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1. Structural mechanism of extranucleosomal DNA readout by the INO80 complex

Author

Kunert, Franziska, Metzner, Felix J., Jung, James, Hoepfler, Markus, Woike, Stephan, Schall, Kevin, Kostrewa, Dirk, Moldt, Manuela, Chen, Jia-Xuan, Bantele, Susanne, Pfander, Boris, Eustermann, Sebastian, Hopfner, Karl-Peter, Kunert, Franziska, Metzner, Felix J., Jung, James, Hoepfler, Markus, Woike, Stephan, Schall, Kevin, Kostrewa, Dirk, Moldt, Manuela, Chen, Jia-Xuan, Bantele, Susanne, Pfander, Boris, Eustermann, Sebastian, and Hopfner, Karl-Peter

Abstract

The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo- electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.

Published
2022

2. Structural mechanism of extranucleosomal DNA readout by the INO80 complex

Author

Kunert, Franziska, Metzner, Felix J., Jung, James, Hopfler, Markus, Woike, Stephan, Schall, Kevin, Kostrewa, Dirk, Moldt, Manuela, Chen, Jia Xuan, Bantele, Susanne, Pfander, Boris, Eustermann, Sebastian, Hopfner, Karl Peter, Kunert, Franziska, Metzner, Felix J., Jung, James, Hopfler, Markus, Woike, Stephan, Schall, Kevin, Kostrewa, Dirk, Moldt, Manuela, Chen, Jia Xuan, Bantele, Susanne, Pfander, Boris, Eustermann, Sebastian, and Hopfner, Karl Peter

Abstract

The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.

Published
2022

3. Track Finding at Belle II

Author

Bertacchi, Valerio, Bilka, Tadeas, Braun, Nils, Casarosa, Giulia, Corona, Luigi, Cunliffe, Sam, Dattola, Filippo, De Marino, Gaetano, De Nuccio, Michael, De Pietro, Giacomo, Van Dong, Thanh, Dujany, Giulio, Ecker, Patrick, Eliachevitch, Michael, Fillinger, Tristan, Frost, Oliver, Fruehwirth, Rudolf, Gebauer, Uwe, Glazov, Alexander, Gosling, Nicolas, Guo, Aiqiang, Hauth, Thomas, Heck, Martin, Kaleta, Mateusz, Kandra, Jakub, Kleinwort, Claus, Kuhr, Thomas, Kurz, Simon, Kvasnicka, Peter, Lettenbichler, Jakob, Lueck, Thomas, Martini, Alberto, Metzner, Felix, Neverov, Dmitrii, Niebuhr, Carsten, Paoloni, Eugenio, Patra, Sourav, Piilonen, Leo, Praz, Cyrille, Prim, Markus Tobias, Pulvermacher, Christian, Racs, Sebastian, Rad, Navid, Rados, Petar, Ritter, Martin, Rizzo, Giuliana, Rostomyan, Armine, Scavino, Bianca, Schlueter, Tobias, Schwenker, Benjamin, Spataro, Stefano, Spruck, Bjoern, Svidras, Henrikas, Tenchini, Francesco, Uematsu, Yuma, Webb, James, Wessel, Christian, Zani, Laura, Bertacchi, Valerio, Bilka, Tadeas, Braun, Nils, Casarosa, Giulia, Corona, Luigi, Cunliffe, Sam, Dattola, Filippo, De Marino, Gaetano, De Nuccio, Michael, De Pietro, Giacomo, Van Dong, Thanh, Dujany, Giulio, Ecker, Patrick, Eliachevitch, Michael, Fillinger, Tristan, Frost, Oliver, Fruehwirth, Rudolf, Gebauer, Uwe, Glazov, Alexander, Gosling, Nicolas, Guo, Aiqiang, Hauth, Thomas, Heck, Martin, Kaleta, Mateusz, Kandra, Jakub, Kleinwort, Claus, Kuhr, Thomas, Kurz, Simon, Kvasnicka, Peter, Lettenbichler, Jakob, Lueck, Thomas, Martini, Alberto, Metzner, Felix, Neverov, Dmitrii, Niebuhr, Carsten, Paoloni, Eugenio, Patra, Sourav, Piilonen, Leo, Praz, Cyrille, Prim, Markus Tobias, Pulvermacher, Christian, Racs, Sebastian, Rad, Navid, Rados, Petar, Ritter, Martin, Rizzo, Giuliana, Rostomyan, Armine, Scavino, Bianca, Schlueter, Tobias, Schwenker, Benjamin, Spataro, Stefano, Spruck, Bjoern, Svidras, Henrikas, Tenchini, Francesco, Uematsu, Yuma, Webb, James, Wessel, Christian, and Zani, Laura

Abstract

This paper describes the track-finding algorithm that is used for event reconstruction in the Belle II experiment operating at the SuperKEKB B-factory in Tsukuba, Japan. The algorithm is designed to balance the requirements of a high efficiency to find charged particles with a good track parameter resolution, a low rate of spurious tracks, and a reasonable demand on CPU resources. The software is implemented in a flexible, modular manner and employs a diverse selection of global and local track-finding algorithms to achieve an optimal performance.

Published
2020
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4. The Full Event Interpretation -- An exclusive tagging algorithm for the Belle II experiment

Author

Keck, Thomas, Abudinen, Fernandi, Bernlochner, Florian U., Cheaib, Racha, Cunliffe, Sam, Feindt, Michael, Ferber, Torben, Gelb, Moritz, Gemmler, Jochen, Goldenzweig, Pablo, Heck, Martin, Hollitt, Sohpie, Kahn, James, Krohn, Jo-Frederik, Kuhr, Thomas, Komarov, Ilya, Ligioi, Luigi, Lubej, Matic, Metzner, Felix, Prim, Markus, Pulvermacher, Christian, Ritter, Martin, Schwab, Judith, Sutcliffe, William, Tamponi, Umberto, Tenchini, Francesco, Toutounji, Nadia E., Urquijo, Phillip, Weyland, Denis, Zupanc, Anze, Keck, Thomas, Abudinen, Fernandi, Bernlochner, Florian U., Cheaib, Racha, Cunliffe, Sam, Feindt, Michael, Ferber, Torben, Gelb, Moritz, Gemmler, Jochen, Goldenzweig, Pablo, Heck, Martin, Hollitt, Sohpie, Kahn, James, Krohn, Jo-Frederik, Kuhr, Thomas, Komarov, Ilya, Ligioi, Luigi, Lubej, Matic, Metzner, Felix, Prim, Markus, Pulvermacher, Christian, Ritter, Martin, Schwab, Judith, Sutcliffe, William, Tamponi, Umberto, Tenchini, Francesco, Toutounji, Nadia E., Urquijo, Phillip, Weyland, Denis, and Zupanc, Anze

Abstract

The Full Event Interpretation is presented: a new exclusive tagging algorithm used by the high-energy physics experiment Belle II. The experimental setup of Belle II allows the precise measurement of otherwise inaccessible $B$ meson decay-modes. The Full Event Interpretation algorithm enables many of these measurements. The algorithm relies on machine learning to automatically identify plausible $B$ meson decay chains based on the data recorded by the detector. Compared to similar algorithms employed by previous experiments, the Full Event Interpretation provides a greater efficiency, yielding a larger effective sample size usable in the measurement., Comment: 11 pages, 7 figures, 1 table

Published
2018
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5. The Full Event Interpretation -- An exclusive tagging algorithm for the Belle II experiment

Author

Keck, Thomas, Abudinen, Fernandi, Bernlochner, Florian U., Cheaib, Racha, Cunliffe, Sam, Feindt, Michael, Ferber, Torben, Gelb, Moritz, Gemmler, Jochen, Goldenzweig, Pablo, Heck, Martin, Hollitt, Sohpie, Kahn, James, Krohn, Jo-Frederik, Kuhr, Thomas, Komarov, Ilya, Ligioi, Luigi, Lubej, Matic, Metzner, Felix, Prim, Markus, Pulvermacher, Christian, Ritter, Martin, Schwab, Judith, Sutcliffe, William, Tamponi, Umberto, Tenchini, Francesco, Toutounji, Nadia E., Urquijo, Phillip, Weyland, Denis, Zupanc, Anze, Keck, Thomas, Abudinen, Fernandi, Bernlochner, Florian U., Cheaib, Racha, Cunliffe, Sam, Feindt, Michael, Ferber, Torben, Gelb, Moritz, Gemmler, Jochen, Goldenzweig, Pablo, Heck, Martin, Hollitt, Sohpie, Kahn, James, Krohn, Jo-Frederik, Kuhr, Thomas, Komarov, Ilya, Ligioi, Luigi, Lubej, Matic, Metzner, Felix, Prim, Markus, Pulvermacher, Christian, Ritter, Martin, Schwab, Judith, Sutcliffe, William, Tamponi, Umberto, Tenchini, Francesco, Toutounji, Nadia E., Urquijo, Phillip, Weyland, Denis, and Zupanc, Anze

Abstract

The Full Event Interpretation is presented: a new exclusive tagging algorithm used by the high-energy physics experiment Belle II. The experimental setup of Belle II allows the precise measurement of otherwise inaccessible $B$ meson decay-modes. The Full Event Interpretation algorithm enables many of these measurements. The algorithm relies on machine learning to automatically identify plausible $B$ meson decay chains based on the data recorded by the detector. Compared to similar algorithms employed by previous experiments, the Full Event Interpretation provides a greater efficiency, yielding a larger effective sample size usable in the measurement., Comment: 11 pages, 7 figures, 1 table

Published
2018
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6. B2BII - Data conversion from Belle to Belle II

Author

Gelb, Moritz, Keck, Thomas, Prim, Markus, Atmacan, Hulya, Gemmler, Jochen, Itoh, Ryosuke, Kronenbitter, Bastian, Kuhr, Thomas, Lubej, Matic, Metzner, Felix, Park, Chanseok, Park, Seokhee, Pulvermacher, Christian, Ritter, Martin, Zupanc, Anze, Gelb, Moritz, Keck, Thomas, Prim, Markus, Atmacan, Hulya, Gemmler, Jochen, Itoh, Ryosuke, Kronenbitter, Bastian, Kuhr, Thomas, Lubej, Matic, Metzner, Felix, Park, Chanseok, Park, Seokhee, Pulvermacher, Christian, Ritter, Martin, and Zupanc, Anze

Abstract

We describe the conversion of simulated and recorded data by the Belle experiment to the Belle~II format with the software package \texttt{b2bii}. It is part of the Belle~II Analysis Software Framework. This allows the validation of the analysis software and the improvement of analyses based on the recorded Belle dataset using newly developed analysis tools.

Published
2018
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