Transcriptomics,Genomics

Dataset Information

16

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays


ABSTRACT: A casual look at the behavior and function of animals and plants clearly shows that many physiological processes are periodic and tied to cyclical changes in a day. As suggested by the persistence of some rhythms in the absence of external cues, organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome. As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons creating a transcript that if translated would be expected to produce a truncated protein. In some cases such as the MYB transcription factor PHOSPATE STARVATION RESPONSE1, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic. In addition to several known non-coding transcripts including miRNA, trans-acting siRNA, and snoRNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or non-coding. Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic. This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known. Overall design: Seedlings of Arabidopsis thaliana accession Col-0 were grown on MS media (supplemented with 2% D-glucose and solidified with 1% agar) 7 days in 12 h light:12 h dark cycles under white fluorescent bulbs at 100 mmol m-2 s-1 before release to constant light and temperature. Samples were collected every 4 h beginning at the time of lights on, ZT0. Single perfect matches, without a 2nd partial match of >18/25 bp were selected giving a total of 1,683,620 unique features. These were mapped to annotated mRNAs as intron, exon, inter-genic region, or flanking probes which span an annotated boundary. Hybridization efficiencies of oligonucleotide probes on tiling arrays vary considerably and some probes tend to be unresponsive. Thus, to avoid spurious decrease of signal in the spectral analysis from poorly responsive probes, we filtered out probes which are lowly expressed (mean < 3) and furthermore show very little variation (standard deviation < 0.25) across the time series leaving a total of 1,609,258 features between both the forward and reverse strand arrays. The twelve measurements for each probes were standardized and Fourier analysis was used to evaluate the RNA expression pattern over the two-day time course. To exploit redundancy of features we grouped all probes for the same exon based on the TAIR7 genome annotation, or applied 200 bp windows centered on each intronic or intergenic probe position while stopping at exon boundaries. We then computed the 24-h spectral power F24 from the average of the standardized probes within a group. To assess the significance of these F24 scores, we built empirical null distributions that take into account the number of probes (weight) that went into the calculation of the spectral power. The family of null distributions was calibrated from the distribution of scores of all probes annotated as intergenic. We parametrized these distributions as exponential functions which gave excellent fits. The p-values for all features were then computed from the fitted distributions. The labeling method which used oligo dT for first strand amplification of the RNA produces a 3’ biased probes; therefore, any annotation unit with at least two features satisfying p < 0.005 was considered circadian regulated. For Fig. 2 the phases for genes were computed from the circular averages of the phase in individual exons using CIRCSTAT.

INSTRUMENT(S): AtTile1F to Arabidopsis Tiling 1.0F

SUBMITTER: Samuel P Hazen   

PROVIDER: GSE13814 | GEO | 2008-12-06

SECONDARY ACCESSION(S): PRJNA110587

REPOSITORIES: GEO

altmetric image

Publications

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.

Hazen Samuel P SP   Naef Felix F   Quisel Tom T   Gendron Joshua M JM   Chen Huaming H   Ecker Joseph R JR   Borevitz Justin O JO   Kay Steve A SA  

Genome biology 20090211 2


BACKGROUND: Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome. RESULTS: As in previous studies, we detected a circadian rhythm for approximately 25% of the prote  ...[more]

Similar Datasets

2014-06-03 | E-GEOD-57891 | ArrayExpress
| GSE81100 | GEO
| GSE67305 | GEO
| GSE36874 | GEO
2016-07-01 | E-GEOD-81100 | ArrayExpress
2014-05-03 | E-GEOD-36874 | ArrayExpress
2014-12-10 | E-GEOD-54651 | ArrayExpress
2014-10-05 | E-GEOD-54650 | ArrayExpress
2014-05-03 | E-GEOD-36873 | ArrayExpress
2013-03-11 | E-GEOD-36871 | ArrayExpress