Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).

Protein cysteine thiols undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates protein-membrane and protein-protein interactions critical to an array of biological processes, from homeostatic lung surfactant function to cellular transformation. The most widely used S-acylation assays, including acyl-biotin exchange (ABE) and acyl resin-assisted capture (Acyl-RAC), utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. ABE and Acyl-RAC have enabled both the proteome-wide identification of S-palmitoylation sites and basic biochemical studies. Yet, these assays generally utilize hundreds of micrograms to milligrams of input material and require numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome this, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment from 20-50 micrograms of input protein. The method is compatible with protein-level detection of Sacylated proteins as well as S-acyl site-based identification and quantification using on-quartz isobaric (tandem mass tag) labeling and LC-MS/MS. Also described are conditions for long-term hydroxylamine storage, which further expedites the assay and minimizes waste. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional intact protein detection and chemoproteomic workflows.

Quantification Quality Control Emerges as A Crucial Factor to Enhance Single Cell Proteomics Data Analysis.

Mass spectrometry (MS)-based single-cell proteomics (SCP) provides us the opportunity to unbiasedly explore biological variability within cells without the limitation of antibody availability. This field is rapidly developed with the main focuses on instrument advancement, sample preparation refinement, and signal boosting methods; however, the optimal data processing and analysis are rarely investigated which holds an arduous challenge because of the high proportion of missing values and batch effect. Here, we introduced a quantification quality control to intensify the identification of differentially expressed proteins (DEPs) by considering both within and across SCP data. Combining quantification quality control with isobaric matching between runs (IMBR) and PSM-level normalization, an additional 12% and 19% of proteins and peptides, with more than 90% of proteins/peptides containing valid values, were quantified. Clearly, quantification quality control was able to reduce quantification variations and q-values with the more apparent cell type separations. In addition, we found that PSM-level normalization performed similarly to other protein-level normalizations but kept the original data profiles without the additional requirement of data manipulation. In proof of concept of our refined pipeline, six uniquely identified DEPs exhibiting varied fold-changes and playing critical roles for melanoma and monocyte functionalities were selected for validation using immunoblotting. Five out of six validated DEPs showed an identical trend with the SCP dataset, emphasizing the feasibility of combining the IMBR, cell quality control, and PSM-level normalization in SCP analysis, which is beneficial for future SCP studies.

Longitudinal cerebral perfusion in presymptomatic genetic frontotemporal dementia: GENFI results.

INTRODUCTION: Effective longitudinal biomarkers that track disease progression are needed to characterize the presymptomatic phase of genetic frontotemporal dementia (FTD). We investigate the utility of cerebral perfusion as one such biomarker in presymptomatic FTD mutation carriers. METHODS: We investigated longitudinal profiles of cerebral perfusion using arterial spin labeling magnetic resonance imaging in 42 C9orf72, 70 GRN, and 31 MAPT presymptomatic carriers and 158 non-carrier controls. Linear mixed effects models assessed perfusion up to 5 years after baseline assessment. RESULTS: Perfusion decline was evident in all three presymptomatic groups in global gray matter. Each group also featured its own regional pattern of hypoperfusion over time, with the left thalamus common to all groups. Frontal lobe regions featured lower perfusion in those who symptomatically converted versus asymptomatic carriers past their expected age of disease onset. DISCUSSION: Cerebral perfusion is a potential biomarker for assessing genetic FTD and its genetic subgroups prior to symptom onset. HIGHLIGHTS: Gray matter perfusion declines in at-risk genetic frontotemporal dementia (FTD). Regional perfusion decline differs between at-risk genetic FTD subgroups . Hypoperfusion in the left thalamus is common across all presymptomatic groups. Converters exhibit greater right frontal hypoperfusion than non-converters past their expected conversion date. Cerebral hypoperfusion is a potential early biomarker of genetic FTD.

Generalized Venous Prominence on Susceptibility-Weighted Imaging Correlates With Global Cerebral Blood Flow Decline.

Objective This study investigated the global correlation between cerebral blood flow (CBF) decline and increased venous prominence, utilizing arterial spin labeling (ASL) and susceptibility-weighted imaging (SWI) MRI techniques. Methods The study was conducted at the Department of Diagnostic Imaging, St. Marina University Hospital, Varna, Bulgaria. Through a retrospective analysis, we examined data from 115 patients undergoing neurological assessment. CBF decline was assessed through ASL MRI, while global venous visibility was evaluated using SWI MRI. Results The analysis revealed a significant positive correlation between CBF decline and venous prominence (Spearman's rho = 0.261, p = 0.005), indicating a systemic interaction between cerebral perfusion and the venous system. Logistic regression further underscored CBF decline as a significant predictive factor for increased venous visibility (odds ratio (OR) = 1.690, p = 0.004). The assessments' high inter-rater reliability (Cohen's kappa = 0.82) supports the consistency and validity of our findings. Conclusion The integration of ASL and SWI MRI provides critical insights into cerebral hemodynamics, emphasizing the significance of these imaging modalities in both neurovascular research and clinical practice. Our findings suggest a systemic relationship between CBF decline and venous system alterations, underscoring the potential for these techniques to enhance our understanding of neurovascular disorders. Future studies should pursue longitudinal and quantitative analyses to deepen our comprehension of these relationships and their clinical implications.

Associations of apolipoprotein E ε4 allele, regional cerebral blood flow, and serum liver function markers in patients with cognitive impairment.

Introduction: The ε4 allele of the apolipoprotein E gene (APOE4) is expressed abundantly in both the brain and peripheral circulation as a genetic risk factor for Alzheimer's disease (AD). Cerebral blood flow (CBF) dysfunction is an essential feature of AD, and the liver plays an important role in the pathogenesis of dementia. However, the associations of APOE4 with CBF and liver function markers in patients with cognitive impairment remains unclear. We aimed to evaluate the associations of APOE4 with CBF measured by arterial spin labeling (ASL) magnetic resonance imaging (MRI) and serum liver function markers in participants who were diagnosed with cognitive impairment. Methods: Fourteen participants with AD and sixteen with amnestic mild cognitive impairment (MCI) were recruited. In addition to providing comprehensive clinical information, all patients underwent laboratory tests and MRI. All participants were divided into carriers and noncarriers of the ε4 allele, and T-tests and Mann-Whitney U tests were used to observe the differences between APOE4 carriers and noncarriers in CBF and liver function markers. Results: Regarding regional cerebral blood flow (rCBF), APOE4 carriers showed hyperperfusion in the bilateral occipital cortex, bilateral thalamus, and left precuneus and hypoperfusion in the right lateral temporal cortex when compared with noncarriers. Regarding serum liver function markers, bilirubin levels (including total, direct, and indirect) were lower in APOE4 carriers than in noncarriers. Conclusion: APOE4 exerts a strong effect on CBF dysfunction by inheritance, representing a risk factor for AD. APOE4 may be related to bilirubin metabolism, potentially providing specific neural targets for the diagnosis and treatment of AD.

MRI Data Analysis in Malformations of Cortical Development.

Brain magnetic resonance imaging (MRI) is a noninvasive imaging modality that utilizes powerful magnets and radio waves to generate detailed images of the brain, making it a valuable tool for investigating malformations of cortical development (MCD). Various MRI techniques, including 3D T1-weighted, multiplanar thin-sliced T2-weighted, and 3D fluid-attenuated inversion recovery (FLAIR) sequences, can provide high-resolution images with excellent spatial and contrast resolution, allowing for a detailed visualization of cortical anatomy and abnormalities. Almost all MCD can be detected and characterized using MRI. Advanced techniques, such as arterial spin labeling MR perfusion, diffusion tensor imaging (DTI), and functional MRI (fMRI), may be used to improve the detection rate of these malformations and to plan surgery in case of drug-resistant epilepsy. However, there are also limitations related to high cost, relatively low availability, need for sedation or anesthesia, and limited sensitivity for detecting subtle focal cortical malformations. Despite these limitations, brain MRI plays a crucial role in the investigation of MCD, providing valuable information for diagnosis, treatment planning, and patient management.

Interaction of Nipah Virus F and G with the Cellular Protein Cortactin Discovered by a Proximity Interactome Assay.

Nipah virus (NiV) is a highly lethal zoonotic virus with a potential large-scale outbreak, which poses a great threat to world health and security. In order to explore more potential factors associated with NiV, a proximity labeling method was applied to investigate the F, G, and host protein interactions systematically. We screened 1996 and 1524 high-confidence host proteins that interacted with the NiV fusion (F) glycoprotein and attachment (G) glycoprotein in HEK293T cells by proximity labeling technology, and 863 of them interacted with both F and G. The results of GO and KEGG enrichment analysis showed that most of these host proteins were involved in cellular processes, molecular binding, endocytosis, tight junction, and other functions. Cytoscape software (v3.9.1) was used for visual analysis, and the results showed that Cortactin (CTTN), Serpine mRNA binding protein 1 (SERBP1), and stathmin 1 (STMN1) were the top 20 proteins and interacted with F and G, and were selected for further validation. We observed colocalization of F-CTTN, F-SERBP1, F-STMN1, G-CTTN, G-SERBP1, and G-STMN1 using confocal fluorescence microscopy, and the results showed that CTTN, SERBP1, and STMN1 overlapped with NiV F and NiV G in HEK293T cells. Further studies found that CTTN can significantly inhibit the infection of the Nipah pseudovirus (NiVpv) into host cells, while SERBP1 and STMN1 had no significant effect on pseudovirus infection. In addition, CTTN can also inhibit the infection of the Hendra pseudovirus (HeVpv) in 293T cells. In summary, this study revealed that the potential host proteins interacted with NiV F and G and demonstrated that CTTN could inhibit NiVpv and HeVpv infection, providing new evidence and targets for the study of drugs against these diseases.

How Promising Are "Ultraprocessed" Front-of-Package Labels? A Formative Study with US Adults.

High levels of food processing can have detrimental health effects independent of nutrient content. Experts and advocates have proposed adding information about food processing status to front-of-package labeling schemes, which currently exclusively focus on nutrient content. How consumers would perceive "ultraprocessed" labels has not yet been examined. To address this gap, we conducted a within-subjects online experiment with a convenience sample of 600 US adults. Participants viewed a product under three labeling conditions (control, "ultraprocessed" label, and "ultraprocessed" plus "high in sugar" label) in random order for a single product. The "ultraprocessed" label led participants to report thinking more about the risks of eating the product and discouraging them from wanting to buy the product more than the control, despite not grabbing more attention than the control. The "ultraprocessed" plus "high in sugar" labels grabbed more attention, led participants to think more about the risks of eating the product, and discouraged them from wanting to buy the product more than the "ultraprocessed" label alone. "Ultraprocessed" labels may constitute promising messages that could work in tandem with nutrient labels, and further research should examine how they would influence consumers' actual intentions and behaviors.

Selective Arylation of RNA 2'-OH Groups via SNAr Reaction with Trialkylammonium Heterocycles.

Small-molecule reactions at the 2'-OH groups of RNA enable useful applications for transcriptome technology and biology. To date, all reactions have involved carbonyl acylation and mechanistically related sulfonylation, limiting the types of modifications and properties that can be achieved. Here we report that electron-deficient heteroaryl species selectively react with 2'-OH groups of RNA in water via SNAr chemistry. In particular, trialkyl-ammonium (TAA)-activated aromatic heterocycles, prepared in one step from aryl chloride precursors, give high conversions to aryl ether adducts with RNAs in aqueous buffer in ~2-3 h. Remarkably, a TAA triazine previously used only for reaction with carboxylic acids, shows unprecedented selectivity for RNA over water, reacting rapidly with 2'-OH groups while exhibiting a half-life in water of >10 days. We further show that a triazine aryl species can be used as a probe at trace-level yields to map RNA structure in vitro. Finally, we prepare a number of functionalized trialkylammonium triazine reagents and show that they can be used to covalently label RNA efficiently for use in vitro and in living cells. This direct arylation chemistry offers a simple and distinct structural scaffold for post-synthetic RNA modification, with the potential for utility in multiple applications in transcriptome research.

Isotopically nonstationary metabolic flux analysis of plants: recent progress and future opportunities.

Metabolic flux analysis (MFA) is a valuable tool for quantifying cellular phenotypes and to guide plant metabolic engineering. By introducing stable isotopic tracers and employing mathematical models, MFA can quantify the rates of metabolic reactions through biochemical pathways. Recent applications of isotopically nonstationary MFA (INST-MFA) to plants have elucidated nonintuitive metabolism in leaves under optimal and stress conditions, described coupled fluxes for fast-growing algae, and produced a synergistic multi-organ flux map that is a first in MFA for any biological system. These insights could not be elucidated through other approaches and show the potential of INST-MFA to correct an oversimplified understanding of plant metabolism.

Deep Ordinal Classification in Forest Areas Using Light Detection and Ranging Point Clouds.

Recent advances in Deep Learning and aerial Light Detection And Ranging (LiDAR) have offered the possibility of refining the classification and segmentation of 3D point clouds to contribute to the monitoring of complex environments. In this context, the present study focuses on developing an ordinal classification model in forest areas where LiDAR point clouds can be classified into four distinct ordinal classes: ground, low vegetation, medium vegetation, and high vegetation. To do so, an effective soft labeling technique based on a novel proposed generalized exponential function (CE-GE) is applied to the PointNet network architecture. Statistical analyses based on Kolmogorov-Smirnov and Student's t-test reveal that the CE-GE method achieves the best results for all the evaluation metrics compared to other methodologies. Regarding the confusion matrices of the best alternative conceived and the standard categorical cross-entropy method, the smoothed ordinal classification obtains a more consistent classification compared to the nominal approach. Thus, the proposed methodology significantly improves the point-by-point classification of PointNet, reducing the errors in distinguishing between the middle classes (low vegetation and medium vegetation).

The Effects of an Educational Intervention About Front-of-Package Labeling on Food and Beverage Selection Among Children and Their Caregivers: Protocol for a Randomized Controlled Trial.

BACKGROUND: Overweight and obesity pose a global public health challenge and have a multifactorial origin. One of these factors includes obesogenic environments, which promote ultraprocessed foods characterized by being high in calories, saturated fats, added sugars, and sodium. In Mexico, it has been estimated that 30% of the total energy consumed comes from processed foods. The Modification to the Official Mexican Standards introduces nutritional information through black octagonal seals that alert consumers about products with excessive amounts of some components for a better food selection in the population. However, the effects of warning labels on processed food selection and purchases among children remain unknown. OBJECTIVE: We aimed to evaluate the impact of a digital educational intervention focusing on front-of-package warning labels on the food selection and purchasing behavior of elementary schoolchildren and their caregivers. METHODS: Children from 4 elementary schools in Mexico City, 2 public and 2 private schools, will participate in a randomized controlled trial. The schools will be chosen by simple random sampling. Schools will be randomized into 2 groups: intervention and control. In the control group, the dyads (caregiver-schoolchildren) will receive general nutritional education, and in the intervention group, they will receive guidance on reading labels and raising awareness about the impact of consuming ultraprocessed products on health. The educational intervention will be conducted via a website. Baseline measurements will be taken for both groups at 3 and 6 months. All participants will have access to an online store through the website, allowing them to engage in exercises for selecting and purchasing food and beverages. In addition, other measures will include a brief 5-question exam to evaluate theoretical understanding, a 24-hour reminder, a survey on food habits and consumption, application of a food preference scale, anthropometric measurements, and recording of school lunch choices. RESULTS: Registration and funding were authorized in 2022, and we will begin data collection in September 2024. Recruitment has not yet taken place, but the status of data analysis and expected results will be published in April 2025. CONCLUSIONS: The study is expected to contribute to evaluating whether reinforcing front-of-package warning labels with education enhances its effects and makes them more sustainable. Conducting this study will allow us to propose whether or not it is necessary to develop new intervention strategies related to front-of-package labeling for a better understanding of the population, improved food choices, and better health outcomes. TRIAL REGISTRATION: ClinicalTrials.gov NCT06102473; https://clinicaltrials.gov/study/NCT06102473. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/54783.

A Facile Method to Append a Bio-ID Tag to Endogenous Mutant Kras Alleles.

KRAS mutations occur in approximately ~50% of colorectal cancers (CRCs) and are associated with poor prognosis and resistance to therapy. While these most common mutations found at amino acids G12, G13, Q61, and A146 have long been considered oncogenic drivers of CRC, emerging clinical data suggest that each mutation may possess different biological functions, resulting in varying consequences in oncogenesis. Currently, the mechanistic underpinnings associated with each allelic variation remain unclear. Elucidating the unique effectors of each KRAS mutant could both increase the understanding of KRAS biology and provide a basis for allele-specific therapeutic opportunities. Biotinylation identification (BioID) is a method to label and identify proteins located in proximity of a protein of interest. These proteins are captured through the strong interaction between the biotin label and streptavidin bead and subsequently identified by mass spectrometry. Here, we developed a protocol using CRISPR-mediated gene editing to generate endogenous BioID2-tagged KrasG12D and KrasG12V isogenic murine colon epithelial cell lines to identify unique protein proximity partners by BioID.

Helicobacter pylori glycan biosynthesis modulates host immune cell recognition and response.

Introduction: The pathogenic bacterium Helicobacter pylori has evolved glycan-mediated mechanisms to evade host immune defenses. This study tests the hypothesis that genetic disruption of H. pylori glycan biosynthesis alters immune recognition and response by human gastric epithelial cells and monocyte-derived dendritic cells. Methods: To test this hypothesis, human cell lines were challenged with wildtype H. pylori alongside an array of H. pylori glycosylation mutants. The relative levels of immune response were measured via immature dendritic cell maturation and cytokine secretion. Results: Our findings indicate that disruption of lipopolysaccharide biosynthesis diminishes gastric cytokine production, without disrupting dendritic cell recognition and activation. In contrast, variable immune responses were observed in protein glycosylation mutants which prompted us to test the hypothesis that phase variation plays a role in regulating bacterial cell surface glycosylation and subsequent immune recognition. Lewis antigen presentation does not correlate with extent of immune response, while the extent of lipopolysaccharide O-antigen elaboration does. Discussion: The outcomes of this study demonstrate that H. pylori glycans modulate the host immune response. This work provides a foundation to pursue immune-based tailoring of bacterial glycans towards modulating immunogenicity of microbial pathogens.

Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse?

Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.

Inconsistent excipient listings in DailyMed: implications for drug safety.

Excipients, or inactive ingredients, are a frequent cause of medication intolerance and allergy. Patients and clinicians concerned about medication allergies and sensitivities rely on the U.S. National Library of Medicine's DailyMed for accurate lists of excipients. Based on our anecdotal discovery of several examples of excipient omissions, we wished to examine the accuracy of DailyMed's listings more systematically in a sample of commonly prescribed medications. The objective of the study is to identify the frequency of inconsistency of excipient reporting within the DailyMed website. We performed a database audit of the Structured Product Labeling XML file provided by the drug manufacturer to the Food and Drug Administration and DailyMed for two randomly selected formulations of each of 50 commonly prescribed medications. For each of the 100 formulations, we compared the excipients listed in the "Description" to those in the "Ingredients and Appearance" sections in DailyMed. The Structured Product Labeling data file provided by the drug manufacturer contained internal inconsistencies of excipients in 39% of the formulations examined. Despite the use of Structured Product Labeling, the drug manufacturer's medication labels provided to the FDA and reported by DailyMed often contain conflicting information about inactive ingredients. Patients with allergies and excipient sensitivity should be aware of these discrepancies and consult multiple sections of the label to identify potential allergy-inducing inactive ingredients.

Rapid in-EPON CLEM: Combining fast and efficient labeling of self-labeling enzyme tags with EM-resistant Janelia Fluor dyes and StayGold.

Correlative light and electron microscopy (CLEM) combines light microscopy (LM) of fluorescent samples to ultrastructural analyses by electron microscopy (EM). Pre-embedding CLEM often suffers from inaccurate correlation between LM and EM modalities. Post-embedding CLEM enables precise registration of structures directly on EM sections, but requires fluorescent markers withstanding EM sample preparation, especially osmium tetroxide fixation, dehydration and EPON embedding. Most fluorescent proteins (FPs) lose their fluorescence during such conventional embedding (CE), but synthetic dyes represent promising alternatives as their stability exceeds those of FP. We analyzed various Janelia Fluor dyes and TMR conjugated to ligands for self-labeling enzymes, such as HaloTag, for fluorescence preservation after CE. We show that TMR, JF525, JF549, JFX549 and JFX554 retain fluorescence, with JFX549 and JFX554 yielding best results overall, also allowing integration of high-pressure freezing and freeze substitution. Furthermore, we found the recently published FP StayGold to resist CE, facilitating dual-fluorescence in-resin CLEM.

Checkmating the Nutri-Score: Will Food Patriotism Prevent the Harmonization of Front-of-Pack Labeling Schemes within the EU?

Front-of-pack labeling schemes are an effective but contested regulatory approach to nudge consumers towards healthy food choices. The Nutri-Score, being implemented by seven European countries, is one of the most elaborated and evidence-based examples. Therefore, the Nutri-Score has been deemed as the frontrunner within the EU Commission's attempt to harmonize front-of-pack labeling among EU member states under its Farm-to-Fork strategy (F2F) by the end of 2022. However, the endeavor is on the brink of failure due to massive resistance by Mediterranean member states and parts of the food industry capitalizing on patriotic narratives (e.g. Made in Italy). This comment investigates the Nutri-Score saga from a political and commercial determinants of health lens. It argues that an EU-wide roll-out of the label hinges on the specific interplay between political structures and stakeholder agency. As shown, the EU's weak decision-making power has been exploited by the No-Nutri-Score alliance.

Size-dependent vector effects of microplastics on bioaccumulation of hydrophobic organic contaminants in earthworm: A dual-dosing study.

The potential of microplastics to act as a vector for anthropogenic contaminants is of rising concern. However, directly quantitatively determining the vector effects of microplastics has been rarely studied. Here, we present a dual-dosing method that simulates the chemical bioaccumulation from soil and microplastics simultaneously, wherein unlabeled hydrophobic organic contaminants (HOCs) were spiked in the soil and their respective isotope-labeled reference compounds were spiked on the polyethylene microplastics. The comparison of the bioavailability, i.e., the freely dissolved concentration in soil porewater and bioaccumulation by earthworm, between the unlabeled and isotope-labeled HOCs was carried out. Relatively higher level of bioavailability of the isotope-labeled HOCs was observed compared to the unlabeled HOCs, which may be attributed to the irreversible desorption of HOCs from soil particles. The average relative fractions of bioaccumulated isotope-labeled HOCs in the soil treated with 1 % microplastics ranged from 6.9 % to 46.4 %, which were higher than those in the soil treated with 0.1 % microplastics. Treatments with the smallest microplastic particles were observed to have the highest relative fractions of bioaccumulated isotope-labeled HOCs, with the exception of phenanthrene, suggesting greater vector effects of smaller microplastic particles. Biodynamic model analysis indicated that the contribution of dermal uptake to the bioaccumulation of isotope-labeled HOCs was higher than that for unlabeled HOCs. This proposed method can be used as a tool to assess the prospective vector effects of microplastics in complex environmental conditions and would enhance the comprehensive understanding of the microplastic vector effects for HOC bioaccumulation.

Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle.

mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.