{"entity": "journal", "iuid": "8b38ade3fa95427290adb632ca1c288c", "timestamp": "2026-07-18T02:51:39.271Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Nat.%20Struct.%20Mol.%20Biol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Nat.%20Struct.%20Mol.%20Biol."}}, "title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "issn-l": "1545-9985", "publications_count": 16, "publications": [{"entity": "publication", "iuid": "98b0419415a549f5811c2936f54fd763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98b0419415a549f5811c2936f54fd763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98b0419415a549f5811c2936f54fd763"}}, "title": "Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex.", "authors": [{"family": "MacLean", "given": "Andrew E", "initials": "AE"}, {"family": "Shikha", "given": "Shikha", "initials": "S", "orcid": "0000-0002-7878-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/2de6231587194596b907dddf06be1b45.json"}}, {"family": "Ferreira Silva", "given": "Mariana", "initials": "M"}, {"family": "Gramelspacher", "given": "Max J", "initials": "MJ", "orcid": "0000-0003-3090-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fb639abc4534915b60c4ac9de0e26ac.json"}}, {"family": "Nilsen", "given": "Aaron", "initials": "A"}, {"family": "Liebman", "given": "Katherine M", "initials": "KM"}, {"family": "Pou", "given": "Sovitj", "initials": "S"}, {"family": "Winter", "given": "Rolf W", "initials": "RW"}, {"family": "Meir", "given": "Amit", "initials": "A", "orcid": "0000-0001-9635-1021", "researcher": {"href": "https://publications.scilifelab.se/researcher/75240761defd4310a72f84c79a5114be.json"}}, {"family": "Riscoe", "given": "Michael K", "initials": "MK", "orcid": "0000-0002-1343-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d664bd5cf8d4e2db165759312e43e65.json"}}, {"family": "Doggett", "given": "J Stone", "initials": "JS", "orcid": "0000-0002-6098-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/08880b0318d44f23ac4264bf0d967ed5.json"}}, {"family": "Sheiner", "given": "Lilach", "initials": "L", "orcid": "0000-0001-5909-2307", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e426f417f194a75ae9fbc76ea24040e.json"}}, {"family": "M\u00fchleip", "given": "Alexander", "initials": "A", "orcid": "0000-0002-1877-2282", "researcher": {"href": "https://publications.scilifelab.se/researcher/921b5acb5b7c402fa06c8c148cbd5340.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "32", "issue": "8", "pages": "1424-1433", "issn-l": "1545-9985"}, "abstract": "The apicomplexan mitochondrial electron transport chain is essential for parasite survival and displays a divergent subunit composition. Here we report cryo-electron microscopy structures of an apicomplexan III2-IV supercomplex and of the drug target complex III2. The supercomplex structure reveals how clade-specific subunits form an apicomplexan-conserved III2-IV interface with a unique, kinked architecture, suggesting that supercomplexes evolved independently in different eukaryotic lineages. A knockout resulting in supercomplex disassembly challenges the proposed role of III2-IV in electron transfer efficiency as suggested for mammals. Nevertheless, knockout analysis indicates that III2-IV is critical for parasite fitness. The complexes from the model parasite Toxoplasma gondii were inhibited with the antimalarial atovaquone, revealing interactions underpinning species specificity. They were also inhibited with endochin-like quinolone (ELQ)-300, an inhibitor in late-stage preclinical development. Notably, in the apicomplexan binding site, ELQ-300 is flipped compared with related compounds in the mammalian enzyme. On the basis of the binding modes and parasite-specific interactions discovered, we designed more potent ELQs with subnanomolar activity against T. gondii. Our findings reveal critical evolutionary differences in the role of supercomplexes in mitochondrial biology and provide insight into cytochrome b inhibition, informing future drug discovery.", "doi": "10.1038/s41594-025-01531-7", "pmid": "40389671", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12350165"}, {"db": "pii", "key": "10.1038/s41594-025-01531-7"}], "notes": [], "created": "2025-11-13T09:40:20.527Z", "modified": "2025-11-13T09:40:21.380Z"}, {"entity": "publication", "iuid": "35f8f501e005484788d085fd0b0a9d6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35f8f501e005484788d085fd0b0a9d6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35f8f501e005484788d085fd0b0a9d6f"}}, "title": "Closed and open structures of the eukaryotic magnesium channel Mrs2 reveal the auto-ligand-gating regulation mechanism.", "authors": [{"family": "Li", "given": "Ping", "initials": "P", "orcid": "0000-0002-7364-3301", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cc17e1d61cb498b88038a9f5dfa6aff.json"}}, {"family": "Liu", "given": "Shiyan", "initials": "S"}, {"family": "Wallerstein", "given": "Johan", "initials": "J"}, {"family": "Villones", "given": "Rhiza Lyne E", "initials": "RLE"}, {"family": "Huang", "given": "Peng", "initials": "P"}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Meloni", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4976-1401", "researcher": {"href": "https://publications.scilifelab.se/researcher/24f1558274e845e7a7351c62d8f627fe.json"}}, {"family": "Lu", "given": "Kefeng", "initials": "K", "orcid": "0000-0001-8200-9380", "researcher": {"href": "https://publications.scilifelab.se/researcher/d38d6efdc9744554b14b3370196467b8.json"}}, {"family": "Steen Jensen", "given": "Kristine", "initials": "K", "orcid": "0000-0001-9174-8361", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b573ed9dbd440c6b4cda217120ff974.json"}}, {"family": "Liin", "given": "Sara I", "initials": "SI", "orcid": "0000-0001-8493-0114", "researcher": {"href": "https://publications.scilifelab.se/researcher/e82a591108f24dcabf50779d88fc8844.json"}}, {"family": "Gourdon", "given": "Pontus", "initials": "P", "orcid": "0000-0002-8631-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc6cdbbcab048fab7a65df6cb796aab.json"}}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "32", "issue": "3", "pages": "491-501", "issn-l": "1545-9985"}, "abstract": "The CorA/Mrs2 family of pentameric proteins are cardinal for the influx of Mg2+ across cellular membranes, importing the cation to mitochondria in eukaryotes. Yet, the conducting and regulation mechanisms of permeation remain elusive, particularly for the eukaryotic Mrs2 members. Here, we report closed and open Mrs2 cryo-electron microscopy structures, accompanied by functional characterization. Mg2+ flux is permitted by a narrow pore, gated by methionine and arginine residues in the closed state. Transition between the conformations is orchestrated by two pairs of conserved sensor-serving Mg2+-binding sites in the mitochondrial matrix lumen, located in between monomers. At lower levels of Mg2+, these ions are stripped, permitting an alternative, symmetrical shape, maintained by the RDLR motif that replaces one of the sensor site pairs in the open conformation. Thus, our findings collectively establish the molecular basis for selective Mg2+ influx of Mrs2 and an auto-ligand-gating regulation mechanism.", "doi": "10.1038/s41594-024-01432-1", "pmid": "39609652", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11919701"}, {"db": "pii", "key": "10.1038/s41594-024-01432-1"}], "notes": [], "created": "2024-11-29T18:28:28.359Z", "modified": "2025-10-25T10:16:19.762Z"}, {"entity": "publication", "iuid": "fb964a37469d46c3b8bea7ec226da10b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb964a37469d46c3b8bea7ec226da10b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb964a37469d46c3b8bea7ec226da10b"}}, "title": "Structural basis for lipid transfer by the ATG2A-ATG9A complex.", "authors": [{"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-3839-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/9892fd666eaf4519bae74ec10977512e.json"}}, {"family": "Dahmane", "given": "Selma", "initials": "S"}, {"family": "Ti", "given": "Rujuan", "initials": "R", "orcid": "0000-0002-5169-8491", "researcher": {"href": "https://publications.scilifelab.se/researcher/b530a2ed7e1246b1842cfa8611ffc75d.json"}}, {"family": "Mai", "given": "Xinyi", "initials": "X", "orcid": "0009-0004-7828-061X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa46a9e3371a409c804847b14923f4a6.json"}}, {"family": "Zhu", "given": "Lizhe", "initials": "L", "orcid": "0000-0001-8252-7807", "researcher": {"href": "https://publications.scilifelab.se/researcher/8275c054d43b45b79f49c1a95b10a806.json"}}, {"family": "Carlson", "given": "Lars-Anders", "initials": "LA", "orcid": "0000-0003-2342-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba0e366ce21e49b48212bbed5a0a7bd1.json"}}, {"family": "Stjepanovic", "given": "Goran", "initials": "G", "orcid": "0000-0002-4841-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/a25e20f893d94f8d963403da7eb2a5e1.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "32", "issue": "1", "pages": "35-47", "issn-l": "1545-9985"}, "abstract": "Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid transfer and re-equilibration between membranes for autophagosome formation. Here we report the cryo-electron microscopy structures of human ATG2A in complex with WD-repeat protein interacting with phosphoinositides 4 (WIPI4) at 3.2 \u00c5 and the ATG2A-WIPI4-ATG9A complex at 7 \u00c5 global resolution. On the basis of molecular dynamics simulations, we propose a mechanism of lipid extraction from the donor membranes. Our analysis revealed 3:1 stoichiometry of the ATG9A-ATG2A complex, directly aligning the ATG9A lateral pore with ATG2A lipid transfer cavity, and an interaction of the ATG9A trimer with both the N-terminal and the C-terminal tip of rod-shaped ATG2A. Cryo-electron tomography of ATG2A liposome-binding states showed that ATG2A tethers lipid vesicles at different orientations. In summary, this study provides a molecular basis for the growth of the phagophore membrane and lends structural insights into spatially coupled lipid transport and re-equilibration during autophagosome formation.", "doi": "10.1038/s41594-024-01376-6", "pmid": "39174844", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41594-024-01376-6"}], "notes": [], "created": "2024-11-27T11:37:36.821Z", "modified": "2025-10-29T14:46:12.392Z"}, {"entity": "publication", "iuid": "744a6ad4f05545bea2cb39642ffe1e88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/744a6ad4f05545bea2cb39642ffe1e88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/744a6ad4f05545bea2cb39642ffe1e88"}}, "title": "Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.", "authors": [{"family": "Horv\u00e1th", "given": "Vivien", "initials": "V", "orcid": "0000-0001-6536-1710", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be63bec9f4a4bf2a0fa907973cef28d.json"}}, {"family": "Garza", "given": "Raquel", "initials": "R"}, {"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME"}, {"family": "Johansson", "given": "Pia A", "initials": "PA"}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Christoforidou", "given": "Georgia", "initials": "G"}, {"family": "Karlsson", "given": "Ofelia", "initials": "O"}, {"family": "Castilla Vallmanya", "given": "Laura", "initials": "L"}, {"family": "Koutounidou", "given": "Symela", "initials": "S", "orcid": "0009-0003-6710-8374", "researcher": {"href": "https://publications.scilifelab.se/researcher/bacb26c356f74e6ba8da4d55b7dc4b15.json"}}, {"family": "Gerdes", "given": "Patricia", "initials": "P", "orcid": "0000-0002-1148-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8571bfad113498c8fdb09fb74d7b2bd.json"}}, {"family": "Pandiloski", "given": "Ninoslav", "initials": "N"}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "31", "issue": "10", "pages": "1543-1556", "issn-l": "1545-9985"}, "abstract": "SVA (SINE (short interspersed nuclear element)-VNTR (variable number of tandem repeats)-Alu) retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized and how their regulatory impact is constrained by an innate epigenetic defense system.", "doi": "10.1038/s41594-024-01320-8", "pmid": "38834915", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11479940"}, {"db": "pii", "key": "10.1038/s41594-024-01320-8"}], "notes": [], "created": "2024-09-03T12:22:35.346Z", "modified": "2024-11-15T06:29:49.161Z"}, {"entity": "publication", "iuid": "a484c8a8f0c0429ab56b31b4e80db6e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a484c8a8f0c0429ab56b31b4e80db6e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a484c8a8f0c0429ab56b31b4e80db6e4"}}, "title": "Structure and interactions of the endogenous human Commander complex.", "authors": [{"family": "Laulumaa", "given": "Saara", "initials": "S", "orcid": "0000-0003-4836-9256", "researcher": {"href": "https://publications.scilifelab.se/researcher/0420474f746b42d2b451fdfd8ae578ed.json"}}, {"family": "Kumpula", "given": "Esa-Pekka", "initials": "EP", "orcid": "0000-0003-0335-5993", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb426bc260a3414d9dabd2a1302813b1.json"}}, {"family": "Huiskonen", "given": "Juha T", "initials": "JT", "orcid": "0000-0002-0348-7323", "researcher": {"href": "https://publications.scilifelab.se/researcher/c858a2e60971462f9e53653320c9eb0f.json"}}, {"family": "Varjosalo", "given": "Markku", "initials": "M", "orcid": "0000-0002-1340-9732", "researcher": {"href": "https://publications.scilifelab.se/researcher/631a0a4964d747399c0b1781e546f0ab.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "31", "issue": "6", "pages": "925-938", "issn-l": "1545-9985"}, "abstract": "The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions.", "doi": "10.1038/s41594-024-01246-1", "pmid": "38459129", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11189303"}, {"db": "pii", "key": "10.1038/s41594-024-01246-1"}], "notes": [], "created": "2024-11-15T13:40:35.645Z", "modified": "2024-11-19T07:36:48.332Z"}, {"entity": "publication", "iuid": "32532dfcd911424f93ddea636563394f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32532dfcd911424f93ddea636563394f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32532dfcd911424f93ddea636563394f"}}, "title": "Snapshots of actin and tubulin folding inside the TRiC chaperonin.", "authors": [{"family": "Kelly", "given": "John J", "initials": "JJ"}, {"family": "Tranter", "given": "Dale", "initials": "D"}, {"family": "Pardon", "given": "Els", "initials": "E", "orcid": "0000-0002-2466-0172", "researcher": {"href": "https://publications.scilifelab.se/researcher/375719a54c844150a4d5cb2b4f3ebb57.json"}}, {"family": "Chi", "given": "Gamma", "initials": "G"}, {"family": "Kramer", "given": "Holger", "initials": "H", "orcid": "0000-0002-6400-0945", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf9fb27444604e999fe8815be9eb336a.json"}}, {"family": "Happonen", "given": "Lotta", "initials": "L", "orcid": "0000-0002-5922-4549", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7af0a6faf6a48e7937a644be472edbe.json"}}, {"family": "Knee", "given": "Kelly M", "initials": "KM"}, {"family": "Janz", "given": "Jay M", "initials": "JM"}, {"family": "Steyaert", "given": "Jan", "initials": "J", "orcid": "0000-0002-3825-874X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a13eb5511e1448fb982b5bd1bb1d6f1.json"}}, {"family": "Bulawa", "given": "Christine", "initials": "C"}, {"family": "Paavilainen", "given": "Ville O", "initials": "VO", "orcid": "0000-0002-3160-7767", "researcher": {"href": "https://publications.scilifelab.se/researcher/f76359e8b92b4b53af80c36d064a1a42.json"}}, {"family": "Huiskonen", "given": "Juha T", "initials": "JT", "orcid": "0000-0002-0348-7323", "researcher": {"href": "https://publications.scilifelab.se/researcher/c858a2e60971462f9e53653320c9eb0f.json"}}, {"family": "Yue", "given": "Wyatt W", "initials": "WW", "orcid": "0000-0001-6959-6007", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be92e7076054a009efe9d23f78b5a48.json"}}], "type": "journal article", "published": "2022-04-21", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "issn-l": "1545-9985"}, "abstract": "The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, including he cytoskeletal proteins actin and tubulin. Although its architecture and how it recognizes folding substrates are emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and cochaperone (PhLP2A) at different folding stages, for structure determination by cryo-EM. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions toward the central space to achieve their native fold. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Further, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging model of client protein folding within TRiC.", "doi": "10.1038/s41594-022-00755-1", "pmid": "35449234", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41594-022-00755-1"}], "notes": [], "created": "2022-04-27T14:22:02.454Z", "modified": "2022-04-27T14:22:02.677Z"}, {"entity": "publication", "iuid": "fcf19a79c0f84e60b324b5b3d59f8cb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcf19a79c0f84e60b324b5b3d59f8cb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcf19a79c0f84e60b324b5b3d59f8cb0"}}, "title": "Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.", "authors": [{"family": "Stsiapanava", "given": "Alena", "initials": "A"}, {"family": "Xu", "given": "Chenrui", "initials": "C"}, {"family": "Nishio", "given": "Shunsuke", "initials": "S", "orcid": "0000-0003-3420-2578", "researcher": {"href": "https://publications.scilifelab.se/researcher/418271e729d04268845cd61f734b44c0.json"}}, {"family": "Han", "given": "Ling", "initials": "L", "orcid": "0000-0001-9310-4789", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f38b9eaca93474280189bb93b118817.json"}}, {"family": "Yamakawa", "given": "Nao", "initials": "N"}, {"family": "Carroni", "given": "Marta", "initials": "M"}, {"family": "Tunyasuvunakool", "given": "Kathryn", "initials": "K"}, {"family": "Jumper", "given": "John", "initials": "J", "orcid": "0000-0001-6169-6580", "researcher": {"href": "https://publications.scilifelab.se/researcher/74b09bf1cdfc4b17b7082781f11aa25a.json"}}, {"family": "de Sanctis", "given": "Daniele", "initials": "D", "orcid": "0000-0003-0391-8290", "researcher": {"href": "https://publications.scilifelab.se/researcher/191f6c2f187a4cf396364ee4316d36e3.json"}}, {"family": "Wu", "given": "Bin", "initials": "B", "orcid": "0000-0002-0883-8006", "researcher": {"href": "https://publications.scilifelab.se/researcher/76dd84c8134245d48bf28f63511fa1ba.json"}}, {"family": "Jovine", "given": "Luca", "initials": "L", "orcid": "0000-0002-2679-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/8507a7657f6b434ebc572453aa172b1e.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "issn-l": "1545-9985", "volume": "29", "issue": "3", "pages": "190-193"}, "abstract": "Glycoprotein 2 (GP2) and uromodulin (UMOD) filaments protect against gastrointestinal and urinary tract infections by acting as decoys for bacterial fimbrial lectin FimH. By combining AlphaFold2 predictions with X-ray crystallography and cryo-EM, we show that these proteins contain a bipartite decoy module whose new fold presents the high-mannose glycan recognized by FimH. The structure rationalizes UMOD mutations associated with kidney diseases and visualizes a key epitope implicated in cast nephropathy.", "doi": "10.1038/s41594-022-00729-3", "pmid": "35273390", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8930769"}, {"db": "pii", "key": "10.1038/s41594-022-00729-3"}], "notes": [], "created": "2022-03-21T10:46:40.880Z", "modified": "2022-12-02T10:15:52.364Z"}, {"entity": "publication", "iuid": "16948fd9c1e947eab8b9487a32da850b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16948fd9c1e947eab8b9487a32da850b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16948fd9c1e947eab8b9487a32da850b"}}, "title": "Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2.", "authors": [{"family": "Matsuoka", "given": "Rei", "initials": "R"}, {"family": "Fudim", "given": "Roman", "initials": "R", "orcid": "0000-0001-5101-3184", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ffbe654828498d90ebcfeac084a082.json"}}, {"family": "Jung", "given": "Sukkyeong", "initials": "S", "orcid": "0000-0002-4730-5245", "researcher": {"href": "https://publications.scilifelab.se/researcher/f65f769bad8a4fd6a4186b7ddaaf6051.json"}}, {"family": "Zhang", "given": "Chenou", "initials": "C"}, {"family": "Bazzone", "given": "Andre", "initials": "A", "orcid": "0000-0002-2419-3519", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c714875986841b788d700b56f4f093c.json"}}, {"family": "Chatzikyriakidou", "given": "Yurie", "initials": "Y"}, {"family": "Robinson", "given": "Carol V", "initials": "CV", "orcid": "0000-0001-7829-5505", "researcher": {"href": "https://publications.scilifelab.se/researcher/109418b5455b4a32bcff02b54d49885b.json"}}, {"family": "Nomura", "given": "Norimichi", "initials": "N", "orcid": "0000-0002-6330-2239", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b604af54f4a49f8a7884fbd70d99101.json"}}, {"family": "Iwata", "given": "So", "initials": "S", "orcid": "0000-0003-1735-2937", "researcher": {"href": "https://publications.scilifelab.se/researcher/dadeb06908fa4d679e2b5344a4484c0d.json"}}, {"family": "Landreh", "given": "Michael", "initials": "M", "orcid": "0000-0002-7958-4074", "researcher": {"href": "https://publications.scilifelab.se/researcher/87494f4204c04be9bce5e9ddcdc92d8a.json"}}, {"family": "Orellana", "given": "Laura", "initials": "L"}, {"family": "Beckstein", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1340-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebdd85d6b214b78bdd2d13df4822ba0.json"}}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "29", "issue": "2", "pages": "108-120", "issn-l": "1545-9985"}, "abstract": "The Na+/H+ exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na+/Li+ exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 \u00c5 resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na+/H+ exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.", "doi": "10.1038/s41594-022-00738-2", "pmid": "35173351", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8850199"}, {"db": "pii", "key": "10.1038/s41594-022-00738-2"}], "notes": [], "created": "2023-11-24T18:05:36.006Z", "modified": "2023-11-24T18:05:36.279Z"}, {"entity": "publication", "iuid": "92dba4d4ec6f45f9ad59022513e674eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92dba4d4ec6f45f9ad59022513e674eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92dba4d4ec6f45f9ad59022513e674eb"}}, "title": "Cryo-EM structure of the yeast respiratory supercomplex.", "authors": [{"family": "Rathore", "given": "Sorbhi", "initials": "S", "orcid": "0000-0001-9178-1006", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2293f9f60f44cfa47f1e3691c1309d.json"}}, {"family": "Berndtsson", "given": "Jens", "initials": "J", "orcid": "0000-0001-6627-8134", "researcher": {"href": "https://publications.scilifelab.se/researcher/7620a5c7c0f245a28771d57d7179abbd.json"}}, {"family": "Marin-Buera", "given": "Lorena", "initials": "L"}, {"family": "Conrad", "given": "Julian", "initials": "J"}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Brzezinski", "given": "Peter", "initials": "P", "orcid": "0000-0003-3860-4988", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3314030ecf94791a713a068d4926c20.json"}}, {"family": "Ott", "given": "Martin", "initials": "M", "orcid": "0000-0001-6367-3091", "researcher": {"href": "https://publications.scilifelab.se/researcher/b27b582dbd2a47bcbb0fb3194277902a.json"}}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "26", "issue": "1", "pages": "50-57", "issn-l": "1545-9985"}, "abstract": "Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III 2IV and III2IV2, at 3.2-\u00c5 and 3.5-\u00c5 resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.", "doi": "10.1038/s41594-018-0169-7", "pmid": "30598556", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41594-018-0169-7"}], "notes": [], "created": "2019-01-03T16:38:40.124Z", "modified": "2021-06-21T13:49:53.118Z"}, {"entity": "publication", "iuid": "c43fdddf24ee4d548364cd7bb3c5885d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c43fdddf24ee4d548364cd7bb3c5885d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c43fdddf24ee4d548364cd7bb3c5885d"}}, "title": "Structure of a functional obligate complex III 2IV2 respiratory supercomplex from Mycobacterium smegmatis.", "authors": [{"family": "Wiseman", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-2994-5839", "researcher": {"href": "https://publications.scilifelab.se/researcher/2098646fa9de4dbc8f7cca8aeabad319.json"}}, {"family": "Nitharwal", "given": "Ram Gopal", "initials": "RG"}, {"family": "Fedotovskaya", "given": "Olga", "initials": "O"}, {"family": "Sch\u00e4fer", "given": "Jacob", "initials": "J"}, {"family": "Guo", "given": "Hui", "initials": "H", "orcid": "0000-0001-7007-2876", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6a0383b19ff4fe78c32a07079f90a51.json"}}, {"family": "Kuang", "given": "Qie", "initials": "Q"}, {"family": "Benlekbir", "given": "Samir", "initials": "S"}, {"family": "Sj\u00f6strand", "given": "Dan", "initials": "D"}, {"family": "\u00c4delroth", "given": "Pia", "initials": "P"}, {"family": "Rubinstein", "given": "John L", "initials": "JL", "orcid": "0000-0003-0566-2209", "researcher": {"href": "https://publications.scilifelab.se/researcher/771d163fc4b543669ee8fd1148bfe24d.json"}}, {"family": "Brzezinski", "given": "Peter", "initials": "P", "orcid": "0000-0003-3860-4988", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3314030ecf94791a713a068d4926c20.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}], "type": "journal article", "published": "2018-12-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "25", "issue": "12", "pages": "1128-1136", "issn-l": "1545-9985"}, "abstract": "In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is coupled to transmembrane proton translocation, thus establishing the electrochemical proton gradient that drives ATP synthesis. We isolated, biochemically characterized, and determined the structure of the obligate III 2IV2 supercomplex from Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The supercomplex has quinol:O2 oxidoreductase activity without exogenous cytochrome c and includes a superoxide dismutase subunit that may detoxify reactive oxygen species produced during respiration. We found menaquinone bound in both the Qo and Qi sites of complex III. The complex III-intrinsic diheme cytochrome cc subunit, which functionally replaces both cytochrome c1 and soluble cytochrome c in canonical electron-transport chains, displays two conformations: one in which it provides a direct electronic link to complex IV and another in which it serves as an electrical switch interrupting the connection.", "doi": "10.1038/s41594-018-0160-3", "pmid": "30518849", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41594-018-0160-3"}], "notes": [], "created": "2019-08-01T08:29:50.182Z", "modified": "2021-06-21T13:56:08.387Z"}, {"entity": "publication", "iuid": "bb07ae26a72248d4bdeaf2ac8614f1c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb07ae26a72248d4bdeaf2ac8614f1c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb07ae26a72248d4bdeaf2ac8614f1c3"}}, "title": "Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.", "authors": [{"family": "Guettou", "given": "Fatma", "initials": "F"}, {"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "Raba", "given": "Michael", "initials": "M"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "21", "issn": "1545-9985", "issue": "8", "pages": "728-731", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Peptide transporters of the PepT family have key roles in the transport of di- and tripeptides across membranes as well as in the absorption of orally administered drugs in the small intestine. We have determined structures of a PepT transporter from Shewanella oneidensis (PepT(So2)) in complex with three different peptides. The peptides bind in a large cavity lined by residues that are highly conserved in human PepT1 and PepT2. The bound peptides adopt extended conformations with their N termini clamped into a conserved polar pocket. A positively charged patch allows differential interactions with the C-terminal carboxylates of di- and tripeptides. Here we identify three pockets for peptide side chain interactions, and our binding studies define differential roles of these pockets for the recognition of different subtypes of peptide side chains.", "doi": "10.1038/nsmb.2860", "pmid": "25064511", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2860"}, {"db": "PDB", "key": "4TPG"}, {"db": "PDB", "key": "4TPH"}, {"db": "PDB", "key": "4TPJ"}], "notes": [], "created": "2017-05-04T15:03:54.823Z", "modified": "2017-09-06T11:42:09.276Z"}, {"entity": "publication", "iuid": "ae4a9ad44aba43cc8e97105e9918c0cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae4a9ad44aba43cc8e97105e9918c0cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae4a9ad44aba43cc8e97105e9918c0cc"}}, "title": "Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity.", "authors": [{"family": "Sadeghi", "given": "Laia", "initials": "L"}, {"family": "Siggens", "given": "Lee", "initials": "L"}, {"family": "Svensson", "given": "J Peter", "initials": "JP"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "21", "issn": "1545-9985", "issue": "3", "pages": "236-243", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Functional centromeres are essential for proper cell division. Centromeres are established largely by epigenetic processes resulting in incorporation of the histone H3 variant CENP-A. Here, we demonstrate the direct involvement of H2B monoubiquitination, mediated by RNF20 in humans or Brl1 in Schizosaccharomyces pombe, in centromeric chromatin maintenance. Monoubiquinated H2B (H2Bub1) is needed for this maintenance, promoting noncoding transcription, centromere integrity and accurate chromosomal segregation. A transient pulse of centromeric H2Bub1 leads to RNA polymerase II-mediated transcription of the centromere's central domain, coupled to decreased H3 stability. H2Bub1-deficient cells have centromere cores that, despite their intact centromeric heterochromatin barriers, exhibit characteristics of heterochromatin, such as silencing histone modifications, reduced nucleosome turnover and reduced levels of transcription. In the H2Bub1-deficient cells, centromere functionality is hampered, thus resulting in unequal chromosome segregation. Therefore, centromeric H2Bub1 is essential for maintaining active centromeric chromatin.", "doi": "10.1038/nsmb.2776", "pmid": "24531659", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2776"}, {"db": "GEO", "key": "GSE49874"}], "notes": [], "created": "2017-05-04T15:03:19.948Z", "modified": "2017-05-30T12:42:32.004Z"}, {"entity": "publication", "iuid": "8073104337864e828f6d9304523cfb9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8073104337864e828f6d9304523cfb9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8073104337864e828f6d9304523cfb9b"}}, "title": "High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.", "authors": [{"family": "Anandapadamanaban", "given": "Madhanagopal", "initials": "M"}, {"family": "Andresen", "given": "Cecilia", "initials": "C"}, {"family": "Helander", "given": "Sara", "initials": "S"}, {"family": "Ohyama", "given": "Yoshifumi", "initials": "Y"}, {"family": "Siponen", "given": "Marina I", "initials": "MI"}, {"family": "Lundstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Kokubo", "given": "Tetsuro", "initials": "T"}, {"family": "Ikura", "given": "Mitsuhiko", "initials": "M"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "20", "issn": "1545-9985", "issue": "8", "pages": "1008-1014", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 \u00c5) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.", "doi": "10.1038/nsmb.2611", "pmid": "23851461", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2611"}, {"db": "pmc", "key": "PMC4972576"}, {"db": "mid", "key": "CAMS4086"}, {"db": "PDB", "key": "4B0A"}], "notes": [], "created": "2017-05-04T15:03:49.726Z", "modified": "2017-09-06T11:42:09.178Z"}, {"entity": "publication", "iuid": "cf2c496c7c344e5a8ad536c44367b83a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf2c496c7c344e5a8ad536c44367b83a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf2c496c7c344e5a8ad536c44367b83a"}}, "title": "Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.", "authors": [{"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "20", "issn": "1545-9985", "issue": "6", "pages": "766-768", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Here we present two structures of the major facilitator (MFS) xylose transporter XylE from Escherichia coli in inward open and partially occluded inward open conformations. These structures provide key information about the transport cycle of XylE and the closely related human GLUT transporters. This is, to our knowledge, the first MFS transporter structure determined in more than one conformational state, which may establish XylE as an important MFS model protein.", "doi": "10.1038/nsmb.2569", "pmid": "23624861", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2569"}, {"db": "PDB", "key": "4JA3"}, {"db": "PDB", "key": "4JA4"}], "notes": [], "created": "2017-05-04T15:03:49.415Z", "modified": "2017-09-06T11:42:09.361Z"}, {"entity": "publication", "iuid": "bb6519b0dd8d478ebba28f1e622005ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb6519b0dd8d478ebba28f1e622005ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb6519b0dd8d478ebba28f1e622005ec"}}, "title": "Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2011-11-06", "journal": {"volume": "18", "issn": "1545-9985", "issue": "12", "pages": "1435-1440", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Transcriptome sequencing allows for analysis of mature RNAs at base pair resolution. Here we show that RNA-seq can also be used for studying nascent RNAs undergoing transcription. We sequenced total RNA from human brain and liver and found a large fraction of reads (up to 40%) within introns. Intronic RNAs were abundant in brain tissue, particularly for genes involved in axonal growth and synaptic transmission. Moreover, we detected significant differences in intronic RNA levels between fetal and adult brains. We show that the pattern of intronic sequence read coverage is explained by nascent transcription in combination with co-transcriptional splicing. Further analysis of co-transcriptional splicing indicates a correlation between slowly removed introns and alternative splicing. Our data show that sequencing of total RNA provides unique insight into the transcriptional processes in the cell, with particular importance for normal brain development.", "doi": "10.1038/nsmb.2143", "pmid": "22056773", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2143"}], "notes": [], "created": "2017-05-04T14:57:22.242Z", "modified": "2021-07-08T12:52:24.403Z"}, {"entity": "publication", "iuid": "44a038e26eb24be997b53892bb9dd3ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44a038e26eb24be997b53892bb9dd3ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44a038e26eb24be997b53892bb9dd3ba"}}, "title": "Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.", "authors": [{"family": "Lantermann", "given": "Alexandra B", "initials": "AB"}, {"family": "Straub", "given": "Tobias", "initials": "T"}, {"family": "Str\u00e5lfors", "given": "Annelie", "initials": "A"}, {"family": "Yuan", "given": "Guo-Cheng", "initials": "GC"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Korber", "given": "Philipp", "initials": "P"}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "17", "issn": "1545-9985", "issue": "2", "pages": "251-257", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we have generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome wide. Using this resource, we found surprising differences from the previously published nucleosome organization of the distantly related yeast Saccharomyces cerevisiae. DNA sequence guides nucleosome positioning differently: for example, poly(dA-dT) elements are not enriched in S. pombe nucleosome-depleted regions. Regular nucleosomal arrays emanate more asymmetrically-mainly codirectionally with transcription-from promoter nucleosome-depleted regions, but promoters harboring the histone variant H2A.Z also show regular arrays upstream of these regions. Regular nucleosome phasing in S. pombe has a very short repeat length of 154 base pairs and requires a remodeler, Mit1, that is conserved in humans but is not found in S. cerevisiae. Nucleosome positioning mechanisms are evidently not universal but evolutionarily plastic.", "doi": "10.1038/nsmb.1741", "pmid": "20118936", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "nsmb.1741"}, {"db": "GEO", "key": "GSE16040"}], "notes": [], "created": "2017-05-04T15:03:08.130Z", "modified": "2017-05-30T14:50:29.888Z"}], "created": "2017-05-09T09:12:22.985Z", "modified": "2020-11-27T13:14:05.118Z"}