Emerging Genome Technologies
Hazen, Samuel , Naef, Felix , Quisel, Thomas , Borevitz, Justin , Kay, Steve .
Detecting circadian clock regulated transcription using genome tiling arrays.
Circadian clock regulation of transcription in plants appears to be rather extensive and many pathways relating to photosynthesis, cold acclimation, and cell wall dynamics, for example, exhibit circadian rhythms at multiple levels. Estimates on the extent of circadian clock regulation are primarily derived from the use of high-density oligonucleotide arrays with features whose majority correspond to the 3’ end of genes annotated as protein coding. Recently, there has been a flourish of work using genome tiling arrays capable of measuring nearly all nonredundant sequences in the genome, far beyond what previous studies were capable of evaluating. In numbers perhaps comparable to the number of protein coding transcripts, noncoding RNAs, which include natural antisense transcripts appear to be a large component of a remarkably complex transcriptome in all organisms examined to date: Arabidopsis, Drosophila, E. coli, human, rice, and yeast. Tiling array experiments have done little to characterize large-scale transcriptional activity beyond to say it exists. We explored circadian clock transcriptional regulation in Arabidopsis by using the AtTILE1 high-density oligonucleotide tiling array. This unbiased approach measured rhythmic antisense transcripts, alternative splicing, noncoding RNAs, and erroneous genome annotation.
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1 - The Scripps Research Institute, Department of Biochemistry, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
2 - Swiss Institute for Experimental Cancer Research
3 - University Of Chicago, Department of Evolution and Ecology
4 - The Scripps Research Institute, Department of Biochemistry
Presentation Type: ASPB Minisymposium
Location: Continental A/Hilton
Date: Sunday, July 8th, 2007
Time: 2:25 PM