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Widespread RNA editing of embedded alu elements in the human transcriptome
Dennis D Y Kim1, Thomas T Y Kim, Thomas Walsh
1Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA.
Genome Research
|September 3, 2004
Summary
Adenosine to inosine (A-to-I) RNA editing frequently targets Alu elements within human genes. This editing process may mark non-standard transcripts for specific cellular pathways.
Area of Science:
- Genomics
- RNA Biology
- Molecular Genetics
Background:
- Alu elements are abundant repetitive sequences in the human genome, often found within gene introns and untranslated regions (UTRs).
- While transcribed Alu sequences can influence RNA splicing, their broader impact on host RNA remains understudied.
- Adenosine to inosine (A-to-I) RNA editing has been observed in repetitive elements within specific human RNAs.
Purpose of the Study:
- To investigate the global prevalence and characteristics of A-to-I RNA editing within transcribed Alu sequences across the human transcriptome.
- To determine the association of Alu-associated RNA editing with specific RNA features and potential functions.
Main Methods:
- Statistical analysis of publicly available full-length human complementary DNAs (cDNAs).
- Identification and characterization of A-to-I editing sites within Alu sequences across diverse human libraries and tissues.
Main Results:
- Alu-associated RNA editing is a widespread phenomenon, detected in approximately 2% of analyzed human cDNAs.
- A-to-I substitutions are predominantly clustered within transcribed sense or antisense Alu sequences.
- Edited bases correlate with retained introns, extended UTRs, or transcripts lacking a corresponding known gene.
Conclusions:
- RNA editing of embedded Alu sequences is a global feature of the human transcriptome.
- Alu-associated RNA editing may serve as a mechanism to identify and potentially regulate non-coding or non-standard RNA transcripts.