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Sense-antisense pairs in mammals: functional and evolutionary considerations
Pedro A F Galante1, Daniel O Vidal, Jorge E de Souza
1Ludwig Institute for Cancer Research, São Paulo Branch, Hospital Alemão Oswaldo Cruz, São Paulo, SP, Brazil. pgalante@compbio.ludwig.org.br
Natural antisense transcripts (NATs) play roles in cellular processes, but many are artifacts from cDNA library construction. A new model explains the origin of functional sense-antisense (S-AS) pairs in mammalian genomes.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Mammalian genomes contain numerous natural antisense transcripts (NATs).
- Sense-antisense (S-AS) pairs are implicated in various cellular functions.
Purpose of the Study:
- To create a comprehensive catalog of S-AS pairs in human and mouse genomes.
- To investigate the functional roles of NATs, including gene expression regulation.
- To identify potential artifacts among NATs.
Main Methods:
- Analysis of public expressed sequence data.
- Utilized 122 massively parallel signature sequencing (MPSS) libraries from human and mouse tissues.
- Computational and experimental approaches were employed.
Main Results:
- Generated a catalog of nearly 20,000 S-AS pairs in human and mouse genomes.
- Identified a significant fraction of NATs as artifacts resulting from genomic priming during cDNA library construction.
- Dissected and proposed new roles for NATs.
Conclusions:
- Proposed an evolutionary and functional model for the origin of S-AS pairs.
- Alternative polyadenylation and retroposition are key mechanisms contributing to functional S-AS pair formation.
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