Epigenetic Modification ◽  
Methylation Status ◽  
Follicular Development ◽  
Restriction Enzymes ◽  
Important Trait ◽  
Specific Restriction ◽  
Polymerase Chain

Litter size is an important trait in the pig industry. Therefore, a lot of effort has been put into improving this trait. DNA methylation is an essential epigenetic modification present in unique DNA sequences. Alterations in methylation can affect transcription and phenotypic variation. The purpose of this study was to investigate the effect of DNA methylation on litter size. Methylation-specific restriction enzymes are simple and useful tools for detecting DNA methylation status. We used a pair of methylation-sensitive isoschizomers, which have the same recognition site, HpaII and MspI. Insulin-like growth factor binding protein 4 (IGFBP4) is a key regulator of ovarian follicular development and fetal growth in eutherian mammals. In this study, we discovered that IGFBP4 was hyper-methylated in the uterus tissue of a larger litter size group using bisulfite sequencing, and validated the positive relationship between the methylation status of IGFBP4 and the total number born of pigs using the porcine methylation-specific restriction enzyme polymerase chain reaction (PMP) assay. We suggest that the IGFPB4 gene can be used as a prognostic biomarker for hyperprolific sows and that the PMP assay is a useful tool for methylation status screening.

scholarly journals Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1381-1387 ◽  
Author(s):  
Moshe Feldman ◽  
Bao Liu ◽  
Gregorio Segal ◽  
Shahal Abbo ◽  
Avraham A Levy ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Tetraploid Wheat ◽  
Diploid Species ◽  
Noncoding Dna ◽  
Polyploid Wheat ◽  
Genomic Changes ◽  
Group I ◽  
Group Ii ◽  
Homoeologous Chromosomes

To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, lowcopy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2021 ◽  
Author(s):  
Richard V Miller ◽  
Rafik Neme ◽  
Derek M Clay ◽  
Jananan S Pathmanathan ◽  
Michael W Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

Abstract The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination.

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