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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...

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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
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Both copy number and sequence variations affect expression of human DEFB4.

M Groth1, C Wiegand, K Szafranski

  • 1Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany. mgroth@fli-leibniz.de

Genes and Immunity
|May 7, 2010
PubMed
Summary

Copy number variations (CNVs) in the beta-defensin cluster (DEFB) impact gene expression. We found that DEFB copy number and specific sequence variations influence DEFB4 expression levels in cells and skin, with implications for immune response.

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Last Updated: Jun 13, 2026

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Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Area of Science:

  • Genomics
  • Immunology
  • Molecular Biology

Background:

  • Copy number variations (CNVs) significantly contribute to genomic variability.
  • The beta-defensin cluster (DEFB) on chromosome 8p23.1 is a well-studied CNV region, with copy numbers ranging from 2 to 12.
  • Low DEFB copy numbers are associated with an increased predisposition to Crohn's disease.

Purpose of the Study:

  • To investigate the relationship between DEFB copy number (CN) and multisite variations (MSVs) and the expression of beta-defensin genes.
  • To analyze DEFB4 expression in B-lymphoblastoid cell lines (LCLs) and normal human epidermal keratinocytes (NHEKs).
  • To examine variant-specific expression (VSE) and the impact of inflammatory stimuli on DEFB4 expression.

Main Methods:

  • DEFB4 expression was analyzed in LCLs and NHEKs.
  • Cells were stimulated with lipopolysaccharide, tumor necrosis factor-alpha (TNF-alpha), and interferon-gamma (IFN-gamma).
  • DEFB4 MSV was quantified in DNA and mRNA to assess VSE. The DEFB4 promoter region was resequenced.

Main Results:

  • A strong correlation was observed between DEFB CN and DEFB4 expression in LCLs, though some cell lines with differing CNs showed similar expression.
  • Quantification of DEFB4 MSV revealed VSE, with one variant consistently showing lower expression.
  • Costimulation of NHEKs with TNF-alpha/IFN-gamma synergistically increased total DEFB4 expression and suppressed VSE.
  • The DEFB4 promoter region exhibited a high density of sequence variations (approximately 1 MSV/41 bp).

Conclusions:

  • DEFB copy number and sequence variations play a crucial role in regulating DEFB4 expression.
  • Inflammatory signals can modulate DEFB4 expression and overcome variant-specific expression patterns.
  • The high variability in the DEFB4 promoter suggests complex regulatory mechanisms influencing gene expression.