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Single Nucleotide Polymorphisms-SNPs01:05

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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,...
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The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent...
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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.
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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Functional Implications of the CLOCK 3111T/C Single-Nucleotide Polymorphism.

Angela R Ozburn1, Kush Purohit2, Puja K Parekh2

  • 1Department of Psychiatry and Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA; Portland Alcohol Research Center, VA Medical Center, Portland, OR, USA.

Frontiers in Psychiatry
|May 6, 2016
PubMed
Summary

Disruptions in circadian rhythms are linked to bipolar disorder (BD). A specific CLOCK gene variation (3111T/C SNP) impacts gene expression, potentially influencing BD manic episodes.

Keywords:
bipolar disordercell culturecircadianclockgene expressionsingle-nucleotide polymorphism

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Area of Science:

  • Neuroscience
  • Genetics
  • Chronobiology

Background:

  • Circadian rhythm disruptions are strongly linked to bipolar disorder (BD).
  • The molecular clock, including the CLOCK protein, regulates circadian rhythms via a feedback loop.
  • Previous research indicates Clock gene manipulation can induce manic-like behaviors in mice.

Purpose of the Study:

  • To investigate the functional impact of the human CLOCK 3111T/C single-nucleotide polymorphism (SNP) on gene expression.
  • To determine how this specific genetic variation in the CLOCK gene affects mRNA levels and circadian gene regulation.

Main Methods:

  • Transfection of mouse embryonic fibroblasts (Clock(-/-)) with human CLOCK gene variants (T or C SNP at position 3111).
  • Measurement of circadian gene expression over a 24-hour period post-transfection.
  • Analysis of mRNA levels for CLOCK and its target gene Per2.

Main Results:

  • The CLOCK 3111C SNP variant led to significantly higher CLOCK mRNA levels compared to the 3111T SNP.
  • Expression of Per2, a downstream target of CLOCK, was also elevated with the CLOCK 3111C variant.
  • These findings suggest the 3'-untranslated region (3'-UTR) SNP influences CLOCK mRNA expression, function, and stability.

Conclusions:

  • The CLOCK 3111T/C SNP in the 3'-UTR of the CLOCK gene has functional consequences on gene expression.
  • This genetic variation may contribute to the association between CLOCK gene polymorphisms and increased manic episodes in bipolar disorder.
  • Further research is warranted to fully elucidate the role of this SNP in BD pathophysiology.