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Small RNAs originated from pseudogenes: cis- or trans-acting?
Xingyi Guo1, Zhaolei Zhang, Mark B Gerstein
1Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Albert Einstein College of Medicine, New York, New York, United States of America.
Plos Computational Biology
|August 4, 2009
Summary
Rice genomes contain numerous pseudogenes, with some generating regulatory small RNAs. This study identifies 11,956 pseudogenes, revealing their potential roles in gene regulation and development.
Area of Science:
- Genomics
- Molecular Biology
- Plant Science
Background:
- Pseudogenes are increasingly recognized for novel regulatory functions beyond their silenced ancestral genes.
- Systematic characterization of rice pseudogenes and their regulatory impact on the rice genome is lacking.
Purpose of the Study:
- To conduct a genome-wide identification and characterization of rice pseudogenes.
- To investigate the potential of rice pseudogenes to produce small RNAs and their regulatory roles.
Main Methods:
- Genome-wide identification of non-transposon-related pseudogenes in rice.
- Analysis of small RNA sequencing data from developing rice grains.
- Bioinformatic analysis to predict small RNA origins and potential regulatory interactions.
Main Results:
- Identified 11,956 non-transposon-related rice pseudogenes, predominantly from gene duplications.
- Found 145 pseudogenes potentially generating antisense small RNAs, many of which are 24-nucleotides long.
- Evidence suggests pseudogene-derived small RNAs can act in cis to repress transcription or in trans to regulate functional genes.
Conclusions:
- Rice protein-coding genes have prevalent pseudogene paralogs, with a subset capable of producing regulatory small RNAs.
- Pseudogene-derived small RNAs may play significant roles in rice development and gene regulation.
- Exapted functions of pseudogenes represent a potentially ubiquitous phenomenon in eukaryotes.
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