scholarly journals The Control of Natural Variation in Cytosine Methylation in Arabidopsis

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 355-363 ◽  
Author(s):  
Nicole C Riddle ◽  
Eric J Richards
Keyword(s):  
Copy Number ◽  
Natural Variation ◽  
Cytosine Methylation ◽  
Gene Copy Number ◽  
Nucleolus Organizer ◽  
Flowering Plant ◽  
Gene Copy ◽  
Rrna Gene ◽  
Nucleolus Organizer Regions ◽  
Plant Arabidopsis Thaliana

Abstract We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA gene repeats at the two nucleolus organizer regions (NOR). Our findings indicate that natural variation in NOR methylation results from a combination of genetic and epigenetic mechanisms. Genetic variation in rRNA gene copy number and trans-acting modifier loci account for some of the natural variation in NOR methylation. Our results also suggest that divergence and inheritance of epigenetic information, independent of changes in underlying nucleotide sequence, may play an important role in maintaining natural variation in cytosine methylation.

scholarly journals Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 283
Author(s):  
Eyal Seroussi
Keyword(s):  
Copy Number ◽  
Sanger Sequencing ◽  
Cytosine Methylation ◽  
Direct Sequencing ◽  
Information Source ◽  
Gene Copy Number ◽  
Cost Effective ◽  
Gene Copy ◽  
Base Editing ◽  
Recent Developments

Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.

scholarly journals Alteration of rRNA gene copy number and expression in patients with intellectual disability and heteromorphic acrocentric chromosomes

2018 ◽  
Vol 19 (2) ◽  
pp. 129-134 ◽  
Author(s):  
Irina S. Kolesnikova ◽  
Alexander A. Dolskiy ◽  
Natalya A. Lemskaya ◽  
Yulia V. Maksimova ◽  
Asia R. Shorina ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Rrna Gene ◽  
Acrocentric Chromosomes

scholarly journals Life History Implications of rRNA Gene Copy Number in Escherichia coli

2004 ◽  
Vol 70 (11) ◽  
pp. 6670-6677 ◽  
Author(s):  
Bradley S. Stevenson ◽  
Thomas M. Schmidt
Keyword(s):  
Escherichia Coli ◽  
Life History ◽  
Copy Number ◽  
Gene Copy Number ◽  
Rrna Operon ◽  
Relative Fitness ◽  
Gene Copy ◽  
Rrna Gene ◽  
Negative Consequences ◽  
Chemostat Cultures

ABSTRACT The role of the rRNA gene copy number as a central component of bacterial life histories was studied by using strains of Escherichia coli in which one or two of the seven rRNA operons (rrnA and/or rrnB) were deleted. The relative fitness of these strains was determined in competition experiments in both batch and chemostat cultures. In batch cultures, the decrease in relative fitness corresponded to the number of rRNA operons deleted, which could be accounted for completely by increased lag times and decreased growth rates. The magnitude of the deleterious effect varied with the environment in which fitness was measured: the negative consequences of rRNA operon deletions increased under culture conditions permitting more-rapid growth. The rRNA operon deletion strains were not more effective competitors under the regimen of constant, limited resources provided in chemostat cultures. Enhanced fitness in chemostat cultures would have suggested a simple tradeoff in which deletion strains grew faster (due to more efficient resource utilization) under resource limitation. The contributions of growth rate, lag time, Ks , and death rate to the fitness of each strain were verified through mathematical simulation of competition experiments. These data support the hypothesis that multiple rRNA operons are a component of bacterial life history and that they confer a selective advantage permitting microbes to respond quickly and grow rapidly in environments characterized by fluctuations in resource availability.

scholarly journals Unstable inheritance of 45S rRNA genes in Arabidopsis thaliana

2016 ◽  
Author(s):  
Fernando A. Rabanal ◽  
Viktoria Nizhynska ◽  
Terezie Mandáková ◽  
Polina Yu. Novikova ◽  
Martin A. Lysak ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Copy Number ◽  
Association Studies ◽  
Recombinant Inbred Lines ◽  
Gene Copy Number ◽  
Rrna Genes ◽  
Gene Copy ◽  
Nucleolar Organizer Regions ◽  
Rrna Gene ◽  
Genome Wide Association Studies

AbstractThe considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. Surprisingly, attempts to map this variation by means of genome-wide association studies (GWAS) failed to identify either of the two likely sources, namely the nucleolar organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA CNV was a phenotype rather than a genotype. To explain these results, we investigated the inheritance and stability of rRNA gene copy number using the variety of genetic resources available in A. thaliana — F2 crosses, recombinant inbred lines, the multiparent advanced generation inter-cross population, and mutation accumulation lines. Our results clearly show that rRNA gene CNV can be mapped to the NORs themselves, with both loci contributing equally to the variation. However, NOR size is unstably inherited, and dramatic copy number changes are visible already within tens of generations, which explains why it is not possible to map the NORs using GWAS. We did not find any evidence of trans-acting loci in crosses, which is also expected since changes due to such loci would take very many generations to manifest themselves. rRNA gene copy number is thus an interesting example of “missing heritability” — a trait that is heritable in pedigrees, but not in the general population.

scholarly journals The Responding Site of the Rex Locus of Drosophila melanogaster

Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 271-276
Author(s):  
Ellen E Swanson
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Ribosomal Rna ◽  
Maternal Effect ◽  
Copy Number ◽  
Mitotic Chromosome ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Rrna Gene ◽  
Chromosome Behavior

ABSTRACT Rex is a dominant, maternal-effect locus in the heterochromatin of the X chromosome Drosophila melanogaster. It causes an early mitotic exchange-like event between heterochromatic elements of an attached- XY in X/attached-XY embryos of Rex mothers. Evidence is presented here that the site of Rex action is the ribosomal RNA gene cluster (the bb locus) only; no other heterochromatin is affected. The Rex locus may be useful in studying regulation of rRNA-gene copy number, mitotic chromosome behavior and heterochromatic function.

The physiological effects of natural variation in growth hormone gene copy number in ram lambs

1997 ◽  
Vol 14 (6) ◽  
pp. 381-390 ◽  
Author(s):  
E. Gootwine ◽  
J.M. Suttie ◽  
J.C. McEwan ◽  
B.A. Veenvliet ◽  
R.P. Littlejohn ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Copy Number ◽  
Natural Variation ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Growth Hormone Gene ◽  
Physiological Effects ◽  
Ram Lambs

The ribosomal RNA genes of Locusta migratoria: copy number and evidence for underreplication in a polyploid tissue

1985 ◽  
Vol 63 (10) ◽  
pp. 1064-1070 ◽  
Author(s):  
M. Oishi ◽  
J. Locke ◽  
G. R. Wyatt
Keyword(s):  
Adult Female ◽  
Copy Number ◽  
Fat Body ◽  
Locusta Migratoria ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Rrna Gene ◽  
Mature Adult ◽  
Restriction Sites ◽  
Vitellogenin Synthesis

From libraries of Locusta migratoria genomic DNA in bacteriophage λ, clones have been isolated that hybridize with one or both of the 18S and 28S components of locust rRNA. Six clones studied show common patterns of restriction sites in the coding sequences and some include an intron in the 28S region. Subcloned sequences from within the 18S and 28S coding regions were used as probes in dot hybridization assays of the rRN A gene copy number in DNA prepared from several locust tissues and stages. The 18S and 28S probes gave similar results, showing about 4000 copies/haploid genome in testis, embryo, and fat body from larvae and immature adults of both sexes. This is by far the greatest rRNA gene copy number yet reported for any insect. DNA from reproductively mature adult female fat body showed a consistent reduction in the copy number by about one-third. Mature adult male fat body DNA showed no significant reduction in the copy number. It therefore appears that the final round of DNA replication in the adult female fat body, which produces 8-ploid and 16-ploid cells active in vitellogenin synthesis, involves underreplication of rDNA.

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