Dataset Information

Identification of the key ubiquitination sites of the OsWRI1a protein in rice

ABSTRACT: OsWRI1a is a key factor regulating the nitrogen response of rice roots, and it is a downstream target gene of RNR10. Previous studies have shown that rice OsWRI1a is subject to ubiquitination modification. To determine the ubiquitination modification sites of OsWRI1a, we conducted mass spectrometry analysis.

INSTRUMENT(S):

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Root, Leaf

SUBMITTER: chengbo shen

LAB HEAD: Shengbo Shen

PROVIDER: PXD067124 | Pride | 2025-12-17

REPOSITORIES: Pride

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			Action	DRS
	24NP16190001.raw	Raw
	NRS11-U.dat	Other

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Project description:The centromere is defined by the presence of a centromere-specific histone H3 variant, CENH3. Establishment and maintenance of the centromeric chromatin (CEN chromatin) is determined by poorly understood epigenetic mechanisms. Interestingly, CEN chromatin in several eukaryotes showed euchromatic characteristics although being embedded within pericentromeric heterochromatin. Specifically, H3K4me2 appeared to be a unique histone modification mark associated with animal centromeres. We developed a genomic tiling array for four fully sequenced rice centromeres. A ChIP-chip approach was used to study the patterns of several euchromatic histone modification marks, including H3K4me2, H3K4me3, H3K36me3, and H3K4K9a, associated with rice centromeres. We demonstrate that the CENH3 subdomains within the four centromeres are depleted with the four histone H3 marks. The vast majority of the four histone marks were associated with the genes located in the H3 subdomains within the centromeric cores. Genes in the centromeres showed similar histone modification patterns as those located outside of the centromeres. Thus, the euchromatic characteristics of rice CEN chromatin are trademarks of the transcribed sequences embedded in the H3 subdomains of the centromeres. We propose that the constitutively expressed genes located in rice centromeres may provide a barrier for loading of CENH3 into the H3 subdomains. The separation of CENH3 into the H3 subdomains is favorable for the three dimensional structure and its associated function of rice centromeres. We developed a genomic tiling array that covers four rice centromeres (Cen4, Cen5, Cen7, and Cen8) using the NimbleGen 3x720K array based on the NimbleGen HD2 platform. We used four antibodies (H3K4me3, H3K4me2, H3K36me3, H3K4K9ac) to perform ChIP-chip experiments. ChIP was conducted using leaf tissue from two-week old rice seedlings. We have 3 biological replicates for each antibody and 6 technological replicates of hybridization with position exchange on the array. Thus, each histone modification included 18 hybridization experiments.

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Identification of the key ubiquitination sites of the OsWRI1a protein in rice

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