{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/checksum.txt"],"Pepxml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/db.pep.xml"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_1_S4-B10_1_13437.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_3_S4-C8_1_13447.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_4_S4-C12_1_13451.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_4_S4-C10_1_13449.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_3_S4-C6_1_13445.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_2_S4-C2_1_13441.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_5_S4-D4_1_13455.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_1_S4-B12_1_13439.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_5_S4-D2_1_13453.d.refined.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_2_S4-C4_1_13443.d.refined.mgf"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_4_S4-C10_1_13449.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_5_S4-D2_1_13453.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_5_S4-D4_1_13455.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_3_S4-C6_1_13445.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_3_S4-C8_1_13447.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_4_S4-C12_1_13451.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_1_S4-B10_1_13437.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Interphase_2_S4-C2_1_13441.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_2_S4-C4_1_13443.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063728/2424001_DDA_Max_Mitose_1_S4-B12_1_13439.d.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["pablo.navarro-gil@pasteur.fr"],"submitter":["Guillaume CHEVREUX"],"technology_type":["Data-dependent acquisition","Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Hyper-transcription","Es cells","Mitotic bookmarking","Myc/max"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063728"],"tissue":["Early Embryonic Cell","Embryonic Stem Cell"],"sample_protocol":["Immunoprecipitation: For immunoprecipitation (IP) assays, E14Tg2a cells were lysed in ice-cold lysis buffer (10 mM Tris-HCl pH 7.5, 5 mM EDTA, 150 mM NaCl, 30 mM sodium pyrophosphate tetrabasic decahydrate [Sigma, S6422], 50 mM sodium fluoride [Sigma, S7920], 10% glycerol, 1% NP-40, supplemented with 1XComplete™ Protease Inhibitor Cocktail, EDTA-free [Roche], PhosSTOP™ phosphatase inhibitors [Roche], and 25 U/mL Benzonase® [Sigma, E1014]). Cells were resuspended in 500 μL lysis buffer per 10x10⁶ cells and incubated on ice for 30 min. Lysates were cleared by centrifugation (10 min, 600 × g, 4 °C) and the supernatants collected. For each IP, 500 μL of lysate was incubated overnight at 4 °C under rotation with 1:100 anti-Max (Proteintech, 10426-1-AP). The following day, 50 μL of Protein G Sepharose beads (Sigma, P9424 or P3296; 50% slurry) pre-blocked with bovine serum albumin (BSA, 500 μg/mL; Roche, 5931665103) and denatured yeast tRNA (1 μg/mL; Invitrogen, AM7119) were added and incubated for 2 h at 4 °C under rotation. Beads were then washed once with 1 mL lysis buffer for 5 min at 4 °C. For mass spectrometry applications, detergent- and glycerol-free conditions were used in final washes. After the initial wash with lysis buffer, beads were washed 4 times with cold Tris-buffered saline (TBS; 200 mM Tris, 1.5 M NaCl, pH 7.6), and a final wash was performed with molecular-grade water. Beads were kept in minimal residual volume of cold water to maintain hydration before downstream processing. Samples preparation prior to LC-MS/MS analysis: Beads from pulldown experiments were incubated overnight at 37°C with 20 μL of 50 mM NH4HCO3 buffer containing 1 µg of sequencing-grade trypsin/Lys C mix. Before LC-MS/MS analysis, the digested peptides were loaded and desalted on evotips provided by Evosep (Odense, Denmark) according to manufacturer’s procedure. LC-MS/MS acquisition: Samples were analyzed on a timsTOF Pro 2 mass spectrometer (Bruker Daltonics, Bremen, Germany) coupled to an Evosep one system (Evosep, Odense, Denmark) operating with the 30SPD method developed by the manufacturer. Briefly, the method is based on a 44-min gradient and a total cycle time of 48 min with a C18 analytical column (0.15 x 150 mm, 1.9µm beads, ref EV-1106) equilibrated at 40°C and operated at a flow rate of 500 nL/min. H2O/0.1 % FA was used as solvent A and ACN/ 0.1 % FA as solvent B. The timsTOF Pro 2 was operated in DDA-PASEF mode1 over a 1.3 sec cycle time. Mass spectra for MS and MS/MS scans were recorded between 100 and 1700 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["MS raw files were processed using PEAKS Online 11 (build 1.9, Bioinformatics Solutions Inc.). Data were searched against the Mus Musculus Swiss-Prot database (downloaded 2024_01, 17,191 entries). Parent mass tolerance was set to 20 ppm, with fragment mass tolerance at 0.05 Da. Semi-Specific tryptic cleavage was selected and a maximum of 2 missed cleavages was authorized. For identification, the following post-translational modifications were included: oxidation (M), deamidation (NQ), Acetylation (K, Protein N-term), Methylation (KR), Dimethylation (KR) and Phosphorylation (STY) as variables and half of a disulfide bridge (C) as fixed. Identifications were filtered based on a 1% FDR (False Discovery Rate) threshold at both peptide and protein group levels. Label free quantification was performed using the PEAKS Online X quantification module, allowing a mass tolerance of 5 ppm, a CCS error tolerance of 0.02 and a-0.25 min retention time shift tolerance for match between runs. Protein abundance was inferred using a top N peptide method and TIC was used for normalization. Multivariate statistics on proteins and peptides were performed using Qlucore Omics Explorer 3.8 (Qlucore AB, Lund, SWEDEN). A positive threshold value of 1 was specified to enable a log2 transformation of abundance data for normalization i.e. all abundance data values below the threshold will be replaced by 1 before transformation. The transformed data were finally used for statistical analysis i.e. evaluation of differentially present proteins or peptides between two groups using a Student’s bilateral t-test. A p-value better than 0.05 was used to filter differential candidates."],"omics_type":["Proteomics"],"labhead":["Pablo NAVARRO GIL"],"instrument_platform":[""],"labhead_affiliation":["UMR7338, Developmental and stem cell biology, Pasteur Institut, FRANCE"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"publication":["Not available"],"submitter_mail":["guillaume.chevreux@ijm.fr"],"submitter_affiliation":["Institut Jacques Monod, CNRS UMR7592"],"submitter_country":["France"],"additional_accession":[]},"is_claimable":false,"name":"Mitotic MAX bookmarking drives MYC-dependent hyper-transcription at TBP-bound promoters","description":"Shortly after cell division, a robust wave of hyper-transcription reactivates the genome1-3. This phenomenon is particularly pronounced in pluripotent cells4, which necessitate rapid transcriptome reactivation to maintain their undifferentiated state and prevent premature differentiation. While recent work has illuminated how specific groups of genes are reactivated4-8, the mechanisms enabling the global, efficient and accurate post-mitotic reactivation of the genome remain unknown. Here we elucidate the direct involvement of the MYC/MAX transcription factors in the post-mitotic reactivation of pluripotent mouse embryonic stem cells. While MYC undergoes extensive phosphorylation and largely dissociates from its DNA binding sites during mitosis, we report that MAX remains bound to its targets, preferentially at promoters, and facilitates early recruitment of MYC following mitosis. Through the application of MYC/MAX heterodimerization inhibitors, we demonstrate their indispensable role in sustaining hyper-transcription in ES cells, including during the critical transition from mitosis to G1 phase. Our findings uncover a novel role for MAX in mitotic bookmarking, highlighting its pivotal role in post-mitotic MYC recruitment and the re-establishment of high global transcription levels. These findings hold significant implications for medically relevant contexts, particularly when cell proliferation is of paramount importance. We anticipate that the study of mitotic bookmarking by MYC and MAX and of the effects of anti-cancer drugs targeting MYC/MAX interactions in such process will be relevant for our understanding of cancer and its potential 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