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| Status |
Public on Apr 23, 2024 |
| Title |
AtSDR4L and DIG1 interact with VAL2 to promote seed-to-seedling transition |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
During the embryonic-to-vegetative transition in plants, many genes that were active in seeds become transcriptionally turned off. Recently, we reported a new transcriptional corepressor of the embryonic program, SEED DORMANCY 4-LIKE (AtSDR4L). Multiple lines of evidence suggest that AtSDR4L plays an essential role in regulating the transition from seed to seedling, possibly by collaborating with components of Polycomb Repressive Complexes (PRCs) and PRC-associated proteins VIVIPAROUS1/ABI3-LIKE (VAL) proteins. Through yeast-two-hybrid (Y2H) assays and genome-wide binding analysis, we demonstrated that AtSDR4L and DIG1 physically interact with VAL2 but not with VAL1. The interactions depend on the C-terminal halves of AtSDR4L and DIG1, and the N-terminal half of VAL2. AtSDR4L binds to target loci in germinating seeds, preceding reduced accumulation of H3K27me3 Atsdr4l seedlings at a few loci important for seed development. These findings suggest AtSDR4L, and potentially DIG1, facilitate the recruitment of PRC2 through VAL2 to inactivate seed development genes, thus promoting the seed-to-seedling transition.
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| Overall design |
Chromatin immunoprecipitation DNA-seq (ChIP-seq) was performed to map the histone modification H3K27me3 in 1 and 3-day-old seedlings of Arabidopsis wilde-type and Atsdr4l mutants. Additionally, ChIP-seq was conducted to investigate AtSDR4L binding in germinating seeds treated with 5 uM ABA.
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| Web link |
https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiae225/7656885#449672485
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| Contributor(s) |
Alizadeh M, Lu B, Song L |
| Citation(s) |
38652698 |
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| Submission date |
Nov 03, 2023 |
| Last update date |
Jul 23, 2024 |
| Contact name |
Liang Song |
| E-mail(s) |
liang.song@botany.ubc.ca
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| Organization name |
University of British Columbia
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| Department |
Botany
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| Lab |
Song Lab
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| Street address |
2231-6270 UNIVERSITY BLVD
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| City |
VANCOUVER |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (18)
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| GSM7881936 |
H3K27me3, Atsdr4l_4, 1 DAI, rep2 |
| GSM7881937 |
H3K27me3, Atsdr4l_5, 1 DAI, rep1 |
| GSM7881938 |
H3K27me3, Atsdr4l_5, 1 DAI, rep2 |
| GSM7881939 |
H3K27me3, WT, 3 DAI, rep1 |
| GSM7881940 |
H3K27me3, WT, 3 DAI, rep2 |
| GSM7881941 |
H3K27me3, Atsdr4l_4, 3 DAI, rep1 |
| GSM7881942 |
H3K27me3, Atsdr4l_4, 3 DAI, rep2 |
| GSM7881943 |
H3K27me3, Atsdr4l_5, 3 DAI, rep1 |
| GSM7881944 |
H3K27me3, Atsdr4l_5, 3 DAI, rep2 |
| GSM7881945 |
Mock IgG, WT, pooled |
| GSM7881946 |
Mock IgG, Atsdr4l_4, pooled |
| GSM7881947 |
Mock IgG, Atsdr4l_5, pooled |
| GSM7881948 |
AtSDR4L, rep 1 |
| GSM7881949 |
AtSDR4L, rep2 |
| GSM7881950 |
WT, mock |
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| Relations |
| BioProject |
PRJNA1035518 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE246997_RAW.tar |
782.2 Mb |
(http)(custom) |
TAR (of BROADPEAK, NARROWPEAK, TDF) |
| GSE246997_filtered_S004_combinedmock.tdf |
53.7 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
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