Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of H3K4me3 and H3K27me3 in HY(Hwayong) and chd1(chr729) rice.

ABSTRACT: We report the application of CHIP-seq technology for high-throughput profiling of histone modifications in HY(Hwayong) and chd1(chr729). By obtaining about 12 million reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide H3K4me3 and H3k27me3 maps of HY(Hwayong) and chd1(chr729). We find that lysine 4 and lysine 27 trimethylation marked genes effectively losed in chd1 compared to HY. Examination of two histone modifications in two rice species.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: yongfeng hu

PROVIDER: E-GEOD-30490 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome.

Hu Yongfeng Y Liu Dengnian D Zhong Xiaocao X Zhang Chengjun C Zhang Qifa Q Zhou Dao-Xiu DX

Proceedings of the National Academy of Sciences of the United States of America 20120326 15

Histone lysine methylation is an important component of the epigenetic system demarcating transcriptionally active and inactive chromatin domains. It is of primary importance in understanding how different histone lysine methylation marks and a specific combination of them are read and interpreted by chromatin proteins to regulate gene expression. In this paper, we report that the rice CHD3 protein CHR729 that was required for many aspects of plant development can interact with dimethylated hist ...[more]

PMID: 22451926

Similar Datasets

Genome-wide maps of H3K4me3 and H3K27me3 in HY(Hwayong) and chd1(chr729) rice.

Project description:We report the application of CHIP-seq technology for high-throughput profiling of histone modifications in HY(Hwayong) and chd1(chr729). By obtaining about 12 million reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide H3K4me3 and H3k27me3 maps of HY(Hwayong) and chd1(chr729). We find that lysine 4 and lysine 27 trimethylation marked genes effectively losed in chd1 compared to HY.

2012-03-10 | GSE30490 | GEO

Rice (Oryza sativa) lysine-acetylation LC-MS/MS

Project description:Lysine acetylation is a dynamic and reversible post-translational modification that plays an imporant role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation sites and proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings.

2016-02-24 | PXD002291 | Pride

Transcriptional analysis of time course in response to HY-PDT on human nasopharyngeal carcinoma cell line CNE-2

Project description:Analysis of photodynamic therapy with hypericin of nasopharyngeal carcinoma cells CNE-2 in different time-points at gene expression level. The hypothesis tested in the present study was that HY-PDT could induce apoptosis on CNE-2 cells via intrinsic pathways. Results provide important information of the response of apoptosis, such as specific oxidative stress genes, mitochondrial related genes, cell cycle related genes, etc. Total RNAs were isolated from the cultured cells treatment with 20 μg/ml HY and irradiation then cultured in dark for 0, 2, 6, 12, 20 h respectively compared to cells treatment with 20 μg/ml HY only then cultured in dark for 20 h.

2011-01-28 | E-GEOD-20134 | biostudies-arrayexpress

CHD1 and H3K4me3 ChIP-seq in prostate cancer cell line PC-3

Project description:Trimethylation of histone H3 at lysine 4 (H3K4me3) is known to be associated with transcriptional activation and CHD1 is known to selectively recognize and bind to H3K4me3 to activate gene transcription. In addition, CHD1 is involved in the maintenance of open chromatin and cooperates with H3K4me3 to control pluripotency of murine embryonic stem cells. To determine the downstream transcriptional targets and pathways of CHD1 and H3K4me3 in PTEN-null PCa cells, ChIP-seq was performed in control versus CHD1 knockdown PC-3 cells.

2017-02-10 | GSE91401 | GEO

Co-dependency of H2B monoubiquitination and nucleosome re-assembly on Chd1

Project description:Monoubiquitination of histone H2B on lysine 123 (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively. Many of the factors such as Rad6/Bre1, the Paf1 complex, and the Bur1/Bur2 complex were identified to be required for proper histone H3K4 and H3K79 trimethylation, and were shown to function by regulating H2BK123ub levels. Here, we have identified Chd1 as a factor that is required for proper maintenance of H2B monoubiquitination levels, but not for H3K4 and H3K79 trimethylation. Loss of Chd1 results in a substantial loss of H2BK123ub levels with little to no effect on the genome-wide pattern of H3K4 and H3K79 trimethylation. Our data shows that nucleosomal occupancy is reduced in gene bodies in both CHD1 null and K123A backgrounds. We have also demonstrated that Chd1’s function in maintaining H2BK123ub levels is conserved from yeast to human. Our study provides evidence that only small levels of H2BK123ub are necessary for full levels of H3K4 and H3K79 trimethylation in vivo, and points to a role for Chd1 in positively regulating gene expression through promoting nucleosome re-assembly coupled with H2B monoubiquitination. Examination of two histone modifications in wild-type and Chd1 null yeast strains using ChIP-seq. Expression profiling in wild-type and Chd1 null yeast strains using RNA-seq.

2012-05-01 | E-GEOD-36334 | biostudies-arrayexpress

Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail

Project description:ISWI-family nucleosome remodeling enzymes need the histone H4 N-terminal tail to mobilize nucleosomes. Here we mapped the H4-tail binding pocket of ISWI. Surprisingly the binding site was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the N-terminal region (NTR) of ISWI, indicating that AutoN does not act as a simple pseudosubstrate as suggested previously. Rather, AutoN cooperated with a hitherto uncharacterized motif, termed AcidicN, to confer H4-tail sensitivity and discriminate between DNA and nucleosomes. A third motif in the NTR, ppHSA, was functionally required in vivo and provided structural stability by clamping the NTR to Lobe 2 of the ATPase domain. This configuration is reminiscent of Chd1 even though Chd1 contains an unrelated NTR. Our results shed light on the intricate structural and functional regulation of ISWI by the NTR and uncover surprising parallels with Chd1. Elife. 2017 Jan 21;6. pii: e21477. doi: 10.7554/eLife.21477. [Epub ahead of print]

2017-02-02 | PXD005831 | Pride

Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance

Project description:Lysine-specific demethylase 1 (LSD1) is involved in gene regulation and development; however, its precise function, molecular targets and underlying mechanisms during development are poorly understood. Here, we show that LSD1 is required for neuronal progenitor cell (NPC) maintenance during cortical development. A ChIP-seq analysis identified a LSD1 binding site (LBAL) downstream of Atrophin1 (ATN1). Surprisingly, tranylcypromine (LSD1 inhibitor) treatment increased H3K4 methylation at LBAL, leading to ATN1 repression and NPC differentiation. Knockdown of LSD1 and ATN1 phenocopied each other in inducing NPC premature differentiation and depletion which could be rescued by ATN1 overexpression, suggesting that LSD1 controls NPC differentiation via regulation of ATN1 methylation status and expression. The involvement of LSD1 in ATN1 expression and NPC maintenance were confirmed in knockout mice. These findings hint at the potential application for the clinical drug, tranylcypromine, in the prevention and/or treatment of ATN1-associated degenerative disease, dentatorubral-pallidoluysian atrophy. Examination of LSD1 binding sites in neuronal progenitor cells.

2015-04-29 | E-GEOD-62770 | biostudies-arrayexpress

Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response

Project description:This SuperSeries is composed of the following subset Series: GSE22102: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (sequencing) GSE24774: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (WT and G9a deficient DCs) GSE24776: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (WT and G9a deficient MEFs) Refer to individual Series

2012-03-02 | E-GEOD-24826 | biostudies-arrayexpress

Histone architecture of stem-cell memory T cells reveals progressive remodeling of epigenetic landscape in antigen-experienced CD8 T cells

Project description:We investigated the genomic landscape of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling [GSE67825], we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in distinct subsets of CD8+ T cells - naïve, stem cell memory, central memory, and effector memory. To gain insight into how histone architecture is remodeled during the differentiation of activated T cells

2015-04-15 | E-GEOD-67881 | biostudies-arrayexpress

Oryza sativa Japonica Group

Project description:Genome-wide maps of H3K4me3 and H3K27me3 in HY(Hwayong) and chd1(chr729) rice.

| PRJNA143507 | ENA