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Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress dependent mRNAs

ABSTRACT: Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress dependent mRNAs

PROVIDER: PRJNA521366 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8545534.fastq.gz	Fastqsanger.gz
	SRR8545535.fastq.gz	Fastqsanger.gz
	SRR8545536.fastq.gz	Fastqsanger.gz
	SRR8545537.fastq.gz	Fastqsanger.gz

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Similar Datasets

Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress dependent mRNAs

Project description:RNA binding proteins (RBPs) participate in almost all steps of gene expression, underscoring their potential as key regulators of RNA homeostasis. We structurally and functionally characterized Mip6, a four-RNA Recognition Motif (RRM)-containing RBP, as a functional and physical interactor of the mRNA export factor Mex67. Mip6 directly interacts with the ubiquitin-associated (UBA) domain of Mex67 through tryptophan 442 of Mip6-RRM4, whose mutation leads to slow growth of yeast cells in vivo. Although Mip6-RRM4 binds to RNA in vitro, Mex67 UBA binding prevents Mip6-RRM4 interaction with RNA. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67-dependent manner and concentrates in cytoplasmic foci under several stressors. Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) experiments showed preferential binding of Mip6 to mRNAs regulated by the stress-response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affected their export and expression levels. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4 dependent transcripts by its direct interaction with Mex67 UBA domain.

2019-08-29 | GSE126236 | GEO

Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs.

Project description:RNA-binding proteins (RBPs) participate in all steps of gene expression, underscoring their potential as regulators of RNA homeostasis. We structurally and functionally characterize Mip6, a four-RNA recognition motif (RRM)-containing RBP, as a functional and physical interactor of the export factor Mex67. Mip6-RRM4 directly interacts with the ubiquitin-associated (UBA) domain of Mex67 through a loop containing tryptophan 442. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67-dependent manner and concentrates in cytoplasmic foci under stress. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation experiments show preferential binding of Mip6 to mRNAs regulated by the stress-response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affects their export and expression levels. Additionally, Mip6 interacts physically and/or functionally with proteins with a role in mRNA metabolism and transcription such as Rrp6, Xrn1, Sgf73, and Rpb1. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4-dependent transcripts through its direct interaction with the Mex67 UBA domain.

| S-EPMC6893359 | biostudies-literature

Msn2 controls the yeast metabolic focus

Project description:Msn2 is a transcription factor required for integration of environmental and metabolic signals. Msn2 is directly regulated by the carbon source sensing PKA and AMP pathways. Here we analyse the role of Msn2 for metabolic adjustment by using point mutants mimicking the dephosphorylated state.

2016-10-08 | GSE81890 | GEO

MSN2-mCherry vs. msn2 microarray

Project description:Transcriptional profiling of Msn2 regulated genes. Both strains are PKAas (TPK1M164G TPK2M147G TPK3M165G) and msn4-delta. One strain has Msn2 C-terminally tagged with mCherry and the other strain is msn2-delta. In this experiment, both strains were exposed to 3 uM 1-NM-PP1, which leads to Msn2 nuclear localization, for 0, 10, 20 and 40 min. The goal was to determine the genes that show a strong upregulation in the presence of Msn2, but no expression change in the absence of Msn2.

2013-10-12 | E-MTAB-1945 | biostudies-arrayexpress

Combined UBA/UBA BS Acid Mine Drainage Biofilm Metagenome

Project description:Combined UBA and UBA BS acid mine drainage biofilm metagenome

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ZNF524 directly binds telomeres and supports their integrity via TRF2/RAP1

Project description:ZNF524 directly binds telomeres and supports their integrity via TRF2/RAP1

| PRJNA806777 | ENA

Saccharum barberi cultivar:Uba

Project description:Saccharum barberi Uba Resequencing genome sequencing

| PRJNA651912 | ENA

Msn2-mediated nucleosome remodeling dynamics

Project description:The aim of this experiment was to determine, using MNAse-Seq, how nucleosomes get remodeled during an Msn2 activation timecourse genome-wide. Diploid strain EY2807/ASH79 with genotype TPK1M164G TPK2M147G TPK3M165G msn4::TRP1/LEU2 MSN2-mCherry NHP6a-iRFP::kanMX was used. This strain is PKAas, so upon addition of the inhibitor 1-NM-PP1, Msn2 translocates to the nucleus and activates gene expression. In this experiment, the diploid strain was exposed to 3 uM 1-NM-PP1 for 0, 5, 10, 20 and 40 min and nucleosome positions determined using by crosslinking, MNAse treatment, nucleosomal DNA purification and paired-end high-throughput sequencing (Illumina). Results from transcriptional profiling of yeast with or without Msn2 expression were also deposited at ArrayExpress under accession number E-MTAB-1945 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1945/ ).

2013-10-12 | E-MTAB-1950 | biostudies-arrayexpress

Msn2-mediated nucleosome remodeling dynamics

Project description:Msn2-mediated nucleosome remodeling dynamics

| PRJEB4737 | ENA

Histone Demethylation by a Family of UBA Domain-containing Proteins

Project description:Histone methyl groups can be removed by histone demethylases. Although LSD1 and JmjC domain-containing proteins have been identified to be histone demethylases, enzymes responsible for many histone methylation states or sites are not identified. Here, we performed a high-content cell-based screening of a cDNA library containing 2,500 nuclear proteins and identified KDM10A as a histone demethylase specific for histone H4 lysine 20 (H4K20). Ectopic expression of KDM10A reduced the global levels of H4K20me1/2/3 in 293T cells. In vitro, KDM10A specifically demethylated H4K20me1/2/3 and generated formaldehyde. The enzymatic activity required Fe(II) and α-ketoglutarate as cofactors. Domain mapping indicated that the demethylase activity required its UBA domain. We also demonstrated that KDM10B, a protein homologous to KDM10A, had H4K20 demethylase activity in vitro and in vivo. ChIP-seq reveals that KDM10A/B demethylated H4K20 methylation at specific genomic loci in vivo. We further demonstrated that KDM10A/B activated the transcription of coding genes by demethylating H4K20me1 in the gene body, and the transcription of repetitive elements by demethylating H4K20me3 in intergenic regions. NMR analyses demonstrated that an HxxxE motif in the UBA domain is crucial for iron binding, mutation of these two residues abolished iron binding and the demethylase activity. Thus, we identified a family of UBA domain-containing proteins as histone demethylases.

2020-03-29 | GSE135986 | GEO

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