Population differences in antifreeze protein gene copy number and arrangement in winter flounder

Genome ◽  
1991 ◽  
Vol 34 (1) ◽  
pp. 174-177 ◽  
Author(s):  
Pliny H. Hayes ◽  
Peter L. Davies ◽  
Garth L. Fletcher
Keyword(s):  
Multigene Family ◽  
Copy Number ◽  
Tandem Repeats ◽  
Freezing Point ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Gene Organization ◽  
Winter Flounder ◽  
Gene Copy ◽  
Intrapopulation Variation

Many marine fish in polar waters produce antifreeze proteins (AFPs) to depress their serum freezing point to below that of seawater. Winter flounder from the east coast of North America contain multiple AFP gene copies organized both as tandem repeats and as linked but irregularly spaced genes, with the tandemly repeated genes encoding the bulk of the circulating AFPs. We report here on AFP gene organization in winter flounder from nine locations ranging from Long Island, NY to Conception Bay, Nfld. There are clear differences in AFP gene copy number and arrangement between some of the populations. The greatest variation is seen in the size of the tandem component in fish from the warmer, deeper locations. This contrasts to the conservation of organization in the dispersed, β-tubulin multigene family used for comparative purposes. We suggest that variation in AFP gene family size and organization reflects a relaxation of selection in some geographical areas in the postglacial period.Key words: gene dosage, multigene family, tandem repeats, intrapopulation variation, glaciation.

scholarly journals Genome instability drives epistatic adaptation in the human pathogen Leishmania

2021 ◽  
Vol 118 (51) ◽  
pp. e2113744118
Author(s):  
Giovanni Bussotti ◽  
Laura Piel ◽  
Pascale Pescher ◽  
Malgorzata A. Domagalska ◽  
K. Shanmugha Rajan ◽  
...  
Keyword(s):  
Translational Control ◽  
Copy Number ◽  
Biomarker Discovery ◽  
Genome Instability ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Snorna Gene ◽  
Ideal System

How genome instability is harnessed for fitness gain despite its potential deleterious effects is largely elusive. An ideal system to address this important open question is provided by the protozoan pathogen Leishmania, which exploits frequent variations in chromosome and gene copy number to regulate expression levels. Using ecological genomics and experimental evolution approaches, we provide evidence that Leishmania adaptation relies on epistatic interactions between functionally associated gene copy number variations in pathways driving fitness gain in a given environment. We further uncover posttranscriptional regulation as a key mechanism that compensates for deleterious gene dosage effects and provides phenotypic robustness to genetically heterogenous parasite populations. Finally, we correlate dynamic variations in small nucleolar RNA (snoRNA) gene dosage with changes in ribosomal RNA 2′-O-methylation and pseudouridylation, suggesting translational control as an additional layer of parasite adaptation. Leishmania genome instability is thus harnessed for fitness gain by genome-dependent variations in gene expression and genome-independent compensatory mechanisms. This allows for polyclonal adaptation and maintenance of genetic heterogeneity despite strong selective pressure. The epistatic adaptation described here needs to be considered in Leishmania epidemiology and biomarker discovery and may be relevant to other fast-evolving eukaryotic cells that exploit genome instability for adaptation, such as fungal pathogens or cancer.

scholarly journals Genome plasticity in Paramecium bursaria revealed by population genomics

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Yu-Hsuan Cheng ◽  
Chien-Fu Jeff Liu ◽  
Yen-Hsin Yu ◽  
Yu-Ting Jhou ◽  
Masahiro Fujishima ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Population Genomics ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Paramecium Bursaria ◽  
Gene Copy ◽  
Genome Plasticity ◽  
Ciliate Species ◽  
Number Variation

Abstract Background Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.

scholarly journals Histidine Operon Deattenuation in dnaAMutants of Salmonella typhimurium Correlates with a Decrease in the Gene Dosage Ratio between tRNAHis and Histidine Biosynthetic Loci

1999 ◽  
Vol 181 (9) ◽  
pp. 2938-2941 ◽  
Author(s):  
Anne-Beatrice Blanc-Potard ◽  
Nara Figueroa-Bossi ◽  
Lionello Bossi
Keyword(s):  
Salmonella Typhimurium ◽  
Copy Number ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Gene Copy

ABSTRACT Expression of the histidine operon of Salmonella typhimurium is increased in dnaA(Ts) mutants at 37°C. This effect requires an intact his attenuator and can be suppressed by increasing the gene copy number of thehisR locus, which encodes the tRNAHis. We present data which suggest that the his deattenuation defect in dnaA(Ts) mutants results from the loss of a gene dosage gradient between the hisR locus, close tooriC, and the his operon, far fromoriC. Some of the conclusions drawn here may apply to other operons as well.

scholarly journals Determination of Cytochrome P450 2D6 (CYP2D6) Gene Copy Number by Real-Time Quantitative PCR

2005 ◽  
Vol 2005 (3) ◽  
pp. 248-253 ◽  
Author(s):  
Laurent Bodin ◽  
Philippe H. Beaune ◽  
Marie-Anne Loriot
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Copy Number ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Rapid Identification ◽  
Gene Copy ◽  
Cyp2d6 Gene ◽  
Real Time Quantitative Pcr ◽  
Gene Copies

Gene dosage by real-time quantitative PCR has proved to be accurate for measuring gene copy number. The aim of this study was to apply this approach to the CYP2D6 gene to allow for rapid identification of poor and ultrarapid metabolizers (0, 1, or more than 2 gene copy number). Using the2−ΔΔCtcalculation method and a duplex reaction, the number of CYP2D6 gene copies was determined. Quantitative PCR was performed on 43 samples previously analyzed by Southern blotting and long PCR including 20 samples with a heterozygous deletion, 11 with normal copy number (2 copies), and 12 samples with duplicated genes. The average ratio ranged from1.02to1.28,1.85to2.21, and2.55to3.30, respectively, for the samples with 1 copy, 2 copies, and 3 copies. This study shows that this method is sensitive enough to detect either a heterozygous gene deletion or duplication.

scholarly journals Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation.

2021 ◽  
Author(s):  
Roberto de la Cerda ◽  
Karsten Hookamp ◽  
Fiona Roche ◽  
Georgia Thompson ◽  
Soukaina Timouma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Gene Dosage ◽  
Expression Patterns ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Expression Patterns ◽  
Group I ◽  
Saccharomyces Pastorianus ◽  
Group Ii

The lager yeasts, Saccharomyces pastorianus, are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus and are divided into two broad groups, Group I and II. The two groups evolved from at least one common hybridisation event but have subsequently diverged with Group I strains losing many S. cerevisiae chromosomes while the Group II strains retain both sub-genomes. The complex genomes, containing orthologous alleles from the parental chromosomes, pose interesting questions regarding gene regulation and its impact on the fermentation properties of the strains. Superimposed on the presence of orthologous alleles are complexities of gene dosage due to the aneuploid nature of the genomes. We examined the contribution of the S. cerevisiae and S. eubayanus alleles to the gene expression patterns of Group I and II strains during fermentation. We show that the relative expression of S. cerevisiae and S. eubayanus orthologues is positively correlated with gene copy number. Despite the reduced S. cerevisiae content in the Group I strain, S. cerevisiae orthologues contribute to biochemical pathways upregulated during fermentation which may explain the retention of specific chromosomes in the strain. Conversely, S. eubayanus genes are significantly overrepresented in the upregulated gene pool in the Group II strain. Comparison of the transcription profiles of Group I and II strains during fermentation identified both common and unique gene expression patterns, with gene copy number being a dominant contributory factor. Thus, the aneuploid genomes create complex patterns of gene expression during fermentation with gene dosage playing a crucial role both within and between strains.

scholarly journals Levels of ornithine decarboxylase genomic sequences, heterogeneous nuclear RNA and mRNA in human myeloma cells resistant to α-difluoromethylornithine

1991 ◽  
Vol 278 (3) ◽  
pp. 871-874 ◽  
Author(s):  
J M Hyttinen ◽  
M Halmekytö ◽  
L Alhonen ◽  
J Jänne
Keyword(s):  
Ornithine Decarboxylase ◽  
Reverse Transcription ◽  
Copy Number ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Dot Blot ◽  
Semiquantitative Assessment ◽  
Myeloma Cells ◽  
Human Myeloma Cells

We previously isolated and characterized a human myeloma cell line overproducing ornithine decarboxylase (ODC) due to gene amplification [Leinonen, Alhonen-Hongisto, Laine, Jänne & Jänne (1987) Biochem. J. 242, 199-203]. We have now employed the PCR combined with reverse transcription to determine semiquantitatively ODC gene dosage and the amounts of heterogeneous nuclear (hn) RNA and of mature mRNA of the enzyme in parental and alpha-difluoromethylornithine-resistant human myeloma cells. Experiments with dilution series revealed that the ODC gene copy number and the amount of both hnRNA and mRNA were increased to the same extent (about 100-fold) in the resistant cells. Similar dot-blot analyses of ODC-specific genomic DNA and total RNA indicated that the ODC gene copy number was increased by a factor of 380 and the amount of ODC mRNA by a factor of 700. Our results indicate that the PCR combined with reverse transcription is at least as useful as blot analyses to give semiquantitative assessment of the amounts of specific DNA or RNA sequences. In addition, the use of the PCR enables the analysis of minute sample amounts in extremely short time.

scholarly journals Determination of gene dosage at the PMP22 and androgen receptor loci by quantitative PCR

1998 ◽  
Vol 44 (4) ◽  
pp. 724-730 ◽  
Author(s):  
Renee A Poropat ◽  
Garth A Nicholson
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Point Mutations ◽  
Gene Copy Number ◽  
Fluorescent Labeling ◽  
Gene Copy ◽  
Target Sequence ◽  
Hereditary Neuropathy ◽  
Deletion Event ◽  
Pcr Product

Abstract Although many genetic diseases are caused by the presence of point mutations in respective genes, an increasing number of diseases are known to be caused by gene copy number changes. We report the development of a rapid and reliable PCR-based method for quantitation of gene copy number with sufficient sensitivity to detect single copy changes without the use of radioactive or fluorescent labeling. The sensitivity of this technique has been demonstrated by the detection of the DNA duplication or deletion occurring in two inherited peripheral neuropathies, Charcot-Marie-Tooth type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), that are caused by a reciprocal duplication or deletion event on chromosome 17p11.2–12. This method relies on the comparison of the amount of PCR product generated from a potentially duplicated or deleted target sequence with the amount of product generated from a disomic reference gene. The value of this ratio (target PCR product:reference PCR product) indicates whether the target sequence is duplicated, deleted, or unchanged. Using primers from within a duplicated or deleted region (PMP22 gene and EW401) and from within a reference region (NF1 gene), we tested 50 CMT1A, 30 HNPP, and 50 unaffected individuals for the presence of a DNA duplication or deletion. Target:reference ratios of 1.58, 1.02, and 0.56 were detected for the CMT1A, unaffected, and HNPP groups, respectively. Thus, differentiation of the three groups of individuals was on the basis of gene copy number. This technique was successfully used to detect the difference in the X chromosome copy number between males and females (target:reference ratios of 1.1 and 2.3, respectively). This approach to the detection of DNA duplications and deletions is sensitive, accurate, and has potential applications in the quantitation of changes in gene copy number associated with diseases characterized by such chromosomal alterations.

scholarly journals Tandem duplications lead to novel expression patterns through exon shuffling in D. yakuba

2016 ◽  
Author(s):  
Rebekah L. Rogers ◽  
Ling Shao ◽  
Kevin R. Thornton
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Tandem Duplication ◽  
De Novo ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Gene Duplications ◽  
Gene Structures ◽  
Tandem Duplications

AbstractOne common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this ‘gene dosage’ hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5ʹ and 3ʹ UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution.Author SummaryThe enclosed work shows that whole gene duplications rarely affect gene expression, in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number. We further explain how tandem duplications that create shuffled gene structures can force upregulation of gene sequences, de novo gene creation, and multifold changes in transcript levels.These results show that tandem duplications can produce new genes that are a source of immediate novelty associated with more extreme expression changes than previously suggested by theory. Further, these gene expression changes are a potential source of both beneficial and pathogenic mutations, immediately relevant to clinical and medical genetics in humans and other metazoans.

scholarly journals Genome instability drives epistatic adaptation in the human pathogen Leishmania

2021 ◽  
Author(s):  
Giovanni Bussotti ◽  
Laura Piel ◽  
Pascale Pescher ◽  
Malgorzata Anna Domagalska ◽  
K. Shanmugha Rajan ◽  
...  
Keyword(s):  
Translational Control ◽  
Copy Number ◽  
Biomarker Discovery ◽  
Genome Instability ◽  
Gene Dosage ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Snorna Gene ◽  
Ideal System

How genome instability is harnessed for fitness gain despite its potential deleterious effects is largely elusive. An ideal system to address this important open question is provided by the protozoan pathogen Leishmania that exploits frequent variations in chromosome and gene copy number to regulate expression levels. Using ecological genomics and experimental evolution approaches we provide first evidence that Leishmania adaptation relies on epistatic interactions between functionally associated gene copy number variations that can inform on pathways driving fitness gain in a given environment. We further uncover post-transcriptional regulation as a key mechanism that compensates for deleterious gene dosage effects and provides phenotypic robustness to genetically heterogenous parasite populations. Finally, we correlate dynamic variations in snoRNA gene dosage to changes in rRNA 2′-O-methylation and pseudouridylation, proposing translational control as an additional layer of parasite adaptation. Leishmania genome instability is thus harnessed for fitness gain by genome-dependent variations in gene expression, and genome-independent, compensatory mechanisms. This allows for polyclonal adaptation and maintenance of genetic heterogeneity despite strong selection. Epistatic adaptation described here needs to be considered in Leishmania epidemiology and biomarker discovery, and may be relevant to other fast evolving, eukaryotic cells that exploit genome instability for adaptation, such as fungal pathogens or cancer.

Sign in / Sign up

Export Citation Format

Share Document