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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

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Published on: January 10, 2025

Alu insertion profiling: array-based methods to detect Alu insertions in the human genome.

Maurizio Cardelli¹, Francesca Marchegiani, Mauro Provinciali

¹Advanced Technology Center for Aging Research, Scientific Technological Area, INRCA-IRCCS, Ancona, Italy.

|April 13, 2012

Summary

This summary is machine-generated.

We developed two Alu insertion profiling (AIP) methods to analyze genetic variability in repetitive Alu sequences. These methods efficiently detect new Alu polymorphisms and mutations across the genome.

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Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Area of Science:

Genetics
Genomics
Molecular Biology

Background:

Genetic variability analysis of Alu sequences was limited by the lack of genome-wide detection methods.
Repetitive elements like Alu sequences are crucial for understanding genome evolution and diversity.

Purpose of the Study:

To introduce and validate two novel Alu insertion profiling (AIP) methods for genome-wide analysis of Alu sequence variability.
To assess the sensitivity of AIP methods for detecting polymorphisms in different Alu subfamilies.

Main Methods:

Development of two Alu insertion profiling (AIP) methods utilizing Alu-flanking genomic fragments hybridized to tiling microarrays.
Application of AIP methods to analyze chromosomes 1 and 6 in two genomic samples.
Validation of identified Alu elements using Polymerase Chain Reaction (PCR) and DNA sequencing.

Main Results:

AIP methods demonstrated high sensitivity in detecting young Alu Ya subfamily insertions (67%-90%) and lower sensitivity for older Alu J and S lineages (2%-8%).
Sample-to-sample differences identified 5-8 loci associated with known Alu polymorphisms.
Four novel intragenic Alu elements, polymorphic in 10 additional individuals, were confirmed.

Conclusions:

Alu insertion profiling (AIP) methods provide an efficient genome-wide approach for detecting Alu polymorphisms and mutations.
These methods enhance the study of genetic diversity and the role of repetitive elements in genome evolution.
The validated AIP protocols can be applied to discover new Alu elements and analyze their population-level variation.