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Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE200713 | GEO | 2022/10/28

REPOSITORIES: GEO

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Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [Polysome]

Project description:N6-methyladenosine (m6A) plays critical roles in gene expression control by recruiting the cytoplasmic reader proteins YTHDF1,2 and 3. Recently, the function of YTHDF proteins and whether they bind to shared or distinct sets of methylated mRNAs in cells has been the subject of debate. Here, we developed TRIBE-STAMP, an approach for single-molecule detection of the target RNAs of two RNA binding proteins simultaneously in cells. Applying TRIBE-STAMP to the YTHDF proteins revealed that most target mRNAs are shared among the three YTHDF proteins. Surprisingly, we also found that individual mRNA molecules can be bound by more than one YTHDF protein throughout their lifetime. Furthermore, we show that YTHDF proteins bind sequentially to target methylated mRNAs, with YTHDF1 binding before YTHDF2 or YTHDF3. Our data reveal shared molecular interactions among the YTHDF proteins and support a model in which YTHDF1 and YTHDF3 are unlikely to promote rapid mRNA decay.

2022-10-28 | GSE201538 | GEO

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [TRIBE_STAMP]

2022-10-28 | GSE200712 | GEO

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [RIP-Seq]

2022-10-28 | GSE201540 | GEO

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules.

Project description:Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules.

| PRJNA826333 | ENA

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [Polysome]

Project description:Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [Polysome]

| PRJNA832158 | ENA

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [TRIBE_STAMP]

Project description:Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [TRIBE_STAMP]

| PRJNA826335 | ENA

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [RIP-Seq]

Project description:Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [RIP-Seq]

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Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein.

Project description:Fatty acid binding proteins (FABPs) carry fatty acids (FAs) and other lipids in the cellular environment, and are thus involved in processes such as FA uptake, transport, and oxidation. These proteins bind either one or two ligands in a binding site, which appears to be inaccessible from the bulk. Thus, the entry of the substrate necessitates a conformational change, whose nature is still unknown. A possible description of the ligand binding process is given by the portal hypothesis, which suggests that the FA enters the protein through a dynamic area known as the portal region. On the other hand, recent simulations of the adipocyte lipid binding protein (ALBP) suggested a different entry site (the alternative portal). In this article, we discuss molecular dynamics simulations of the apo-intestinal-FABP (I-FABP) in the presence of palmitate molecule(s) in the simulation box. The simulations were carried out to study whether the FA can enter the protein during the simulations (as in the ALBP) and where the ligand entry site is (the portal region, the alternative portal or a different domain). The analysis of the simulations revealed a clear difference between the ALBP and the I-FABP. In the latter case, the palmitate preferentially adsorbed to the portal region, which was more mobile than the rest of the protein. However, no ligand entry was observed in the multi-nanosecond-long simulations, in contrast to ALBP. These findings suggest that, although the main structural motif of the FABPs is common, the fine details of each individual protein structure grossly modulate its reactivity.

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m<sup>6</sup>A-binding YTHDF proteins promote stress granule formation.

Project description:Diverse RNAs and RNA-binding proteins form phase-separated, membraneless granules in cells under stress conditions. However, the role of the prevalent mRNA methylation, m6A, and its binding proteins in stress granule (SG) assembly remain unclear. Here, we show that m6A-modified mRNAs are enriched in SGs, and that m6A-binding YTHDF proteins are critical for SG formation. Depletion of YTHDF1/3 inhibits SG formation and recruitment of mRNAs to SGs. Both the N-terminal intrinsically disordered region and the C-terminal m6A-binding YTH domain of YTHDF proteins are important for SG formation. Super-resolution imaging further reveals that YTHDF proteins appear to be in a super-saturated state, forming clusters that often reside in the periphery of or at the junctions between SG core clusters, and potentially promote SG formation by reducing the activation energy barrier and critical size for SG condensate formation. Our results suggest a new function of the m6A-binding YTHDF proteins in regulating SG formation.

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