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SRX669386: GSM1464771: ChIP-1-130516; Arabidopsis thaliana; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 16.4M spots, 591.2M bases, 379.8Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: FYRN and FYRC domains of the histone demethylase, JMJ14, mediated chromatin binding and transgene silencing through a pair of NAC transcription factors
show Abstracthide Abstract
JmjC domain containing protein 14 (JMJ14) is an H3K4-specific histone demethylase that plays important roles in RNA-mediated gene silencing and flowering time regulation in Arabidopsis. However, how JMJ14 is recruited to their target genes remains unclear. Here, we show that the C-terminal FYRN and FYRC domains of JMJ14 are required for RNA silencing and flowering time regulation. Chromatin binding of JMJ14 is lost upon deletion of its FYRN and FYRC domains, along with increased H3K4me3. FYRN and FYRC domains interact with a pair of NAC domain containing transcription factors, NAC050 and NAC052. Genome-wide analysis revealed that JMJ14 and NAC050/052 share a set of common target genes with CTTGNNNNNCAAG consensus sequences. Mutations in either NAC052 or NAC050 impair RNA-mediated gene silencing. Thus, our findings demonstrate an important role of FYRN and FYRC in targeting JMJ14 through direct interaction with NAC050/052 transcription factors, which reveals a novel mechanism of recruiting a histone demethylases to its target loci in higher plants. Overall design: anti-HA ChIP-seq were performed with six samples: Col, NAC050-HA, NAC052-HA, jmj14-1, JMJ14-HA and JMJ14-FYR-HA. Anti-H3K4me3 ChIP were performed with four samples: Col, jmj14-1, JMJ14-HA and JMJ14-FYR-HA. (NAC050-HA indicates PNAC050::NAC050-HA nac050-1, NAC052-HA indicates PNAC052::NAC052-HA nac052-2, JMJ14-HA indicates PJMJ14::JMJ14-HA jmj14-1, JMJ14-FYR-HA indicates PJMJ14::JMJ14-FYR-HA jmj14-1)
Sample: ChIP-1-130516
SAMN02951816 • SRS674003 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Selection: ChIP
Layout: SINGLE
Construction protocol: Chromatin Immunoprecipitation (ChIP) assays were performed using 1 g 12-day-old seedlings as previously described with minor modifications (Lu F. et al., 2010, Cell research 20(3):387-390). For anti-HA ChIP, chromatin was fragmented by Micrococcal nuclease (MNase, NEB M0247S) in the MNase digestion buffer (50 mM Tris pH 8.0, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2) instead of sonication before nuclei lysis. Antibodies used in ChIP were anti-H3K4me3 (Millipore 07-473) and anti-HA (Sigma H6908). The ChIP-Seq libraries were constructed using NEBNext® DNA Library Prep Master Mix Set for Illumina® (NEB, E6040S). ChIPed DNA was ligated with Illumina single-end genome sequencing adaptors, size fractionated to obtain 300-bp fragments
Experiment attributes:
GEO Accession: GSM1464771
External link:
Runs: 1 run, 16.4M spots, 591.2M bases, 379.8Mb
Run# of Spots# of BasesSizePublished


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