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| Status |
Public on Mar 16, 2023 |
| Title |
A VEL3 histone deacetylase complex establishes a maternal epigenetic state controlling progeny seed dormancy |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Mother plants play an important role in the control of dormancy and dispersal characters of their progeny. In Arabidopsis seed dormancy is imposed by the embryo-surrounding tissues of the endosperm and seed coat. Here we show that the VERNALIZATION5/VIN3-LIKE 3 (VEL3) gene maintains maternal control over progeny seed dormancy by establishing an epigenetic state early in endosperm development that primes the depth of primary seed dormancy later established during seed maturation. VEL3 relocates MSI1 to the nucleolus and associates with other components of the histone deacetylase complex (HDAC). Furthermore VEL3 preferentially associates with pericentromeric chromatin and is required for deacetylation and H3K27me3 deposition and is required for gene repression via PRC2 and HDAC at pericentromeric regions established in the central cell. Interestingly, the epigenetic state established by the maternal VEL3 is retained trans-generationally in mature seeds, and controls seed dormancy in part through the repression of programmed cell death-associated gene ORE1. Our data demonstrates a novel mechanism by which maternal control of progeny seed physiology persists post-shedding, maintaining parental control of seed behaviour.
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| Overall design |
RNA-seq was performed in globular seeds, mature endosperm and 24 hours water imbibed endosperm (24HAI) for Col0 and vel3. H3K27me3 and H3K9ac ChIP-seq was performed in mature endosperm for Col0 and vel3. VEL3 ChIP-seq was performed in VEL3-GFP siliques.
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| Contributor(s) |
Chen X, Penfield S |
| Citation(s) |
37072400 |
| Submission date |
May 11, 2022 |
| Last update date |
May 12, 2023 |
| Contact name |
Xiaochao Chen |
| E-mail(s) |
xiaochao.chen@jic.ac.uk
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| Organization name |
John Innes Centre
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| Department |
Crop Genetics
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| Lab |
Penfield Lab
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| Street address |
Norwich Research Park, Colney Ln
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| City |
Norwich |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
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| Platforms (3) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
| GPL24025 |
BGISEQ-500 (Arabidopsis thaliana) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (38)
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| GSM6133419 |
RNA-seq, vel3, globular, R1 |
| GSM6133420 |
RNA-seq, vel3, globular, R2 |
| GSM6133421 |
RNA-seq, vel3, globular, R3 |
| GSM6133422 |
RNA-seq, Col0, mature, R1 |
| GSM6133423 |
RNA-seq, Col0, mature, R2 |
| GSM6133424 |
RNA-seq, Col0, mature, R3 |
| GSM6133425 |
RNA-seq, vel3, mature, R1 |
| GSM6133426 |
RNA-seq, vel3, mature, R2 |
| GSM6133427 |
RNA-seq, vel3, mature, R3 |
| GSM6133428 |
RNA-seq, Col0, 24HAI, R1 |
| GSM6133429 |
RNA-seq, Col0, 24HAI, R2 |
| GSM6133430 |
RNA-seq, Col0, 24HAI, R3 |
| GSM6133431 |
RNA-seq, vel3, 24HAI, R1 |
| GSM6133432 |
RNA-seq, vel3, 24HAI, R2 |
| GSM6133433 |
RNA-seq, vel3, 24HAI, R3 |
| GSM6133434 |
H3K27me3, Col0, input, R1 |
| GSM6133435 |
H3K27me3, Col0, IP, R1 |
| GSM6133436 |
H3K27me3, Col0, input, R2 |
| GSM6133437 |
H3K27me3, Col0, IP, R2 |
| GSM6133438 |
H3K27me3, vel3, input, R1 |
| GSM6133439 |
H3K27me3, vel3, IP, R1 |
| GSM6133440 |
H3K27me3, vel3, input, R2 |
| GSM6133441 |
H3K27me3, vel3, IP, R2 |
| GSM6133442 |
VEL3, input, R1 |
| GSM6133443 |
VEL3, IP, R1 |
| GSM6133444 |
VEL3, input, R2 |
| GSM6133445 |
VEL3, IP, R2 |
| GSM7028002 |
H3K9ac, Col0, input, R1 |
| GSM7028003 |
H3K9ac, Col0, input, R2 |
| GSM7028004 |
H3K9ac, Col0, IP, R1 |
| GSM7028005 |
H3K9ac, Col0, IP, R2 |
| GSM7028006 |
H3K9ac, vel3, input, R1 |
| GSM7028007 |
H3K9ac, vel3, input, R2 |
| GSM7028008 |
H3K9ac, vel3, IP, R1 |
| GSM7028009 |
H3K9ac, vel3, IP, R2 |
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| Relations |
| BioProject |
PRJNA837279 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE202802_24HAI_endosperm_TPM.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
| GSE202802_Col0_H3K9ac.bw |
17.0 Mb |
(ftp)(http) |
BW |
| GSE202802_H3K27me3_Col0_R1.bw |
14.9 Mb |
(ftp)(http) |
BW |
| GSE202802_H3K27me3_Col0_R2.bw |
14.9 Mb |
(ftp)(http) |
BW |
| GSE202802_H3K27me3_vel3_R1.bw |
14.6 Mb |
(ftp)(http) |
BW |
| GSE202802_H3K27me3_vel3_R2.bw |
14.7 Mb |
(ftp)(http) |
BW |
| GSE202802_VEL3_R1.bw |
18.1 Mb |
(ftp)(http) |
BW |
| GSE202802_VEL3_R2.bw |
18.4 Mb |
(ftp)(http) |
BW |
| GSE202802_globular_seeds_TPM.csv.gz |
1.9 Mb |
(ftp)(http) |
CSV |
| GSE202802_mature_endosperm_TPM.csv.gz |
35.7 Kb |
(ftp)(http) |
CSV |
| GSE202802_vel3_H3K9ac.bw |
17.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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