{"entity": "journal", "iuid": "13295f3984d543ca816e46cc2b34831f", "timestamp": "2026-10-05T20:28:49.931Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Mol.%20Cell.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Mol.%20Cell"}}, "title": "Mol. Cell", "issn": "1097-4164", "issn-l": "1097-2765", "publications_count": 11, "publications": [{"entity": "publication", "iuid": "00ab4a882a5c45daaf75dcb38a32836b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00ab4a882a5c45daaf75dcb38a32836b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00ab4a882a5c45daaf75dcb38a32836b"}}, "title": "Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation.", "authors": [{"family": "Marsh", "given": "Audrey J", "initials": "AJ"}, {"family": "Pirogov", "given": "Sergei", "initials": "S"}, {"family": "Kaur", "given": "Yadwinder", "initials": "Y"}, {"family": "Ruffridge", "given": "Abby J", "initials": "AJ"}, {"family": "Sajwan", "given": "Suresh", "initials": "S"}, {"family": "Gibson", "given": "Tyler J", "initials": "TJ"}, {"family": "Hunt", "given": "George", "initials": "G"}, {"family": "Harrison", "given": "Melissa M", "initials": "MM"}, {"family": "Mannervik", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2025-06-19", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "85", "issue": "12", "pages": "2409-2424.e8", "issn-l": "1097-2765"}, "abstract": "Immediately after fertilization, the genome is transcriptionally quiescent. Maternally encoded pioneer factors reprogram the chromatin state and facilitate transcription of the zygotic genome. In Drosophila, transcription is initiated by the pioneer factor Zelda. While Zelda-occupied sites are enriched with histone acetylation, a post-translational mark associated with active cis-regulatory regions, the functional relationship between Zelda and histone acetylation remained unclear. We show that Zelda-mediated recruitment of the histone acetyltransferase CREB-binding protein (CBP) is essential for zygotic transcription. CBP catalytic activity is necessary for the release of RNA polymerase II (RNA Pol II) into elongation and for embryonic development. However, CBP also activates transcription independent of acetylation through RNA Pol II recruitment. Neither CBP-mediated acetylation nor CBP itself is required for the pioneering function of Zelda. Our data suggest that pioneer-factor-mediated recruitment of CBP is a conserved mechanism required to activate zygotic transcription but is separable from the function of pioneer factors in restructuring chromatin accessibility.", "doi": "10.1016/j.molcel.2025.05.009", "pmid": "40441155", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2081331"}, {"db": "pmc", "key": "PMC12181052"}, {"db": "pii", "key": "S1097-2765(25)00414-9"}], "notes": [], "created": "2025-07-18T10:23:07.052Z", "modified": "2025-07-18T10:23:07.057Z"}, {"entity": "publication", "iuid": "f5a075e23b8e4e9b9f7cac3107cdb0c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5a075e23b8e4e9b9f7cac3107cdb0c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5a075e23b8e4e9b9f7cac3107cdb0c3"}}, "title": "Retron-Eco1 assembles NAD+-hydrolyzing filaments that provide immunity against bacteriophages.", "authors": [{"family": "Carabias", "given": "Arturo", "initials": "A"}, {"family": "Camara-Wilpert", "given": "Sarah", "initials": "S"}, {"family": "Mestre", "given": "Mario Rodr\u00edguez", "initials": "MR"}, {"family": "Lop\u00e9z-M\u00e9ndez", "given": "Blanca", "initials": "B"}, {"family": "Hendriks", "given": "Ivo A", "initials": "IA"}, {"family": "Zhao", "given": "Ruiliang", "initials": "R"}, {"family": "Pape", "given": "Tillmann", "initials": "T"}, {"family": "Fuglsang", "given": "Anders", "initials": "A"}, {"family": "Luk", "given": "Sean Hoi-Ching", "initials": "SH"}, {"family": "Nielsen", "given": "Michael L", "initials": "ML"}, {"family": "Pinilla-Redondo", "given": "Rafael", "initials": "R"}, {"family": "Montoya", "given": "Guillermo", "initials": "G"}], "type": "journal article", "published": "2024-05-18", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "issn-l": "1097-2765"}, "abstract": "Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD+ during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD+ hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity.", "doi": "10.1016/j.molcel.2024.05.001", "pmid": "38788717", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(24)00394-0"}], "notes": [], "created": "2024-06-04T06:49:00.455Z", "modified": "2024-06-04T06:49:00.458Z"}, {"entity": "publication", "iuid": "471d923bbe2e40549d5e26d86452b93b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/471d923bbe2e40549d5e26d86452b93b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/471d923bbe2e40549d5e26d86452b93b"}}, "title": "METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.", "authors": [{"family": "Ast", "given": "Tslil", "initials": "T"}, {"family": "Itoh", "given": "Yuzuru", "initials": "Y"}, {"family": "Sadre", "given": "Shayan", "initials": "S"}, {"family": "McCoy", "given": "Jason G", "initials": "JG"}, {"family": "Namkoong", "given": "Gil", "initials": "G"}, {"family": "Wengrod", "given": "Jordan C", "initials": "JC"}, {"family": "Chicherin", "given": "Ivan", "initials": "I"}, {"family": "Joshi", "given": "Pallavi R", "initials": "PR"}, {"family": "Kamenski", "given": "Piotr", "initials": "P"}, {"family": "Suess", "given": "Daniel L M", "initials": "DLM"}, {"family": "Amunts", "given": "Alexey", "initials": "A"}, {"family": "Mootha", "given": "Vamsi K", "initials": "VK"}], "type": "journal article", "published": "2024-01-04", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "issn-l": "1097-2765"}, "abstract": "Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [Fe4S4]2+ cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.", "doi": "10.1016/j.molcel.2023.12.016", "pmid": "38199006", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(23)01035-3"}], "notes": [], "created": "2024-01-18T08:16:21.153Z", "modified": "2024-01-18T08:16:21.156Z"}, {"entity": "publication", "iuid": "a174b1424221463aab2826373c39a254", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a174b1424221463aab2826373c39a254.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a174b1424221463aab2826373c39a254"}}, "title": "FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress.", "authors": [{"family": "Brunner", "given": "Andr\u00e4", "initials": "A"}, {"family": "Li", "given": "Qiuzhen", "initials": "Q"}, {"family": "Fisicaro", "given": "Samuele", "initials": "S"}, {"family": "Kourtesakis", "given": "Alexandros", "initials": "A"}, {"family": "Viili\u00e4inen", "given": "Johanna", "initials": "J"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Pandey", "given": "Vijaya", "initials": "V"}, {"family": "Mayank", "given": "Adarsh K", "initials": "AK"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "Wohlschlegel", "given": "James A", "initials": "JA"}, {"family": "Spruck", "given": "Charles", "initials": "C"}, {"family": "Rantala", "given": "Juha K", "initials": "JK"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "83", "issue": "20", "pages": "3720-3739.e8", "issn-l": "1097-2765"}, "abstract": "Fanconi anemia (FA) signaling, a key genomic maintenance pathway, is activated in response to replication stress. Here, we report that phosphorylation of the pivotal pathway protein FANCD2 by CHK1 triggers its FBXL12-dependent proteasomal degradation, facilitating FANCD2 clearance at stalled replication forks. This promotes efficient DNA replication under conditions of CYCLIN E- and drug-induced replication stress. Reconstituting FANCD2-deficient fibroblasts with phosphodegron mutants failed to re-establish fork progression. In the absence of FBXL12, FANCD2 becomes trapped on chromatin, leading to replication stress and excessive DNA damage. In human cancers, FBXL12, CYCLIN E, and FA signaling are positively correlated, and FBXL12 upregulation is linked to reduced survival in patients with high CYCLIN E-expressing breast tumors. Finally, depletion of FBXL12 exacerbated oncogene-induced replication stress and sensitized cancer cells to drug-induced replication stress by WEE1 inhibition. Collectively, our results indicate that FBXL12 constitutes a vulnerability and a potential therapeutic target in CYCLIN E-overexpressing cancers.", "doi": "10.1016/j.molcel.2023.07.026", "pmid": "37591242", "labels": {"Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "mid", "key": "NIHMS1925612"}, {"db": "pmc", "key": "PMC10592106"}, {"db": "pii", "key": "S1097-2765(23)00599-3"}], "notes": [], "created": "2023-11-30T13:13:01.784Z", "modified": "2023-11-30T13:13:01.788Z"}, {"entity": "publication", "iuid": "02450d13be864bfb9e9d001f75977793", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02450d13be864bfb9e9d001f75977793.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02450d13be864bfb9e9d001f75977793"}}, "title": "MYC assembles and stimulates topoisomerases 1 and 2 in a \"topoisome\".", "authors": [{"family": "Das", "given": "Subhendu K", "initials": "SK"}, {"family": "Kuzin", "given": "Vladislav", "initials": "V"}, {"family": "Cameron", "given": "Donald P", "initials": "DP"}, {"family": "Sanford", "given": "Suzanne", "initials": "S"}, {"family": "Jha", "given": "Rajiv Kumar", "initials": "RK"}, {"family": "Nie", "given": "Zuqin", "initials": "Z"}, {"family": "Rosello", "given": "Marta Trullols", "initials": "MT"}, {"family": "Holewinski", "given": "Ronald", "initials": "R"}, {"family": "Andresson", "given": "Thorkell", "initials": "T"}, {"family": "Wisniewski", "given": "Jan", "initials": "J"}, {"family": "Natsume", "given": "Toyoaki", "initials": "T"}, {"family": "Price", "given": "David H", "initials": "DH"}, {"family": "Lewis", "given": "Brian A", "initials": "BA"}, {"family": "Kouzine", "given": "Fedor", "initials": "F"}, {"family": "Levens", "given": "David", "initials": "D"}, {"family": "Baranello", "given": "Laura", "initials": "L"}], "type": "journal article", "published": "2022-01-06", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "82", "issue": "1", "pages": "140-158.e12", "issn-l": "1097-2765"}, "abstract": "High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must manage this interfering torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with topoisomerase 1 (TOP1) and TOP2 that was confirmed in vitro and in cells. Beyond recruiting topoisomerases, MYC directly stimulates their activities. We identify a MYC-nucleated \"topoisome\" complex that unites TOP1 and TOP2 and increases their levels and activities at promoters, gene bodies, and enhancers. Whether TOP2A or TOP2B is included in the topoisome is dictated by the presence of MYC versus MYCN, respectively. Thus, in vitro and in cells, MYC assembles tools that simplify DNA topology and promote genome function under high output conditions.", "doi": "10.1016/j.molcel.2021.11.016", "pmid": "34890565", "labels": {"CRISPR Functional Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(21)00996-5"}, {"db": "pmc", "key": "PMC8750365"}, {"db": "mid", "key": "NIHMS1763797"}], "notes": [], "created": "2022-02-16T12:44:58.771Z", "modified": "2022-02-16T12:45:54.830Z"}, {"entity": "publication", "iuid": "aa77f0add8444723b1c5c4eaa9e8c52b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa77f0add8444723b1c5c4eaa9e8c52b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa77f0add8444723b1c5c4eaa9e8c52b"}}, "title": "(p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains.", "authors": [{"family": "Roghanian", "given": "Mohammad", "initials": "M"}, {"family": "Van Nerom", "given": "Katleen", "initials": "K"}, {"family": "Takada", "given": "Hiraku", "initials": "H"}, {"family": "Caballero-Montes", "given": "Julien", "initials": "J"}, {"family": "Tamman", "given": "Hedvig", "initials": "H"}, {"family": "Kudrin", "given": "Pavel", "initials": "P"}, {"family": "Talavera", "given": "Ariel", "initials": "A"}, {"family": "Dzhygyr", "given": "Ievgen", "initials": "I"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC"}, {"family": "Garcia-Pino", "given": "Abel", "initials": "A"}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V"}], "type": "journal article", "published": "2021-08-19", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "81", "issue": "16", "pages": "3310-3322.e6", "issn-l": "1097-2765"}, "abstract": "Amino acid starvation is sensed by Escherichia coli RelA and Bacillus subtilis Rel through monitoring the aminoacylation status of ribosomal A-site tRNA. These enzymes are positively regulated by their product-the alarmone nucleotide (p)ppGpp-through an unknown mechanism. The (p)ppGpp-synthetic activity of Rel/RelA is controlled via auto-inhibition by the hydrolase/pseudo-hydrolase (HD/pseudo-HD) domain within the enzymatic N-terminal domain region (NTD). We localize the allosteric pppGpp site to the interface between the SYNTH and pseudo-HD/HD domains, with the alarmone stimulating Rel/RelA by exploiting intra-NTD autoinhibition dynamics. We show that without stimulation by pppGpp, starved ribosomes cannot efficiently activate Rel/RelA. Compromised activation by pppGpp ablates Rel/RelA function in vivo, suggesting that regulation by the second messenger (p)ppGpp is necessary for mounting an acute starvation response via coordinated enzymatic activity of individual Rel/RelA molecules. Control by (p)ppGpp is lacking in the E. coli (p)ppGpp synthetase SpoT, thus explaining its weak synthetase activity.", "doi": "10.1016/j.molcel.2021.07.026", "pmid": "34416138", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1097-2765(21)00595-5"}], "notes": [], "created": "2021-12-03T09:33:53.260Z", "modified": "2021-12-03T09:33:53.266Z"}, {"entity": "publication", "iuid": "2ba033fd1efc4e399b47b8681da72993", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ba033fd1efc4e399b47b8681da72993.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ba033fd1efc4e399b47b8681da72993"}}, "title": "Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP.", "authors": [{"family": "Crowe-McAuliffe", "given": "Caillan", "initials": "C"}, {"family": "Takada", "given": "Hiraku", "initials": "H"}, {"family": "Murina", "given": "Victoriia", "initials": "V"}, {"family": "Polte", "given": "Christine", "initials": "C"}, {"family": "Kasvandik", "given": "Sergo", "initials": "S"}, {"family": "Tenson", "given": "Tanel", "initials": "T"}, {"family": "Ignatova", "given": "Zoya", "initials": "Z", "orcid": "0000-0002-9478-8825", "researcher": {"href": "https://publications.scilifelab.se/researcher/15d0b4be02ca4c1884f0ad793462901c.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC"}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd50ba35f7c74d7e9d4f42fbc49739f2.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ea83b1d20f43f9872edbf89b275e5d.json"}}], "type": "journal article", "published": "2021-01-07", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "issn-l": "1097-2765", "volume": "81", "issue": "1", "pages": "115-126.e7"}, "abstract": "In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality control (RQC) pathways. RQC begins with the splitting of stalled ribosomes, leaving an unfinished polypeptide still attached to the large subunit. Ancient and conserved NEMF family RQC proteins target these incomplete proteins for degradation by the addition of C-terminal \"tails.\" How such tailing can occur without the regular suite of translational components is, however, unclear. Using single-particle cryo-electron microscopy (EM) of native complexes, we show that C-terminal tailing in Bacillus subtilis is mediated by NEMF protein RqcH in concert with RqcP, an Hsp15 family protein. Our structures reveal how these factors mediate tRNA movement across the ribosomal 50S subunit to synthesize polypeptides in the absence of mRNA or the small subunit.", "doi": "10.1016/j.molcel.2020.11.002", "pmid": "33259810", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(20)30780-2"}], "notes": [], "created": "2020-12-10T11:26:33.440Z", "modified": "2021-11-10T12:27:47.555Z"}, {"entity": "publication", "iuid": "8b9e53481baa45fdb771e7322b8713ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b9e53481baa45fdb771e7322b8713ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b9e53481baa45fdb771e7322b8713ea"}}, "title": "Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.", "authors": [{"family": "Nicholls", "given": "Thomas J", "initials": "TJ"}, {"family": "Sp\u00e5hr", "given": "Henrik", "initials": "H"}, {"family": "Jiang", "given": "Shan", "initials": "S"}, {"family": "Siira", "given": "Stefan J", "initials": "SJ"}, {"family": "Koolmeister", "given": "Camilla", "initials": "C"}, {"family": "Sharma", "given": "Sushma", "initials": "S"}, {"family": "Kauppila", "given": "Johanna H K", "initials": "JHK"}, {"family": "Jiang", "given": "Min", "initials": "M"}, {"family": "Kaever", "given": "Volkhard", "initials": "V"}, {"family": "Rackham", "given": "Oliver", "initials": "O"}, {"family": "Chabes", "given": "Andrei", "initials": "A"}, {"family": "Falkenberg", "given": "Maria", "initials": "M"}, {"family": "Filipovska", "given": "Aleksandra", "initials": "A"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG"}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM"}], "type": "journal article", "published": "2019-12-05", "journal": {"volume": "76", "issn": "1097-4164", "issue": "5", "pages": "784-796.e6", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length and are assumed to constitute the final stage of RNA turnover. Here we demonstrate that REXO2 is a specialized dinucleotide-degrading enzyme that shows no preference between RNA and DNA dinucleotide substrates. A heart- and skeletal-muscle-specific knockout mouse displays elevated dinucleotide levels and alterations in gene expression patterns indicative of aberrant dinucleotide-primed transcription initiation. We find that dinucleotides act as potent stimulators of mitochondrial transcription initiation in vitro. Our data demonstrate that increased levels of dinucleotides can be used to initiate transcription, leading to an increase in transcription levels from both mitochondrial promoters and other, nonspecific sequence elements in mitochondrial DNA. Efficient RNA turnover by REXO2 is thus required to maintain promoter specificity and proper regulation of transcription in mammalian mitochondria.", "doi": "10.1016/j.molcel.2019.09.010", "pmid": "31588022", "labels": {"Protein Science Facility (PSF)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(19)30695-1"}, {"db": "PDB", "key": "6RCI", "description": "Crystal structure of REXO2"}, {"db": "PDB", "key": "6RCL", "description": "Crystal structure of REXO2-D199A-AA"}, {"db": "PDB", "key": "6RCN", "description": "Crystal structure of REXO2-D199A-dAdA"}], "notes": [], "created": "2019-12-12T11:38:57.069Z", "modified": "2024-01-16T13:48:43.339Z"}, {"entity": "publication", "iuid": "ce017bfd92fb49769abbc2215c8978a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce017bfd92fb49769abbc2215c8978a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce017bfd92fb49769abbc2215c8978a0"}}, "title": "SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization.", "authors": [{"family": "Orre", "given": "Lukas Minus", "initials": "LM"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}, {"family": "Pan", "given": "Yanbo", "initials": "Y"}, {"family": "Arslan", "given": "Taner", "initials": "T"}, {"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Fernandez Woodbridge", "given": "Alejandro", "initials": "A"}, {"family": "Frings", "given": "Oliver", "initials": "O"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2019-01-03", "journal": {"volume": "73", "issn": "1097-4164", "issue": "1", "pages": "166-182.e7", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "Subcellular localization is a main determinant of protein function; however, a global view of cellular proteome organization remains relatively unexplored. We have developed a robust mass spectrometry-based analysis pipeline to generate a proteome-wide view of subcellular localization for proteins mapping to 12,418 individual genes across five cell lines. Based on more than 83,000 unique classifications and correlation profiling, we investigate the effect of alternative splicing and protein domains on localization, complex member co-localization, cell-type-specific localization, as well as protein relocalization after growth factor inhibition. Our analysis provides information about the cellular architecture and complexity of the spatial organization of the proteome; we show that the majority of proteins have a single main subcellular location, that alternative splicing rarely affects subcellular location, and that cell types are best distinguished by expression of proteins exposed to the surrounding environment. The resource is freely accessible via www.subcellbarcode.org.", "doi": "10.1016/j.molcel.2018.11.035", "pmid": "30609389", "labels": {"Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(18)31005-0"}], "notes": [], "created": "2019-01-07T11:26:59.608Z", "modified": "2024-01-16T13:48:44.861Z"}, {"entity": "publication", "iuid": "a1e96d19911348b0881541e490d67a58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1e96d19911348b0881541e490d67a58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1e96d19911348b0881541e490d67a58"}}, "title": "A Unique ISR Program Determines Cellular Responses to Chronic Stress.", "authors": [{"family": "Guan", "given": "Bo-Jhih", "initials": "BJ"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Jobava", "given": "Raul", "initials": "R"}, {"family": "Elroy-Stein", "given": "Orna", "initials": "O"}, {"family": "Valasek", "given": "Leos S", "initials": "LS"}, {"family": "Cargnello", "given": "Marie", "initials": "M"}, {"family": "Gao", "given": "Xing-Huang", "initials": "XH"}, {"family": "Krokowski", "given": "Dawid", "initials": "D"}, {"family": "Merrick", "given": "William C", "initials": "WC"}, {"family": "Kimball", "given": "Scot R", "initials": "SR"}, {"family": "Komar", "given": "Anton A", "initials": "AA"}, {"family": "Koromilas", "given": "Antonis E", "initials": "AE"}, {"family": "Wynshaw-Boris", "given": "Anthony", "initials": "A"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Hatzoglou", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-12-07", "journal": {"volume": "68", "issn": "1097-4164", "issue": "5", "pages": "885-900.e6", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "The integrated stress response (ISR) is a homeostatic mechanism induced by endoplasmic reticulum (ER) stress. In acute/transient ER stress, decreased global protein synthesis and increased uORF mRNA translation are followed by normalization of protein synthesis. Here, we report a dramatically different response during chronic ER stress. This chronic ISR program is characterized by persistently elevated uORF mRNA translation and concurrent gene expression reprogramming, which permits simultaneous stress sensing and proteostasis. The program includes PERK-dependent switching to an eIF3-dependent translation initiation mechanism, resulting in partial, but not complete, translational recovery, which, together with transcriptional reprogramming, selectively bolsters expression of proteins with ER functions. Coordination of transcriptional and translational reprogramming prevents ER dysfunction and inhibits \"foamy cell\" development, thus establishing a molecular basis for understanding human diseases associated with ER dysfunction.", "doi": "10.1016/j.molcel.2017.11.007", "pmid": "29220654", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(17)30842-0"}, {"db": "pmc", "key": "PMC5730339"}, {"db": "mid", "key": "NIHMS919694"}, {"db": "GEO", "description": "A unique ISR Program Determines Cellular Responses to Chronic Stress", "key": "GSE90070"}], "notes": [], "created": "2018-01-10T09:45:07.638Z", "modified": "2020-01-21T13:56:11.026Z"}, {"entity": "publication", "iuid": "dc1955ed9ae2463f8a8d503bd7ab63cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc1955ed9ae2463f8a8d503bd7ab63cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc1955ed9ae2463f8a8d503bd7ab63cb"}}, "title": "PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription.", "authors": [{"family": "Zhao", "given": "Honglei", "initials": "H"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Sumida", "given": "Noriyuki", "initials": "N"}, {"family": "Mill\u00e1n-Ari\u00f1o", "given": "Llu\u00eds", "initials": "L"}, {"family": "Scholz", "given": "Barbara A", "initials": "BA"}, {"family": "Svensson", "given": "J Peter", "initials": "JP"}, {"family": "Chen", "given": "Xingqi", "initials": "X"}, {"family": "Ronnegren", "given": "Anna L", "initials": "AL"}, {"family": "Mallet de Lima", "given": "Carolina Diettrich", "initials": "CD"}, {"family": "Varnoosfaderani", "given": "Farzaneh Shahin", "initials": "FS"}, {"family": "Shi", "given": "Chengxi", "initials": "C"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Yammine", "given": "Samer", "initials": "S"}, {"family": "Israelsson", "given": "Maria", "initials": "M"}, {"family": "Rathje", "given": "Li-Sophie", "initials": "LS"}, {"family": "N\u00e9meti", "given": "Bal\u00e1zs", "initials": "B"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Imreh", "given": "M\u00e1rta P", "initials": "MP"}, {"family": "G\u00f6nd\u00f6r", "given": "Anita", "initials": "A"}], "type": "journal article", "published": "2015-09-17", "journal": {"volume": "59", "issn": "1097-4164", "issue": "6", "pages": "984-997", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor CTCF. They not only mediate chromatin fiber interactions but also promote the recruitment of circadian genes to the lamina. Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Furthermore, depletion of H3K9me2/3, inhibition of PARP activity by olaparib, or downregulation of PARP1 or CTCF expression counteracts both recruitment to the envelope and circadian transcription. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity.", "doi": "10.1016/j.molcel.2015.07.019", "pmid": "26321255", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1097-2765(15)00577-8"}, {"db": "GEO", "key": "GSE26880"}, {"db": "GEO", "key": "GSE58534"}], "notes": [], "created": "2017-05-02T12:59:01.424Z", "modified": "2021-07-08T13:01:30.938Z"}], "created": "2017-05-09T09:12:28.825Z", "modified": "2020-11-27T13:14:01.297Z"}