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Two novel proteins with opposing m6A writing functions interact with HAKAI [RNA-seq]

ABSTRACT: Using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, were discovered as novel components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA. Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation. In addition, HIZ1 was found to be involved in root hair development upon auxin transport inhibition in a HAKAI-dependent manner. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ1 appears to be a HAKAI-dependent negative regulator of m6A deposition and HIZ2 is a novel and essential member of the Arabidopsis m6A writer complex.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE188610 | GEO | 2022/01/21

REPOSITORIES: GEO

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Two novel proteins with opposing m6A writing functions interact with HAKAI [meRIP-seq]

Project description:Using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, were discovered as novel components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA. Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation. In addition, HIZ1 was found to be involved in root hair development upon auxin transport inhibition in a HAKAI-dependent manner. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ1 appears to be a HAKAI-dependent negative regulator of m6A deposition and HIZ2 is a novel and essential member of the Arabidopsis m6A writer complex.

2022-01-20 | GSE174573 | GEO

Two zinc finger proteins with functions in m6A writing interact with HAKAI

Project description:The methyltransferase complex (m6A writer), which catalyzes the deposition of N6-methyladenosine (m6A) in mRNAs, is highly conserved across most eukaryotic organisms, but its components and interactions between them are still far from fully understood. Using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, were discovered as novel components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA. Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation. In addition, HIZ1 was found to be involved in root hair development upon auxin transport inhibition in a HAKAI-dependent manner. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ1 appears to be a HAKAI-dependent negative regulator of m6A deposition and HIZ2 is a novel and essential member of the Arabidopsis m6A writer complex.

2022-02-09 | PXD026287 | Pride

Hakai is required for stabilizing core components of the m6A mRNA methylation machinery

Project description:N6-methyladenosine RNA (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions, including circadian clock, metabolism and embryonic stem cell differentiation. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila. Its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerisation and interaction with other members of the m6A machinery, while its catalytic activity seems dispensable. Finally, we demonstrate that the loss of Hakai destabilizes the level of several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Thus, our work adds new functional and molecular insights into the mechanism of the m6A mRNA writer complex.

2021-04-26 | GSE158663 | GEO

Hakai is required for stabilization of core components of the m6A mRNA methylation machinery

Project description:N6-methyladenosine (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila and human cells. In Drosophila, its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerisation and interaction with other members of the m6A machinery, while its catalytic activity is dispensable. Finally, we demonstrate that the loss of Hakai destabilizes several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Our work adds new functional and molecular insights into the mechanism of the m6A mRNA writer complex.

2021-04-29 | PXD022294 | Pride

m6A-RIP-seq of mRNA in yw, Mettl3, Mettl14 and Hakai flies

Project description:In order to obtain a stringent m6A methylome in Drosophila adults, we performed m6A-RIP-seq in yw control (male and female), Mettl3 (male), Mettl14 (male) and Hakai (male) mutant flies. We find that the effective m6A modification, which depends on the writer complex, is mostly distributed in 5’ UTR and near start codon in Drosophila, in contrast to the mammalian system. We define a set of high-confident m6A methylation sites shared by Mettl3, Mettl14 and Hakai, indicating that Hakai is a core component of the m6A writer complex. We also find differential methylation pattern in certain loci between male and female flies.

2021-03-01 | GSE155662 | GEO

Two zinc finger proteins with functions in m6A writing interact with HAKAI

Project description:Two zinc finger proteins with functions in m6A writing interact with HAKAI

| PRJNA779683 | ENA

Two novel proteins with opposing m6A writing functions interact with HAKAI [RNA-seq]

Project description:Two novel proteins with opposing m6A writing functions interact with HAKAI [RNA-seq]

| PRJNA779686 | ENA

Two novel proteins with opposing m6A writing functions interact with HAKAI [meRIP-seq]

Project description:Two novel proteins with opposing m6A writing functions interact with HAKAI [meRIP-seq]

| PRJNA730562 | ENA

A novel RNA m6A modulator Zc3h13 plays an anchor role in facilitating nuclear RNA methylation and mouse embryonic stem cell self-renewal

Project description:N6-methyladenosine (m6A) is an abundant modification in eukaryotic mRNA, regulating mRNA dynamics by influencing mRNA stability, splicing, export and translation. Recent studies discovered m6A methyltransferases (?writer?), demethylases (?eraser?) and binding proteins (?reader?), which modulate m6A methylation. However, the precise m6A regulating machinery still remains incompletely understood. Here we demonstrate that ZC3H13, a zinc finger protein, plays an essential role in modulating m6A methylation on polyadenylated RNA in the nucleus. ZC3H13 exists in an evolutionary-conserved macromolecular complex containing WTAP, Virilizer and Hakai. We confirm the interaction among those proteins and demonstrate that knockdown of Zc3h13 in mouse embryonic stem cell (mESC) significantly decreases global m6A level on mRNA, mainly at 3? untranslated regions (3? UTR). Interestingly, fractionation assays show that upon Zc3h13 knockdown a great majority of WTAP, Virilizer and Hakai translocate to the cytoplasm and the nuclear presence of the methyltransferase Mettl3 and Mettl14 also decrease significantly. In contrast, knockdown of WTAP, Virilizer or Hakai does not change the nuclear localization of Zc3h13. This suggests that Zc3h13 is required for nuclear localization of the Zc3h13-WTAP-Virilizer-Hakai complex, which is important for RNA m6A methylation. Finally, Zc3h13 depletion, as does WTAP, Virilizer or Hakai, impairs self-renewal and triggers mESC differentiation. Taken together, our findings demonstrate that Zc3h13 plays an essential role in anchoring WTAP, Virilizer and Hakai in the nucleus to facilitate m6A methylation and to regulate mESC self-renewal.

2018-03-14 | GSE94148 | GEO

Serrate modulates N6-Methyladenosine (m6A) RNA modification in Arabidopsis

Project description:N6-methyladenosine (m6A) is the most common prevalent internal modifications found in many of the eukaryotic mRNA and plays an important role in RNA metabolism including pre-mRNA processing, mRNA stability, RNA splicing, RNA export and nuclear retention. Serrate is a component of the Dicer complex, plays as a key factor in RNA metabolism. We here reported SERRATE acts as a key regulator of mRNA m6A modification in Arabidopsis. Loss function of SE results in significant global m6A level reduction in the se-1 mutant comparing to the Col-0. SE positively regulates the transcription of MTA and MTB. In addition, SE physically interacts and functionally works with the m6A writer complex MTA and MTB which affects the binding of m6A methylase to mRNA. Taking together, our data provides a molecular framework that SE modulates m6A mRNA modification in Arabidopsis.

2023-11-01 | GSE241248 | GEO

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