 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 10, 2021 |
| Title |
A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). We show that mutations of all four SANT genes in the sant-null mutant cause increased expression of the flowering repressors FLC, MAF4, and MAF5, resulting in a late flowering phenotype. Transcriptome deep sequencing reveals that while the SANT proteins and HDA6 regulate the expression of largely overlapping sets of genes, TE silencing is unaffected in sant-null mutants. Our global histone H3 acetylation profiling shows that SANT proteins and HDA6 modulate gene expression through deacetylation. Collectively, our findings suggest that Harbinger transposon-derived SANT domain-containing proteins are required for histone deacetylation and flowering time control in plants.
|
| |
|
| Overall design |
For RNA-seq: three independent biological replicates of wild-type(Col-0), hhp1, mbd 1/2/4, sant1234-null and hda6 were used for RNA deep sequencing assay. Total RNA was extracted from 12-day-old Arabidopsis seedlings growing on 1/2 MS medium plates with TRIzol reagent (Invitrogen). mRNA-seq libraries were built according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)) and paired-end sequenced on an Illumina NovaSeq 6000 platform. For ChIP-seq: three biological replicates of 12-day-old wild-type(Col-0), sant1234-null and hda6 seedlings growing on 1/2 MS medium plates were used for histone H3 modification ChIP-seq experiment. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) and then paired-end sequenced on Illumina NovaSeq 6000 platform. We used anti-acetylated Histone H3 antibody (Merck Millipore, 06-599). Each replicate contained two dataset: ChIP and input (to avoid background interference).
|
| |
|
| Contributor(s) |
Zhou X, Zhang C |
| Citation(s) |
33960113 |
| Submission date |
Feb 22, 2021 |
| Last update date |
Aug 16, 2021 |
| Contact name |
Xishi Zhou |
| E-mail(s) |
zhouxishi@caas.cn
|
| Organization name |
Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences
|
| Lab |
Cuijun Zhang
|
| Street address |
No 7, Pengfei Road
|
| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
|
| Samples (33)
|
|
| Relations |
| BioProject |
PRJNA704076 |
| SRA |
SRP307581 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE167288_H3Ac_peak_hda6_vs_WT.csv.gz |
500.1 Kb |
(ftp)(http) |
CSV |
| GSE167288_H3Ac_peak_sant1234-null_vs_WT.csv.gz |
504.7 Kb |
(ftp)(http) |
CSV |
| GSE167288_TE_hda6_vs_WT_exp.txt.gz |
439.7 Kb |
(ftp)(http) |
TXT |
| GSE167288_TE_hhp1_vs_WT_exp.txt.gz |
428.6 Kb |
(ftp)(http) |
TXT |
| GSE167288_TE_mbd124_vs_WT_exp.txt.gz |
433.1 Kb |
(ftp)(http) |
TXT |
| GSE167288_TE_sant1234-null_vs_WT_exp.txt.gz |
434.4 Kb |
(ftp)(http) |
TXT |
| GSE167288_WT_chipseq_RPKM_gene.txt.gz |
755.7 Kb |
(ftp)(http) |
TXT |
| GSE167288_gene_hda6_vs_WT_exp.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE167288_gene_hhp1_vs_WT_exp.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE167288_gene_mbd124_vs_WT_exp.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE167288_gene_sant1234-null_vs_WT_exp.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE167288_hda6_chipseq_RPKM_gene.txt.gz |
753.9 Kb |
(ftp)(http) |
TXT |
| GSE167288_sant1234-null_chipseq_RPKM_gene.txt.gz |
756.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...