Gene Expression
Nebulas
Gene Expression NebulasSummary: The circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. Overexpressing OsPRR37 weakens the transcriptomic rhythms and alters the phases of rhythmic genes. In total, 3,210 differentially expressed genes (DEGs) are identified, among which 1,863 rhythmic DEGs show a correlation between the change of absolute amplitudes and the mean expression levels. We further reveal that OsPRR37 functions as a transcriptional repressor to repress the expression levels and amplitudes of day-phased clock genes. More importantly, OsPRR37 confers expanded regulation on the evening-phased rhythmic DEGs by repressing the morning-phased rhythmic DEGs. Further study shows that OsPRR37 expands its regulation on flowering pathways by repressing Ehd1. Thus, our results demonstrate an expanded regulation mechanism of the circadian clock on the diurnal rhythms of the transcriptome.
Overall Design: Totally 36 samples were analyzed by using Illumina HiSeq2500, in which 18 for GL and 18 for OsPRR37-OE5. The precise sampling times were set as 4:00, 8:00, 12:00, 16:00, 20:00, and 0:00 over a single day with three biological repeats for each time point.
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| Growth Protocol: | Natural long-day conditions |
| Treatment Protocol: | All plant materials were planted according to a randomized block design with three replicates. The precise sampling times were set as 4:00, 8:00, 12:00, 16:00, 20:00, and 0:00 over a single day. |
| Extract Protocol: | Total RNA was isolated from each leaf sample with aTRIzol reagent (Invitrogen, Carlsbad,CA, USA) according to the manufacturer's instructions. The total RNA was treated with RNase-free DNase I (New England Biolabs, Ipswich, MA, USA) to eliminate genomic DNA contamination. |
| Library Construction Protocol: | The cDNA library was constructed according to the protocol that is provided with the NEBNext Ultra RNA Library Prep Kit for Illumina, NEB #E7530 (New England Biolabs, Inc.). |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Unspecific |