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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize...
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Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number
The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the...
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Salivary amylase gene (AMY1) copy number variation has only a minor correlation with body composition in Chinese adults
BackgroundAccording to the WHO, about 39% of the global adult population were overweight or obese in 2016. Obesity has high heritability, with more...
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Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data
BackgroundCopy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer...
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scGAL: unmask tumor clonal substructure by jointly analyzing independent single-cell copy number and scRNA-seq data
BackgroundAccurately deciphering clonal copy number substructure can provide insights into the evolutionary mechanism of cancer, and clustering...
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A chromosome-level genome assembly for Onobrychis viciifolia reveals gene copy number gain underlying enhanced proanthocyanidin biosynthesis
Sainfoin ( Onobrychis viciifolia ), which belongs to subfamily Papilionoideae of Leguminosae, is a vital perennial forage known as “holy hay” due to...
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Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
BackgroundDuring evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than...
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Engineering plasmid copy number heterogeneity for dynamic microbial adaptation
Natural microbial populations exploit phenotypic heterogeneity for survival and adaptation. However, in engineering biology, limiting the sources of...
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Ribosomal DNA copy number alteration in blood sample from gastric cancer patients
BackgroundRibosomal DNA (rDNA) is the most abundant and important housekee** gene in the cell. It usually acted as DNA damage sensor in DNA damage...
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Measurement of transgene copy number in transgenic tobacco plants producing human interferon-γ (hIFN-γ) using quantitative real-time PCR
In transgenic plants, the transgene copy numbers can highly affect the level of expression and genetic stability of the transgene. Hence, the first...
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Completing a genomic characterisation of microscopic tumour samples with copy number
BackgroundGenomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential,...
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Genome-wide investigation to assess copy number variants in the Italian local chicken population
BackgroundCopy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the...
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Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation
Lipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low...
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Diffuse large B-cell lymphoma with DNA copy number changes in a Japanese black calf
A 2-month-old Japanese Black calf exhibited mandibular and superficial cervical lymph node swelling. Fine needle aspiration cytology of the...
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CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a...
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Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses
16S rRNA gene copy number (16S GCN) varies among bacterial species and this variation introduces potential biases to microbial diversity analyses...
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dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations
BackgroundCopy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods...
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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this...
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High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR
Metabarcoding has become the workhorse of community ecology. Sequencing a taxonomically informative DNA fragment from environmental samples gives...
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Investigation of the mechanism of copy number variations involving the α-globin gene cluster on chromosome 16: two case reports and literature review
Thalassemia is one of the most common single-gene disorder worldwide. An important genetic cause of thalassemia is copy number variations (CNVs) in...
