概要: 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.
项目整体设计: 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.
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.
处理方案:
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.
提取方案:
RNA samples were isolated using TRIzol reagent (Invitrogen).
建库方案:
The RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced on Illumina HiSeq 2000 with PE150 method.
测序信息
分子类型:
poly(A)+ RNA
库的片段类型:
PAIRED; SINGLE
库的链类型:
-; Forward; Reverse
测序平台:
ILLUMINA
测序仪型号:
Illumina HiSeq 2000
链特异性:
Unspecific; Specific
样本
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样本描述:
生物条件:
实验变量:
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质量评估:
数据来源
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物种
种族
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组织
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细胞系
疾病
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发育阶段
突变/变异
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Condition Detail
生长方案
处理方案
提取方案
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分子类型
库的片段类型
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加标（Spike-In）
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平均测序片段长度_1
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文章
Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence.
