Tiling arrays reveal plant circadian RNAs
Genome tiling arrays uncover extensive circadian-regulated transcription across the Arabidopsis genome.
Source
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
Study at a glance
- Design
- Animal / in-vitro — Arabidopsis genome tiling arrays on a 2-day circadian time course
- N
- N=12 · 12 samples at 4-hour resolution over 2 days
- Population
- Arabidopsis thaliana plants under circadian free-run
- Outcome
- Extensive circadian transcription including exons, introns, and natural antisense transcripts beyond annotated clock genes
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Tiling arrays reveal plant circadian RNAs
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Arabidopsis thaliana.
Earth's rotation. In addition to reacting directly to external stimuli, many organisms time their behavior in anticipation of periodic changes in the environment.
Whole-genome tiling arrays.
The endogenous timing mechanism known as circadian clocks is widespread across life and is primarily based on interlocking transcriptional feedback loops and regulated protein turnover [].
What they did
Sampled a 2-day circadian time course at 4-hour resolution on whole-genome tiling arrays.
What they found
Known clock genes cycle as expected; many additional exons/ncRNA features show circadian rhythms.
The limits
What it doesn't show
Two-day series limits period precision versus longer time courses.
Key terms
- Circadian clock
- ~24 h endogenous timing system.
- Tiling array
- Dense probes across the genome.
- Arabidopsis
- Plant model organism.
- PRR genes
- PSEUDO-RESPONSE REGULATOR clock genes.
- Spectral analysis
- Tests rhythmic hybridization.
- ncRNA
- Noncoding RNA features.
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Topic:
Common questions
Organism?
Arabidopsis.
Resolution?
4 h.
Duration?
2 days.
Platform?
Tiling arrays.
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