Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-seq analysis of bZIP73 binding sites in rice seedlings (Zhonghua11)

ABSTRACT: Leaf tissues harvested from 50 two-week-old rice seedlings of bZIP73Jap::Flag OE lines were immediately fixed with 1% formaldehyde for chromatin isolation. DNA was extracted immunoprecipitated using anti-Flag antibodies, and the precipitated DNA was purified using the PCR Purification Kit (Qiagen, Germany). Raw genome DNA was used as input. Both input and ChIP DNA samples were sequenced twice.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Shujun Ou

PROVIDER: E-MTAB-6771 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Ineffective hematopoiesis is a hallmark of myelodysplastic syndromes (MDS). Hematopoietic alterations in MDS patients strictly correlate with microenvironment dysfunctions, eventually affecting also the mesenchymal stromal cells (MSCs) compartment. Stromal cells are indeed epigenetically reprogrammed to cooperate with leukemic cells and propagate the disease as "tumor unit"; therefore, changes on MSCs epigenetic profile might contribute to the hematopoietic perturbations typical of MDS. Here, we unveil that the histone variant macroH2A1 (mH2A1) regulates the crosstalk between epigenetics and inflammation in MDS-MSCs, potentially affecting their hematopoietic support ability. We show that the mH2A1 splicing isoform mH2A1.1 accumulates in MDS-MSCs, correlating with the expression of the Toll-like receptor 4 (TLR4), an important pro-tumor activator of MSC phenotype associated to a pro-inflammatory behavior. MH2A1.1-TLR4 axis was further investigated in HS-5 stromal cells after ectopic mH2A1.1 overexpression (mH2A1.1-OE). Proteomic data confirmed the activation of a pro-inflammatory signature associated to TLR4 and nuclear factor kappa B (NFkB) activation. Moreover, mH2A1.1-OE proteomic profile identified several upregulated proteins associated to DNA and histones hypermethylation, including S-adenosylhomocysteine hydrolase, a strong inhibitor of DNA methyltransferase and of the methyl donor S-adenosyl-methionine (SAM). HPLC analysis confirmed higher SAM/SAH ratio along with a metabolic reprogramming. Interestingly, an increased LDHA nuclear localization was detected both in mH2A1.1-OE cells and MDS-MSCs, probably depending on MSC inflammatory phenotype. Finally, coculturing healthy mH2A1-OE MSCs with CD34+ cells, we found a significant reduction in the number of CD34+ cells, which was reflected in a decreased number of colony forming units (CFU -Cs). These results suggest a key role of mH2A1.1 in driving the crosstalk between epigenetic signaling, inflammation and cell metabolism networks in MDS-MSCs.

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ChIP-seq analysis of bZIP73 binding sites in rice seedlings (Zhonghua11)

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