Gene Expression
Nebulas
Gene Expression NebulasSummary: In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. Under starvation and submergence, Kbu andKcr appeared to be less dynamic than H3K9ac and the three marks displayed changes in different sets of genes. Kbu and Kcr seemed to have a function to poise stress-induced gene activation. The results suggest that histone Kbu and Kcr provide a platform for histone acetylation during gene activation and that the proportional mixture of distinct histone lysine acylations which are regulated by environmental cues and has functionally consequence in chromatin modification and gene expression in plants.
Overall Design: RNA-seq and H3K9ac, Kbu, and Kcr ChIP-seq of rice seedlings under normal conditions and starvation and submergence treatments; RNA-seq and H3K9ac ChIP-seq of rice leaf in 4 diurnal times.
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| Growth Protocol: | Rice seeds were germinated and grown on the hormone-free, half-strength Murashige & Skoog (MS) medium under 16/8 hrs light/dark at 30/25°C. |
| Treatment Protocol: | For starvation treatment, seedlings were moved into dark culture at 10 DAG 6:00pm and treated for 48 hours. For submergence treatment, seedlings were submerged in distilled water at 12DAG 12:00am and treated for 6 hours. Seedling leaves from each group were harvested at 12DAG 6:00pm for chromatin and total RNA extraction. |
| Extract Protocol: | RNA samples were isolated using TRIzol reagent (Invitrogen). |
| Library Construction Protocol: | The RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced on Illumina HiSeq 2000 with PE150 method. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED; SINGLE |
| Library Strand: | -; Forward; Reverse |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2000 |
| Strand-Specific: | Unspecific; Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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