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Series GSE124296 Query DataSets for GSE124296
Status Public on May 04, 2019
Title H3K4me3 profiling in HUB1 Arabidopsis mutant seedlings
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution in defining gene expression programs are poorly defined in plant systems. Differently from S. cerevisiae in which a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with SET1), this activity involves multiple histone methyltransferases (HMTs) in Arabidopsis thaliana, among which the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. Here we report that SDG2 co-regulates hundreds genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of the evolutionarily conserved COMPASS complex. Accordingly, S2Lb associates with the AtCOMPASS core subunit WDR5a within a high-molecular weight complex and is required for proper H3K4me3 enrichment over genes highly occupied by RNA Polymerase II. S2Lb knock-out plants display little transcriptomic defects, suggesting that H3K4me3 deposition is important for optimal gene induction rather than for determining on/off transcriptional states. We further report that S2Lb and H3K4me3 are accurately targeted over most genes in hub1 mutant plants lacking histone H2B monoubiquitination. Collectively, our study indicates that a plant-specific COMPASS-like complex acting mainly through an H2Bub-independent mechanism is a major determinant of H3K4me3 deposition in Arabidopsis.
 
Overall design 8 ChIP-seq libraries were sequenced. Two biological replicates each consisting of one Input and one IP for each genotype (WT and hub1-3 mutant)
 
Contributor(s) Barneche F, Benhamed M, Concia L, Rougée M, Bourbousse C
Citation(s) 31113491
Submission date Dec 21, 2018
Last update date May 24, 2019
Contact name Lorenzo Concia
E-mail(s) colore@gmail.com, concia@bio.ens.psl.eu
Phone 769929568
Organization name École Normale Supérieure
Department Institut de Biologie
Lab Plant and Algal Genomics Lab
Street address 46 Rue d'Ulm
City Paris
ZIP/Postal code 75020
Country France
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (8)
GSM3528363 WT_Input_BR1
GSM3528364 WT_Input_BR2
GSM3528365 HUB1_Input_BR1
This SubSeries is part of SuperSeries:
GSE124319 ChIP-seq and RNA-seq in HUB1 and SWD2 Arabidopsis mutant seedlings
Relations
BioProject PRJNA511488
SRA SRP174262

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124296_RAW.tar 359.4 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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