Dataset Information

Expansion of the circadian transcriptome in Brassica rapa supports genome wide diversification of homeolog gene expression patterns

ABSTRACT: Following divergence from Arabidopsis thaliana, Brassica rapa underwent a whole genome triplication followed by extensive genome fractionation. Preferential retention of circadian clock genes suggest that expansion of the circadian network may play an important role during B. rapa domestication. To characterize the circadian transcriptome network, RNA-seq was performed in the B. rapa oil-type variety R500 following photocycle and thermocycle circadian time courses. The photocycle (LDHH) time course consisted of growing plants for 15 days at 20°C under a 12h light/12h dark photoperiod and transfering plants to constant light and 20°C 24h prior to harvesting leaf tissue every 2h for 48h starting at ZT24 with 2 biological replicates at every time point. The thermocycle (LLHC) time course consisted of growing plants for 15 days under constant light with a 12h 20°C/12h 10°C thermoperiod and transfering plants to constant light and 20°C 24h prior to harvesting leaf tissue every 2h for 48h starting at ZT24 with 2 biological replicates at every time point.

ORGANISM(S): Brassica rapa subsp. trilocularis

PROVIDER: GSE123654 | GEO | 2020/01/31

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcription appears to be modified globally by changes in temperature, there is a specific set of transcripts that continue to oscillate in constant conditions following temperature entrainment. These transcripts show a significant overlap with a previously defined set of transcripts oscillating in response to a photocycle. Further, these overlapping transcripts maintain the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. These findings suggest that a single transcriptional clock in the adult fly head is able to integrate information from both light and temperature. Experiment Overall Design: y w flies that had been reared in constant darkness initially at 25 C and later in a 12-hr 18 C/ 12-hr 25 C thermocycle for more than 4 days were harvested every four hours during an additional 18 C/25 C thermo cycle (also indicated as a cold/ambient or CA cycle) or an additional day at constant 25 C (also indicated as ambient/ambient or AA) . Relative to time CA0 as the time of the onset of the 18 C cryophase or AA0 as the time of the onset of the subjective cryophase during constant 25 C, samples were collected in a CA2- CA6-CA10-CA14-CA18-CA22 and AA2-AA6-AA10-AA14-AA18-AA22 schedule. Heads were isolated by breaking up frozen flies and passing them through a set of sieves. RNA was prepared using guanidine-thiocyanate extraction followed by purification over a CsCl gradient. Additional purification of the RNA samples was achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA probe was generated from 25 Î¼g of purified RNA and hybridized as described previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu

Project description:Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcription appears to be modified globally by changes in temperature, there is a specific set of transcripts that continue to oscillate in constant conditions following temperature entrainment. These transcripts show a significant overlap with a previously defined set of transcripts oscillating in response to a photocycle. Further, these overlapping transcripts maintain the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. These findings suggest that a single transcriptional clock in the adult fly head is able to integrate information from both light and temperature. Experiment Overall Design: cn bw flies that had been reared in constant darkness initially at 25 C and later in a 12-hr 18 C/ 12-hr 25 C thermocycle for more than 4 days were harvested every four hours during an additional two days at constant 25 C (also indicated as ambient/ambient or AA days 1 and 2) . Relative to time AA0 as the time of the onset of the subjective cryophase during constant 25 C, samples were collected in a AA2-AA6-AA10-AA14-AA18-AA22-AA26-AA30-AA34-AA38-AA42-AA46 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using guanidine-thiocyanate extraction followed by Experiment Overall Design: purification over a CsCl gradient. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 Î¼g of purified RNA and hybridized as described Experiment Overall Design: previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu

Project description:Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcription appears to be modified globally by changes in temperature, there is a specific set of transcripts that continue to oscillate in constant conditions following temperature entrainment. These transcripts show a significant overlap with a previously defined set of transcripts oscillating in response to a photocycle. Further, these overlapping transcripts maintain the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. These findings suggest that a single transcriptional clock in the adult fly head is able to integrate information from both light and temperature. Experiment Overall Design: y w; tim01 flies that had been reared in constant darkness initially at 25 C and later in a 12-hr 18 C/ 12-hr 25 C thermocycle for more than 4 days were harvested every four hours during an additional 18 C/25 C thermo cycle (also indicated as a cold/ambient or CA cycle) or an additional day at constant 25 C (also indicated as ambient/ambient or AA) . Relative to time CA0 as the time of the onset of the 18 C cryophase or AA0 as the time of the onset of the subjective cryophase during constant 25 C, samples were collected in a CA2- Experiment Overall Design: CA6-CA10-CA14-CA18-CA22 and AA2-AA6-AA10-AA14-AA18-AA22 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using guanidine-thiocyanate extraction followed by Experiment Overall Design: purification over a CsCl gradient. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 Î¼g of purified RNA and hybridized as described Experiment Overall Design: previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu

Project description:Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcription appears to be modified globally by changes in temperature, there is a specific set of transcripts that continue to oscillate in constant conditions following temperature entrainment. These transcripts show a significant overlap with a previously defined set of transcripts oscillating in response to a photocycle. Further, these overlapping transcripts maintain the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. These findings suggest that a single transcriptional clock in the adult fly head is able to integrate information from both light and temperature. Experiment Overall Design: y w flies that had been reared in constant darkness initially at 25 C and later in a 12-hr 18 C/ 12-hr 25 C thermocycle for more than 4 days were harvested every four hours during an additional 18 C/25 C thermo cycle (also indicated as a cold/ambient or CA cycle) or an additional day at constant 25 C (also indicated as ambient/ambient or AA) . Relative to time CA0 as the time of the onset of the 18 C cryophase or AA0 as the time of the onset of the subjective cryophase during constant 25 C, samples were collected in a CA2- Experiment Overall Design: CA6-CA10-CA14-CA18-CA22 and AA2-AA6-AA10-AA14-AA18-AA22 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using guanidine-thiocyanate extraction followed by Experiment Overall Design: purification over a CsCl gradient. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 Î¼g of purified RNA and hybridized as described Experiment Overall Design: previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu

Dataset Information

Expansion of the circadian transcriptome in Brassica rapa supports genome wide diversification of homeolog gene expression patterns

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure