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Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
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Alu insertion variants alter gene transcript levels.

Lindsay M Payer1, Jared P Steranka1, Maria S Kryatova1

  • 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

Genome Research
|November 20, 2021
PubMed
Summary
This summary is machine-generated.

Commonly occurring Alu elements, a type of DNA repeat, can significantly impact gene expression and potentially influence disease risk. This study reveals how these genetic variations affect gene regulation.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Human Evolution

Background:

  • Alu elements are abundant interspersed repeats in the human genome and a major source of structural variation.
  • The regulatory impact of Alu insertions on gene expression is not fully understood, despite associations with expression quantitative trait loci (eQTLs).

Purpose of the Study:

  • To directly assess the regulatory effects of polymorphic Alu insertions independently of other variants.
  • To investigate whether Alu elements can introduce or disrupt gene regulatory functions.

Main Methods:

  • Utilized ectopic luciferase reporter assays to screen 110 Alu insertion variants for regulatory effects.
  • Employed CRISPR gene editing to create cell lines with different endogenous Alu genotypes.
  • Analyzed reporter constructs with surrounding genomic context to differentiate regulatory mechanisms.

Main Results:

  • Observed a range of regulatory effects, with some Alu insertions significantly up- or down-regulating gene expression.
  • Identified three polymorphic Alu loci associated with breast cancer that showed significant regulatory activity in reporter assays.
  • Demonstrated that Alu genotype can alter the expression of cancer-associated genes like PTHLH, RANBP9, and MYC.

Conclusions:

  • Common polymorphic Alu elements can modulate gene transcript levels.
  • Alu genotype represents a potential factor contributing to human disease risk, particularly in cancer.