Biology subjects

Geri, J. B.

Publications and source records attributed to Geri, J. B..

4 recordsLinked to original sources

bioRxiv2026

Single residues within the YTHDF intrinsically disordered region control m6A-dependent mRNA decay

Intrinsically disordered regions (IDRs) mediate protein interactions, condensate partitioning, and regulatory control in RNA-binding proteins, yet the residue-level logic underlying IDR function has remained difficult to define using conventional fragment- and truncation-based approaches. Here, we apply cytosine and adenine base-editor screens to map residue-level regulation within the intrinsically disordered region of YTHDF2, a cytoplasmic reader that couples m6A to mRNA decay. By tiling base edits across YTHDF2 in a YTHDF1/YTHDF3-null background, we identify IDR residues that regulate YTHDF2-dependent cellular fitness. Interestingly, we identified residues that limit YTHDF2 decay activity. Their mutation disrupts endogenous protein-protein interactions and generates hyperactive YTHDF2 variants that promote m6A-dependent mRNA decay and alter recruitment to cytoplasmic RNA granules, without affecting intrinsic m6A binding or protein stability. These findings define the residue-level regulatory logic of the YTHDF2 IDR and establish base-editor screening as a strategy to uncover functional mechanisms encoded within IDR regions.

systems biology↗

bioRxiv2025

Spatial deconstruction of the plasma membrane

The plasma membrane of cells is known to be heterogeneous with regards to the spatial distribution of proteins and lipids, but the nature and origins of this heterogeneity are unclear. In this study we perform fluorescence microscopy on plasma membrane sheets and find that most proteins occur in protein-rich domains separated by intervening protein-poor regions. We show that the protein-rich domains and protein-poor regions are at least partially preserved in plasma membrane-derived vesicles that lack cytoskeletal elements, permitting their separation and isolation by density centrifugation. Compositional analysis by nuclear magnetic resonance and mass spectrometry shows that different proteins and lipids exhibit characteristic tendencies to partition into the protein-rich domains. This differential partitioning is correlated with the function of the different proteins, suggesting segregation based on cellular processes. Likewise, ordered lipids including cholesterol and sphingomyelin differentially segregate, being more abundant in the protein-rich domains. We propose that the collective assembly of certain proteins and lipids creates the heterogenous distribution of membrane components and the emergence of protein-rich domains. These domains could create distinct environments for the function and segregation of various membrane processes.

biophysics↗

bioRxiv2025

Global Protein-Ligand Binding Affinity Profiling via Photocatalytic Labeling

Protein-ligand binding, selectivity, and affinity dictate the effects of drugs and endogenous molecules in cells. Currently, potential protein-ligand interactions are identified by qualitative interpretation of proteomic, transcriptomic, or genomic data, then binding affinities of hits are measured using purified proteins or engineered reporter systems to validate and quantify the strength of individual interactions. Few methods enable simultaneous target identification and biophysical affinity measurement, and these either apply to specific enzyme classes or proteins with ligand-dependent shifts in stability. Here we describe a general platform, termed Affinity Map, which leverages competitive binding analysis, high fidelity photocatalytic labeling, and high throughput proteomics for global quantitative binding affinity profiling. We show that this method is applicable to major classes of ligands, including small molecules, linear peptides, cyclic peptides, and proteins, and can measure affinities between unmodified ligands and proteins in cell lysates, organ extracts, and live cell surfaces.

biochemistry↗

bioRxiv2021

Small molecule photocatalysis enables drug target identification via energy transfer

The identification of cellular targets that can be exploited for therapeutic benefit, broadly known as target ID, remains a fundamental goal in drug discovery. In recent years, the application of new chemical and biological technologies that accelerate target ID has become commonplace within drug discovery programs, as a complete understanding of how molecules react in a cellular environment can lead to increased binding selectivity, improved safety profiles, and clinical efficacy. Established approaches using photoaffinity labelling (PAL) are often costly and time-consuming due to poor signal-to-noise coupled with extensive probe optimization. Such challenges are exacerbated when dealing with low abundance membrane proteins or multiple protein target engagement, typically rendering target ID unfeasible. Herein, we describe a general platform for photocatalytic small molecule target ID, which hinges upon the generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead from the drug, catalytic signal amplification results in multiple labelling events per drug, leading to unprecedented levels of target enrichment. Through the development of cell permeable photo-catalyst conjugates, this method has enabled the quantitative target and off target identification of several drugs including (+)-JQ1, paclitaxel, and dasatinib. Moreover, this methodology has led to the target ID of two GPCRs - ADORA2A and GPR40 - a class of drug target seldom successfully uncovered in small molecule PAL campaigns.

molecular biology↗