Publications | IMP Scientific Papers | Research Institute of Molecular Pathology (IMP)

de Almeida, BP., Schaub, C., Pagani, M., Secchia, S., Furlong, EEM., Stark, A. (2024)

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.

Nature. 626(7997):207-211

Lorenzo-Orts, L., Strobl, M., Steinmetz, B., Leesch, F., Pribitzer, C., Roehsner, J., Schutzbier, M., Dürnberger, G., Pauli, A. (2024)

eIF4E1b is a non-canonical eIF4E protecting maternal dormant mRNAs.

Corresponding preprint EMBO Rep. 25(1):404-427

Ciriello, G., Magnani, L., Aitken, SJ., Akkari, L., Behjati, S., Hanahan, D., Landau, DA., Lopez-Bigas, N., Lupiáñez, DG., Marine, JC., Martin-Villalba, A., Natoli, G., Obenauf, AC., Oricchio, E., Scaffidi, P., Sottoriva, A., Swarbrick, A., Tonon, G., Vanharanta, S., Zuber, J. (2024)

Cancer Evolution: A Multifaceted Affair.

Cancer Discov. 14(1):36-48

Lorenzo-Orts, L., Pauli, A. (2024)

The molecular mechanisms underpinning maternal mRNA dormancy.

Biochem Soc Trans.

Riabov Bassat, D., Visanpattanasin, S., Vorländer, MK., Fin, L., Phillips, AW., Plaschka, C. (2024)

Structural basis of human U5 snRNP late biogenesis and recycling.

Nat Struct Mol Biol.

Pinheiro, D., Mitchel, J. (2024)

Pulling the strings on solid-to-liquid phase transitions in cell collectives.

Curr Opin Cell Biol. 86:102310

Vogel, A., Arnese, R., Gudino Carrillo, RM., Sehr, D., Deszcz, L., Bylicki, A., Meinhart, A., Clausen, T. (2024)

UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome.

Nat Commun. 15(1):6272

Vorländer, MK., Rothe, P., Kleifeld, J., Cormack, ED., Veleti, L., Riabov-Bassat, D., Fin, L., Phillips, AW., Cochella, L., Plaschka, C. (2024)

Mechanism for the initiation of spliceosome disassembly.

Nature. 632(8024):443-450

Fedl, AS., Tagoh, H., Gruenbacher, S., Sun, Q., Schenk, RL., Froussios, K., Jaritz, M., Busslinger, M., Schwickert, TA. (2024)

Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development.

Nat Immunol. 25(9):1663-1677

Deneke, VE., Blaha, A., Lu, Y., Suwita, JP., Draper, JM., Phan, CS., Panser, K., Schleiffer, A., Jacob, L., Humer, T., Stejskal, K., Krssakova, G., Roitinger, E., Handler, D., Kamoshita, M., Vance, TDR., Wang, X., Surm, JM., Moran, Y., Lee, JE., Ikawa, M., Pauli, A. (2024)

A conserved fertilization complex bridges sperm and egg in vertebrates.

Corresponding preprint Cell.

Leesch, F., Lorenzo-Orts, L., Pribitzer, C., Grishkovskaya, I., Roehsner, J., Chugunova, A., Matzinger, M., Roitinger, E., Belačić, K., Kandolf, S., Lin, TY., Mechtler, K., Meinhart, A., Haselbach, D., Pauli, A. (2023)

A molecular network of conserved factors keeps ribosomes dormant in the egg.

Corresponding preprint Nature.

Klaus, L., de Almeida, BP., Vlasova, A., Nemčko, F., Schleiffer, A., Bergauer, K., Hofbauer, L., Rath, M., Stark, A. (2023)

Systematic identification and characterization of repressive domains in Drosophila transcription factors.

EMBO J. 42(3):e112100

Leiendecker, L., Neumann, T., Jung, PS., Cronin, SM., Steinacker, TL., Schleiffer, A., Schutzbier, M., Mechtler, K., Kervarrec, T., Laurent, E., Bachiri, K., Coyaud, E., Murali, R., Busam, KJ., Itzinger-Monshi, B., Kirnbauer, R., Cerroni, L., Calonje, E., Rütten, A., Stubenrauch, F., Griewank, KG., Wiesner, T., Obenauf, AC. (2023)

Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers.

Cancer Discov. 13(1):70-84

Taniguchi-Sugiura, Y., Tanaka, EM. (2023)

Artificial Insemination in Axolotl.

Methods Mol Biol. 2562:417-423

Murawala, P., Oliveira, CR., Okulski, H., Yun, MH., Tanaka, EM. (2023)

Baculovirus Production and Infection in Axolotls.

Methods Mol Biol. 2562:369-387

Kawaguchi, A., Tanaka, EM. (2023)

Chromosome Conformation Capture for Large Genomes.

Methods Mol Biol. 2562:291-318

Nowoshilow, S., Tanaka, EM. (2023)

Navigation and Use of Custom Tracks within the Axolotl Genome Browser.

Methods Mol Biol. 2562:273-289

Masselink, W., Tanaka, EM. (2023)

Ethyl Cinnamate-Based Tissue Clearing Strategies.

Methods Mol Biol. 2562:123-133

Amann, SJ., Keihsler, D., Bodrug, T., Brown, NG., Haselbach, D. (2023)

Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM.

Structure. 31(1):4-19

Reiter, F., de Almeida, BP., Stark, A. (2023)

Enhancers display constrained sequence flexibility and context-specific modulation of motif function.

Genome Res.

Schmoellerl, J., Barbosa, IAM., Minnich, M., Andersch, F., Smeenk, L., Havermans, M., Eder, T., Neumann, T., Jude, J., Fellner, M., Ebert, A., Steininger, M., Delwel, R., Grebien, F., Zuber, J. (2023)

EVI1 drives leukemogenesis through aberrant ERG activation.

Blood. 141(5):453-466

Pacheco-Fiallos, B., Vorländer, MK., Riabov-Bassat, D., Fin, L., O'Reilly, FJ., Ayala, FI., Schellhaas, U., Rappsilber, J., Plaschka, C. (2023)

mRNA recognition and packaging by the human transcription-export complex.

Nature.

Davidson, IF., Barth, R., Zaczek, M., van der Torre, J., Tang, W., Nagasaka, K., Janissen, R., Kerssemakers, J., Wutz, G., Dekker, C., Peters, JM. (2023)

CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion.

Corresponding preprint Nature. 616(7958):822-827

Hoi, DM., Junker, S., Junk, L., Schwechel, K., Fischel, K., Podlesainski, D., Hawkins, PME., van Geelen, L., Kaschani, F., Leodolter, J., Morreale, FE., Kleine, S., Guha, S., Rumpel, K., Schmiedel, VM., Weinstabl, H., Meinhart, A., Payne, RJ., Kaiser, M., Hartl, M., Boehmelt, G., Kazmaier, U., Kalscheuer, R., Clausen, T. (2023)

Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.

Cell. 186(10):2176-2192.e22

Ishihara, K., Mukherjee, A., Gromberg, E., Brugués, J., Tanaka, EM., Jülicher, F. (2023)

Topological morphogenesis of neuroepithelial organoids.

Nat Phys. 19(2):177-183

Gert, KRB., Panser, K., Surm, J., Steinmetz, BS., Schleiffer, A., Jovine, L., Moran, Y., Kondrashov, F., Pauli, A. (2023)

Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries.

Corresponding preprint Nat Commun. 14(1):3506

Jacobs, J., Pagani, M., Wenzl, C., Stark, A. (2023)

Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila.

Science. 381(6654):198-204

Gruenbacher, S., Jaritz, M., Hill, L., Schäfer, M., Busslinger, M. (2023)

Essential role of the Pax5 C-terminal domain in controlling B cell commitment and development.

J Exp Med. 220(12)

Hill, L., Jaritz, M., Tagoh, H., Schindler, K., Kostanova-Poliakova, D., Sun, Q., Schwickert, TA., Leeb, M., Busslinger, M. (2023)

Enhancers of the PAIR4 regulatory module promote distal VH gene recombination at the Igh locus.

EMBO J. 42(15):e112741

Hodáková, Z., Grishkovskaya, I., Brunner, HL., Bolhuis, DL., Belačić, K., Schleiffer, A., Kotisch, H., Brown, NG., Haselbach, D. (2023)

Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5.

EMBO J. 42(16):e113348

Pinheiro, D. (2023)

How embryos sort themselves out.

Nat Rev Mol Cell Biol. 24(12):856

Falcon, F., Tanaka, EM., Rodriguez-Terrones, D. (2023)

Transposon waves at the water-to-land transition.

Curr Opin Genet Dev. 81:102059

Jessberger, G., Várnai, C., Stocsits, RR., Tang, W., Stary, G., Peters, JM. (2023)

Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei.

Genome Res. 33(12):2094-107

Otsuki, L., Tanaka, EM. (2022)

Positional Memory in Vertebrate Regeneration: A Century's Insights from the Salamander Limb.

Cold Spring Harb Perspect Biol. 14(6)

Binner, MI., Kogan, A., Panser, K., Schleiffer, A., Deneke, VE., Pauli, A. (2022)

The Sperm Protein Spaca6 is Essential for Fertilization in Zebrafish.

Corresponding preprint Front Cell Dev Biol. 9:806982

Peycheva, M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, UE., Pavri, R. (2022)

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations.

Science. 377(6612):eabj5502

Kaiser, FMP., Gruenbacher, S., Oyaga, MR., Nio, E., Jaritz, M., Sun, Q., van der Zwaag, W., Kreidl, E., Zopf, LM., Dalm, VASH., Pel, J., Gaiser, C., van der Vliet, R., Wahl, L., Rietman, A., Hill, L., Leca, I., Driessen, G., Laffeber, C., Brooks, A., Katsikis, PD., Lebbink, JHG., Tachibana, K., van der Burg, M., De Zeeuw, CI., Badura, A., Busslinger, M. (2022)

Biallelic PAX5 mutations cause hypogammaglobulinemia, sensorimotor deficits, and autism spectrum disorder.

J Exp Med. 219(9)

Morreale, FE., Kleine, S., Leodolter, J., Junker, S., Hoi, DM., Ovchinnikov, S., Okun, A., Kley, J., Kurzbauer, R., Junk, L., Guha, S., Podlesainski, D., Kazmaier, U., Boehmelt, G., Weinstabl, H., Rumpel, K., Schmiedel, VM., Hartl, M., Haselbach, D., Meinhart, A., Kaiser, M., Clausen, T. (2022)

BacPROTACs mediate targeted protein degradation in bacteria.

Corresponding preprint Cell. 185(13):2338-2353.e18

Neumayr, C., Haberle, V., Serebreni, L., Karner, K., Hendy, O., Boija, A., Henninger, JE., Li, CH., Stejskal, K., Lin, G., Bergauer, K., Pagani, M., Rath, M., Mechtler, K., Arnold, CD., Stark, A. (2022)

Differential cofactor dependencies define distinct types of human enhancers.

Nature. 606(7913):406-413

de Almeida, BP., Reiter, F., Pagani, M., Stark, A. (2022)

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.

Nat Genet. 54(5):613-624

Jurado, S., Fedl, AS., Jaritz, M., Kostanova-Poliakova, D., Malin, SG., Mullighan, CG., Strehl, S., Fischer, M., Busslinger, M. (2022)

The PAX5-JAK2 translocation acts as dual-hit mutation that promotes aggressive B-cell leukemia via nuclear STAT5 activation.

EMBO J. 41(7):e108397

Rauschmeier, R., Reinhardt, A., Gustafsson, C., Glaros, V., Artemov, AV., Dunst, J., Taneja, R., Adameyko, I., Månsson, R., Busslinger, M., Kreslavsky, T. (2022)

Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis.

J Exp Med. 219(2)

Nemčko, F., Stark, A. (2022)

Proteome-scale identification of transcriptional activators in human cells.

Mol Cell. 82(3):497-499

Pre-printSchoeberl, U. E., Fitz, J., Froussios, K., Valieris, R., Makharova, M., Ourailidis, I., Bauer, B., Neumann, T., Wiedemann, E., Steininger, M., Garcia, A. C., Mastrovito, M., Mouquet, H., Tojal Da Silva, I., Pavri, R. (2022)

Somatic hypermutation spectra are independent of the local transcriptional and epigenetic landscape

bioRxiv . 2022.05.21.492925

Pinter, T., Fischer, M., Schäfer, M., Fellner, M., Jude, J., Zuber, J., Busslinger, M., Wöhner, M. (2022)

Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development.

Front Immunol. 13:979606

Obenauf, AC. (2022)

Mechanism-based combination therapies for metastatic cancer.

Sci Transl Med. 14(655):eadd0887

Stock, J., Kazmar, T., Schlumm, F., Hannezo, E., Pauli, A. (2022)

A self-generated Toddler gradient guides mesodermal cell migration.

Corresponding preprint Sci Adv. 8(37):eadd2488

Vorländer, MK., Pacheco-Fiallos, B., Plaschka, C. (2022)

Structural basis of mRNA maturation: Time to put it together.

Curr Opin Struct Biol. 75:102431

Hendy, O., Serebreni, L., Bergauer, K., Muerdter, F., Huber, L., Nemčko, F., Stark, A. (2022)

Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers.

Mol Cell. 82(19):3598-3612.e7

Lust, K., Maynard, A., Gomes, T., Fleck, JS., Camp, JG., Tanaka, EM., Treutlein, B. (2022)

Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration.

Science. 377(6610):eabp9262

Polikarpova, A., Ellinghaus, A., Schmidt-Bleek, O., Grosser, L., Bucher, CH., Duda, GN., Tanaka, EM., Schmidt-Bleek, K. (2022)

The specialist in regeneration-the Axolotl-a suitable model to study bone healing?

NPJ Regen Med. 7(1):35

Glotzer, GL., Tardivo, P., Tanaka, EM. (2022)

Canonical Wnt signaling and the regulation of divergent mesenchymal Fgf8 expression in axolotl limb development and regeneration.

Elife. 11

Lin, TY., Taniguchi-Sugiura, Y., Murawala, P., Hermann, S., Tanaka, EM. (2022)

Inducible and tissue-specific cell labeling in Cre-ERT2 transgenic Xenopus lines.

Dev Growth Differ. 64(5):243-253

Echeverri, K., Fei, J., Tanaka, EM. (2022)

The Axolotl's journey to the modern molecular era.

Curr Top Dev Biol. 147:631-658

Zhong, Y., Walker, SK., Pritykin, Y., Leslie, CS., Rudensky, AY., van der Veeken, J. (2022)

Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families.

Nat Immunol. 23(1):122-134

Wöhner, M., Pinter, T., Bönelt, P., Hagelkruys, A., Kostanova-Poliakova, D., Stadlmann, J., Konieczny, SF., Fischer, M., Jaritz, M., Busslinger, M. (2022)

The Xbp1-regulated transcription factor Mist1 restricts antibody secretion by restraining Blimp1 expression in plasma cells.

Front Immunol. 13:859598

Wu, SS., Lee, H., Szép-Bakonyi, R., Colozza, G., Boese, A., Gert, KR., Hallay, N., Lee, JH., Kim, J., Zhu, Y., Linssen, MM., Pilat-Carotta, S., Hohenstein, P., Theussl, HC., Pauli, A., Koo, BK. (2022)

SCON-a Short Conditional intrON for conditional knockout with one-step zygote injection.

Corresponding preprint Exp Mol Med.

Pre-printAhel J, Fletcher A, Grabarczyk DB, Roitinger E, Deszcz L, Lehner A, Virdee S, Clausen T. (2021)

E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

bioRxiv. 2021.05.10.443411

Cabrera-Quio, LE., Schleiffer, A., Mechtler, K., Pauli, A. (2021)

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition.

PLoS Genet. 17(2):e1009390

Cura Costa, E., Otsuki, L., Rodrigo Albors, A., Tanaka, EM., Chara, O. (2021)

Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration.

Elife. 10

Davidson, IF., Peters, JM. (2021)

Genome folding through loop extrusion by SMC complexes.

Nat Rev Mol Cell Biol. 22(7):445-464

Pre-printKellner MJ, Matl M, Ross JJ, Schnabl J, Handler D, Heinen R, Schaeffer J, Hufnagl P, Indra A, Dekens MPS, Fritsche-Polanz R, Födinger M, Zuber J, Vienna Covid-19 Detection Initiative (VCDI), Allerberger F, Pauli A, Brennecke J (2021)

Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics.

medRxiv. 2021.01.19.21250079

Deneke, VE., Pauli, A. (2021)

The Fertilization Enigma: How Sperm and Egg Fuse.

Annu Rev Cell Dev Biol.

Hajdusits, B., Suskiewicz, MJ., Hundt, N., Meinhart, A., Kurzbauer, R., Leodolter, J., Kukura, P., Clausen, T. (2021)

McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.

Corresponding preprint Elife. 10

Grabarczyk, DB., Petrova, OA., Deszcz, L., Kurzbauer, R., Murphy, P., Ahel, J., Vogel, A., Gogova, R., Faas, V., Kordic, D., Schleiffer, A., Meinhart, A., Imre, R., Lehner, A., Neuhold, J., Bader, G., Stolt-Bergner, P., Böttcher, J., Wolkerstorfer, B., Fischer, G., Grishkovskaya, I., Haselbach, D., Kessler, D., Clausen, T. (2021)

HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain.

Nat Chem Biol.

Fujihara, Y., Herberg, S., Blaha, A., Panser, K., Kobayashi, K., Larasati, T., Novatchkova, M., Theussl, HC., Olszanska, O., Ikawa, M., Pauli, A. (2021)

The conserved fertility factor SPACA4/Bouncer has divergent modes of action in vertebrate fertilization.

Corresponding preprint Proc Natl Acad Sci U S A. 118(39)

Calderón, L., Schindler, K., Malin, SG., Schebesta, A., Sun, Q., Schwickert, T., Alberti, C., Fischer, M., Jaritz, M., Tagoh, H., Ebert, A., Minnich, M., Liston, A., Cochella, L., Busslinger, M. (2021)

Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation.

Sci Immunol. 6(61)

Haas L, Elewaut A, Gerard CL, Umkehrer C, Pedersen M, Leiendecker L, Krecioch I, Hoffmann D, Novatchkova M, Kuttke M, Neumann T, Pires de Silva I, Witthock H, Cuendet MA, Carotta S, Harrington KJ, Zuber J, Scolyer RA, Long GV, Wilmott JS, Michielin O, Vanharanta S, Wiesner T, Obenauf AC. (2021)

Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma

Nature Cancer . 2:693–708

Pre-printGert,KR., Cabrera Quio,LE., Novatchkova,M., Guo,Y., Cairns,BR., Pauli,A. (2021)

Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

bioRxiv . 2021.11.03.467109

Bauer, BW., Davidson, IF., Canena, D., Wutz, G., Tang, W., Litos, G., Horn, S., Hinterdorfer, P., Peters, JM. (2021)

Cohesin mediates DNA loop extrusion by a "swing and clamp" mechanism.

Cell. 184(21):5448-5464.e22

de Almeida, M., Hinterndorfer, M., Brunner, H., Grishkovskaya, I., Singh, K., Schleiffer, A., Jude, J., Deswal, S., Kalis, R., Vunjak, M., Lendl, T., Imre, R., Roitinger, E., Neumann, T., Kandolf, S., Schutzbier, M., Mechtler, K., Versteeg, GA., Haselbach, D., Zuber, J. (2021)

AKIRIN2 controls the nuclear import of proteasomes in vertebrates.

Nature. 599(7885):491-496

Gutiérrez-Pérez, P., Santillán, EM., Lendl, T., Wang, J., Schrempf, A., Steinacker, TL., Asparuhova, M., Brandstetter, M., Haselbach, D., Cochella, L. (2021)

miR-1 sustains muscle physiology by controlling V-ATPase complex assembly.

Sci Adv. 7(42):eabh1434

Leiendecker, L., Jung, PS., Obenauf, AC. (2021)

Targeting CD56 with an antibody-drug conjugate in Merkel cell carcinoma.

Br J Dermatol.

Bassat, E., Tanaka, EM. (2021)

The cellular and signaling dynamics of salamander limb regeneration.

Curr Opin Cell Biol. 73:117-123

Smeenk, L., Ottema, S., Mulet-Lazaro, R., Ebert, A., Havermans, M., Varea, AA., Fellner, M., Pastoors, D., van Herk, S., Erpelinck-Verschueren, C., Grob, T., Hoogenboezem, RM., Kavelaars, FG., Matson, DR., Bresnick, EH., Bindels, EM., Kentsis, A., Zuber, J., Delwel, R. (2021)

Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia.

Cancer Discov. 11(11):2868-2883

Haas, L., Elewaut, A., Gerard, CL., Umkehrer, C., Leiendecker, L., Pedersen, M., Krecioch, I., Hoffmann, D., Novatchkova, M., Kuttke, M., Neumann, T., da Silva, IP., Witthock, H., Cuendet, MA., Carotta, S., Harrington, KJ., Zuber, J., Scolyer, RA., Long, GV., Wilmott, JS., Michielin, O., Vanharanta, S., Wiesner, T., Obenauf, AC. (2021)

Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma.

Nat Cancer. 2(7):693-708

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