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ALBA proteins facilitate cytoplasmic YTHDF-mediated reading of m6A in plants

ABSTRACT: N6-methyladenosine (m6A) exerts many of its regulatory effects on eukaryotic mRNAs by recruiting cytoplasmic YT521-B homology domain family (YTHDF) proteins. Here, we show that in Arabidopsis, the interaction between m6A and the major YTHDF protein ECT2 also involves the mRNA-binding ALBA protein family. ALBA and YTHDF proteins physically associate via a deeply conserved short linear motif in the intrinsically disordered region of YTHDF proteins, their mRNA targets overlap, and ALBA4 binding sites are juxtaposed to m6A sites. These binding sites correspond to pyrimidine-rich elements previously found to be important for m6A binding of ECT2. Accordingly, both biological effects of ECT2 and its binding to m6A targets in vivo require ALBA association. Our results introduce the YTHDF-ALBA complex as the functional cytoplasmic m6A-reader in plants and define a molecular foundation for the concept of facilitated m6A reading that increases the potential for combinatorial control of biological m6A effects.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Root, Leaf

SUBMITTER: Mathias Tankmar

LAB HEAD: Peter Brodersen

PROVIDER: PXD052232 | Pride | 2024-11-18

REPOSITORIES: Pride

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			Action	DRS
	20190627_FJ_LHB_Mathias_23.raw	Raw
	20190627_FJ_LHB_Mathias_24.raw	Raw
	20190627_FJ_LHB_Mathias_25.raw	Raw
	20190627_FJ_LHB_Mathias_29.raw	Raw
	20190627_FJ_LHB_Mathias_30.raw	Raw

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A YTHDF-PABP axis is required for m6A-mediated organogenesis in plants

Project description:N6-methyladenosine (m6A) in mRNA is key to eukaryotic gene regulation. Many m6A functions involve RNA-binding proteins that recognize m6A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3 and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR-elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4 and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.

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YTHDF3 improves translation initiation of mRNAs with N6-methyladenosine methylation at 5’ untranslated region by facilitating eIF2AK2 recruitment in oxaliplatin-resistant colorectal cancer - RIP-seq dataset

Project description:Oxaliplatin as a first-line drug frequently causes the chemo-resistance on colorectal cancer (CRC). N6-methyladenosine (m6A) methylation has been largely acknowledged in multiple biological functions. However, the molecular mechanisms underlying the m6A methylation in modulating anticancer drug resistance in CRC are still obscure. In present study, RIP-seq was conducted to investigate the occupancy of N6-methyladenosine RNA binding protein 3 (YTHDF3) served as “readers” that can recognize m6A modification site in HCT116 cells with oxaliplatin resistance (HCT116R). Then, YTHDF3 was knockdown by siRNA in HCT116 cells with oxaliplatin resistance, and RIP-seq was further conducted to investigate m6A methylation of HCT116, HCT116R and HCT116R cells with YTHDF3 knockdown.

2022-02-04 | E-MTAB-11321 | biostudies-arrayexpress

Phoshorylation regulated UBF1 and ECT2 Binding on ribosomal DNA

Project description:Epithelial Cell Transforming Sequence 2 (ECT2), a guanine nucleotide exchange factor (GEF) for Rho GTPases, is overexpressed in many cancers and is involved in signal transduction pathways that promote cancer cell proliferation, invasion and tumorigenesis. Recently, we demonstrated that a significant pool of ECT2 localizes to the nucleolus of non small cell lung cancer (NSCLC) cells where it binds the transcription factor Upstream Binding Factor 1 (UBF1) on the promoter regions of the ribosomal DNA (rDNA) and activates rDNA transcription, transformed growth and tumor formation. Here we investigate the mechanism by which ECT2 engages UBF1 on rDNA. Mutagenesis of ECT2 demonstrates that the tandem BRCT domain of ECT2 mediates binding to UBF1. Biochemical and mass spectrometry analysis reveals that Protein Kinase Ci (PKCi) directly phosphorylates UBF1 at Ser412 to generate a phosphopeptide binding epitope that binds the ECT2 BRCT domain. Lentiviral shRNA knockdown and reconstitution experiments demonstrate that both a functional ECT2 BRCT domain and the UBF1 Ser412 phosphorylation site are required for UBF1 mediated ECT2 recruitment to rDNA, elevated rRNA synthesis and transformed growth. Taken together, our study provides new molecular insight into ECT2 mediated regulation of rDNA transcription in cancer cells and provides a rationale for therapeutic targeting of UBF1 and ECT2 stimulated rDNA transcription for the treatment of NSCLC.

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2015-07-08 | E-GEOD-65347 | biostudies-arrayexpress

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Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

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