Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [RNA-seq]

ABSTRACT: Histone post-translational modifications (PTMs), such as acetylation and recently identified lysine 2-hydroxyisobutyrylation (Khib), act as active epigenomic marks in plants. SANT domain-containing proteins (SANT1/2/3/4), derived from PIF/Harbinger transposases, form a novel complex with histone deacetylase 6 (HDA6) to regulate gene expression via histone deacetylation. However, whether SANT1/2/3/4 coordinate different types of PTMs to regulate transcription and mediate responses to specific stresses in plants remain unclear. Here, in addition to modulating histone deacetylation, we found that SANT1/2/3/4 proteins acted like HDA6 or HDA9, in regulating the removal of histone Khib. H3KAc and histone Khib coordinated by SANT1/2/3/4 act in concert to regulate gene expression, with H3KAc playing a predominant role and Khib acting complementarily to H3KAc. SANT1/2/3/4 mutation significantly increased the expression of heat-inducible genes with concurrent change of H3KAc levels under normal and heat stress conditions, resulting in enhanced thermotolerance. Interestingly, hda6 mutant plants exhibited a reduced thermotolerance, suggesting that SANT1/2/3/4 negatively regulate plant thermotolerance independently of HDA6. This study revealed the critical roles of Harbinger transposon-derived SANT domain-containing proteins in transcriptional regulation by coordinating different types of histone PTMs and in the regulation of plant thermotolerance.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE243706 | GEO | 2025/09/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [ChIP-seq]

Project description:Histone post-translational modifications (PTMs), such as acetylation and recently identified lysine 2-hydroxyisobutyrylation (Khib), act as active epigenomic marks in plants. SANT domain-containing proteins (SANT1/2/3/4), derived from PIF/Harbinger transposases, form a novel complex with histone deacetylase 6 (HDA6) to regulate gene expression via histone deacetylation. However, whether SANT1/2/3/4 coordinate different types of PTMs to regulate transcription and mediate responses to specific stresses in plants remain unclear. Here, in addition to modulating histone deacetylation, we found that SANT1/2/3/4 proteins acted like HDA6 or HDA9, in regulating the removal of histone Khib. H3KAc and histone Khib coordinated by SANT1/2/3/4 act in concert to regulate gene expression, with H3KAc playing a predominant role and Khib acting complementarily to H3KAc. SANT1/2/3/4 mutation significantly increased the expression of heat-inducible genes with concurrent change of H3KAc levels under normal and heat stress conditions, resulting in enhanced thermotolerance. Interestingly, hda6 mutant plants exhibited a reduced thermotolerance, suggesting that SANT1/2/3/4 negatively regulate plant thermotolerance independently of HDA6. This study revealed the critical roles of Harbinger transposon-derived SANT domain-containing proteins in transcriptional regulation by coordinating different types of histone PTMs and in the regulation of plant thermotolerance.

2025-09-01 | GSE243705 | GEO

A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

Project description: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.

2021-05-10 | GSE167288 | GEO

Arabidopsis RPD3-type histone deacetylases form multiple plant-specific complexes that are required for preventing overexpression of stress-induced genes (ChIP-Seq)

Project description:Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicated that HDA6 and HDA19 function together with other components of the histone deacetylase complexes and co-regulate the expression of a number of genes. HDA6 and HDA19 have been thought to repress gene transcription by histone deacetylation. We found that the histone deacetylase complexes can also repress gene expression via certain histone-deacetylation-independent mechanisms. In the mutants of the histone deacetylase complexes, the expression of a number of stress-induced genes was up-regulated. Several mutants of the histone deacetylase complexes showed severe retardation in growth. Considering that the growth retardation is thought to be a trade-off for the increase of stress tolerance, we predict that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under non-stress conditions.

2021-06-10 | GSE166088 | GEO

Arabidopsis RPD3-type histone deacetylases form multiple plant-specific complexes that are required for preventing overexpression of stress-induced genes (RNA-Seq)

2021-06-10 | GSE166089 | GEO

SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications

Project description:SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications

| PRJNA1019665 | ENA

SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis

Project description:Although the interplay of covalent histone acetylation/deacetylation and ATP-dependent chromatin remodeling is crucial for the regulation of chromatin structure and gene expression in eukaryotes, the underlying molecular mechanism in plants remains largely unclear. Here we show a direct interaction between Arabidopsis SWI3B, an essential subunit of the SWI/SNF chromatin-remodeling complex, and the RPD3/HDA1-type histone deacetylase HDA6 both in vitro and in vivo. Furthermore, SWI3B and HDA6 co-repress the transcription of a subset of transposons. Both SWI3B and HDA6 maintain transposon silencing by decreasing histone H3 acetylation but increasing histone H3 lysine 9 di-methylation, DNA methylation and nucleosome occupancy. Our findings reveal that SWI3B and HDA6 may act in the same corepressor complex to maintain transposon silencing in Arabidopsis.

2021-06-20 | GSE133235 | GEO

SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [RNA-seq]

Project description:SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [RNA-seq]

| PRJNA1019667 | ENA

SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [ChIP-seq]

Project description:SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [ChIP-seq]

| PRJNA1019666 | ENA

Proteomic profiling of histone acetylation pattern in Arabidopsis

Project description:The levels of acetylated and non-acetylated histone peptide forms were quantified in A. thaliana plants with loss of function of HDA6, and plants exposed to HDAs inhibitors (trichostatin and sodium butyrate)during germination .

2019-10-14 | PXD014739 | Pride

A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

Project description:A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

| PRJNA704076 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data