2022

Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.: Author(s) : Dai Y, Guo H, Liu N, Chen W, Ai X, Li H, Sun B, Hou X, Rety S, Xi X,; Journal : EMBO Rep; 2022; G-quadruplexes (G4s) are unusual stable DNA structures that cause genomicinstability. To overcome the potential barriers formed by G4s, cells have evolveddifferent families of proteins that unfold G4s. Pif1 is a DNA helicase fromsuperfamily 1 (SF1) conserved from bacteria to humans with high G4-unwindingactivity. Here, we present the first X-ray crystal structure of the Thermusoshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1recognizes the entire native G4 via a cluster of amino acids at domains 1B/2Bwhich constitute a G4-Recognizing Surface (GRS). The overall structure of the G4maintains its three-layered propeller-type G4 topology, without significantreorganization of G-tetrads upon protein binding. The three G-tetrads in G4 arerecognized by GRS residues mainly through electrostatic, ionic interactions, andhydrogen bonds formed between the GRS residues and the ribose-phosphate backbone.Compared with previously solved structures of SF2 helicases in complex with G4,our structure reveals how helicases from distinct superfamilies adopt differentstrategies for recognizing and unfolding G4s.
The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling: Author(s) : Plana-Carmona M, Stik G, Bulteau R, Segura-Morales C, Alcázar N, Wyatt C, Klonizakis A, de Andrés-Aguayo L, Gasnier M, Tian T, Torcal Garcia G, Vila-Casadesús M, Plachta N, Serrano M, Francesconi M, Graf T,; Journal : Stem Cell Reports; 2022; IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how Il6 expression is regulated and whether it plays a role during embryo development remains unknown. Here, we describe that IL-6 is necessary for C/EBPα-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPα overexpression activates both Il6 and Il6ra genes in B cells and in PSCs. In embryo development, Cebpa is enriched in the trophectoderm of blastocysts together with Il6, while Il6ra is mostly expressed in the inner cell mass (ICM). In addition, Il6 expression in blastocysts requires Cebpa. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. The observed requirement of C/EBPα-regulated IL-6 signaling for pluripotency during somatic cell reprogramming thus recapitulates a physiologic mechanism in which the trophectoderm acts as niche for the ICM through the secretion of IL-6.
Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain.: Author(s) : Torres-Campana D, Horard B, Denaud S, Benoit G, Loppin B, Orsi G,; Journal : PLoS Genet; 2022; The formation of a diploid zygote is a highly complex cellular process that isentirely controlled by maternal gene products stored in the egg cytoplasm. Thishighly specialized transcriptional program is tightly controlled at the chromatinlevel in the female germline. As an extreme case in point, the massive and specificovarian expression of the essential thioredoxin Deadhead (DHD) is criticallyregulated in Drosophila by the histone demethylase Lid and its partner, the histonedeacetylase complex Sin3A/Rpd3, via yet unknown mechanisms. Here, we identified Snr1and Mod(mdg4) as essential for dhd expression and investigated how these epigenomiceffectors act with Lid and Sin3A to hyperactivate dhd. Using Cut&Run chromatinprofiling with a dedicated data analysis procedure, we found that dhd isintriguingly embedded in an H3K27me3/H3K9me3-enriched mini-domain flanked by DNAregulatory elements, including a dhd promoter-proximal element essential for itsexpression. Surprisingly, Lid, Sin3a, Snr1 and Mod(mdg4) impact H3K27me3 and thisregulatory element in distinct manners. However, we show that these effectorsactivate dhd independently of H3K27me3/H3K9me3, and that dhd remains silent in theabsence of these marks. Together, our study demonstrates an atypical and criticalrole for chromatin regulators Lid, Sin3A, Snr1 and Mod(mdg4) to triggertissue-specific hyperactivation within a unique heterochromatin mini-domain.
Titration of Apparent In-Cellula Affinities of Protein-Protein Interactions.: Author(s) : Cluet D, Vergier B, Levy N, Dehau L, Thurman A, Amri I, Spichty M,; Journal : Chembiochem; 2022; A genetic assay permits simultaneous quantification of two interacting proteinsand their bound fraction at the single-cell level using flow cytometry. Apparentin-cellula affinities of protein-protein interactions can be extracted from theacquired data through a titration-like analysis. The applicability of thisapproach is demonstrated on a diverse set of interactions with proteins fromdifferent families and organisms and with in-vitro dissociation constants rangingfrom picomolar to micromolar.

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2022

Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.

The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling

Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain.

Titration of Apparent In-Cellula Affinities of Protein-Protein Interactions.

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