Alu expression in human cell lines and their retrotranspositional potential.

Area of Science:

• Genomics
• Molecular Biology
• Human Genetics

Background:

• Alu elements are abundant repetitive sequences in the human genome.
• Most Alu elements are inactive, but a few 'source elements' can generate new insertions.
• Identifying active Alu sources requires understanding RNA polymerase III (pol III) transcription.

Purpose of the Study:

• To identify active Alu source elements by determining pol III transcribed loci.
• To assess the retrotransposition potential of pol III-bound Alu elements.

Main Methods:

• Genome-wide analyses to identify pol III-bound Alu loci in normal and transformed cell lines.
• Scoring pol III-bound Alus for estimated retrotransposition potential (ERP) based on sequence features.

Main Results:

• The majority of pol III-bound Alus belong to older subfamilies (Alu S and Alu J).
• Most pol III-bound Alu loci candidates lack sequence features crucial for retrotransposition.
• Potentially active Alu loci (high ERP) are predominantly from young Alu subfamilies.

Conclusions:

• Alu expression is variable, influenced by cell type, growth conditions, and transformation state.
• Many pol III-transcribed Alu loci lack retrotransposition capabilities.
• Younger Alu subfamilies are more likely to be active, with variable contributions to somatic genetic damage in vivo.