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Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [ChIP-Seq]

ABSTRACT: Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [ChIP-Seq]

PROVIDER: PRJNA586758 | ENA |

REPOSITORIES: ENA

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Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [ChIP-Seq]

Project description:Chromatin remodeling and histone modifications are important for development and floral phase transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of ISWI chromatin remodeling complexes in Arabidopsis thaliana. We found that ARID5, a subunit of a plant-specific ISWI complex, can regulate development and floral phase transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral phase transition

2019-11-01 | GSE139636 | GEO

Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [RNA-Seq]

2019-11-01 | GSE139637 | GEO

Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis

Project description:Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis

| PRJNA586755 | ENA

Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [RNA-Seq]

Project description:Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis [RNA-Seq]

| PRJNA586757 | ENA

Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates floral phase transition in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-11-01 | GSE139638 | GEO

A plant-specific ISWI subunit is involved in fertility by inhibiting the pistil overgrowth

Project description:we identified the forkhead-associated domain 2 (FHA2) as a plant-specific subunit of an ISWI chromatin-remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. A reduced-fertility phenotype was observed in both the fha2 and rlt1/2 mutant plants and the phenotype was ascribed to overgrowth of the pistil during the floral development. However, the early-flowering phenotype of the rlt1/2 mutant was not shared by the fha2 mutant. Consistently, our RNA-seq analysis indicated that the fha2 mutant affects a subset of rlt1/2-regulated genes but not genes involved in the regulation of flowering time. This study demonstrates that FHA2 functions as a previously uncharacterized subunit of the Arabidopsis ISWI complex to exclusively regulate the pistil growth during the floral development.

2020-05-19 | GSE145514 | GEO

Affinity Purification of ISWI chromatin remodeler in Trypanosoma cruzi

Project description:Chromatin remodeling is a general mechanism involved in DNA-dependent processes, including gene expression regulation. ISWI ATPase is the catalytic subunit in diverse chromatin remodeling complexes that changing histone–DNA interactions and therefore play a pivotal role in different nuclear processes. Here, the ISWI remodeler was fused to GFP (NH and CO fusions) and its partners were determined by affinity purification-mass spectrometry (MS) assay. This approach identified known ISWI partners (NLP, RCCP and FYRP), previously characterized in T. brucei, and new components of TcISWI complex (DRBD2, DHH1 and proteins containing SMC domains).

2020-05-22 | PXD017869 | Pride

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [MNase-seq]

Project description:MNase-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells MNase-seq from Drosophila S2 nuclei after CTCF/CP190 or ISWI-specific RNAi treatment

2014-08-11 | E-GEOD-51599 | biostudies-arrayexpress

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [ChIP-seq]

Project description:H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells Histone H3 ChIP-seq from Drosophila S2 cells after CTCF/CP190 or ISWI-specific RNAi treatment

2014-08-11 | E-GEOD-51598 | biostudies-arrayexpress

Role of CHR4 during floral transition

Project description:Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that mediate floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-seq analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, the qem2 mutation is in CHROMATIN REMODELING 4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.

2020-03-02 | PXD016457 | Pride

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