Bioinformatics Core Facility BMC
print


Breadcrumb Navigation


Content

Publications

2019

  • Cernilogar FM, Hasenöder S, Wang Z, Scheibner K, Burtscher I, Sterr M, Smialowski P, Groh S, Evenroed IM, Gilfillan GD, Lickert H, Schotta G. Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2. Nucleic Acids Res. 2019 Jul 27.doi: 10.1093/nar/gkz627
  • Prayitno K, Schauer T, Regnard C, Becker PB. Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement. EMBO Rep. 2019 Jul 9:e48138. doi: 10.15252/embr.201948138
  • Harpprecht L, Baldi S, Schauer T, Schmidt A, Bange T, Robles MS, Kremmer E, Imhof A, Becker PB. A Drosophila cell-free system that senses DNA breaks and triggers phosphorylation signalling. Nucleic Acids Res. 2019 May 31. pii: gkz473. doi: 10.1093/nar/gkz473
  • Borsos M, Perricone SM, Schauer T, Pontabry J, de Luca KL, de Vries SS, Ruiz-Morales ER, Torres-Padilla ME, Kind J. Genome-lamina interactions are established de novo in the early mouse embryo. Nature. 2019 May 22. doi:
    10.1038/s41586-019-1233-0.
  • Cooper JC, Lukacs A, Reich S, Schauer T, Imhof A, Phadnis N. Altered localization of hybrid incompatibility proteins in Drosophila. Mol Biol Evol. 2019 Apr 30. pii: msz105. doi: 10.1093/molbev/msz105
  • Höpfler M, Kern MJ, Straub T, Prytuliak R, Habermann BH, Pfander B, Jentsch S. Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance. EMBO J. 2019 Apr 23. pii: e100368. doi: 10.15252/embj.2018100368.
  • Pernice HF, Schieweck R, Jafari M, Straub T, Bilban M, Kiebler MA, Popper B. Altered Glutamate Receptor Ionotropic Delta Subunit 2 Expression in Stau2-Deficient Cerebellar Purkinje Cells in the Adult Brain. Int J Mol Sci. 2019
    Apr 11;20(7). doi: 10.3390/ijms20071797
  • Benitz S, Straub T, Mahajan UM, Mutter J, Czemmel S, Unruh T, Wingerath B, Deubler S, Fahr L, Cheng T, Nahnsen S, Bruns P, Kong B, Raulefs S, Ceyhan GO, Mayerle J, Steiger K, Esposito I, Kleeff J, Michalski CW, Regel I. Ring1b-dependent epigenetic remodelling is an essential prerequisite for pancreatic carcinogenesis. Gut. 2019 Apr 6.
    doi: 10.1136/gutjnl-2018-317208
  • Buschle A, Mrozek-Gorska P, Krebs S, Blum H, Cernilogar FM, Schotta G, Pich D, Straub T, Hammerschmidt W. Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation. bioRxiv. https://doi.org/10.1101/573659

2018

  • Baldi S, Jain DS, Harpprecht L, Zabel A, Scheibe M, Butter F, Straub T, Becker PB. Genome-wide Rules of Nucleosome Phasing in Drosophila. Mol Cell. 2018 Oct 19. pii: S1097-2765(18)30803-7. 
    doi: 10.1016/j.molcel.2018.09.032
  • Diana Pauly, Nicole Schäfer, Felix Grassmann, Anna M Pfaller, Tobias Straub, Bernhard HF Weber, Stefanie M. Hauck, Antje Grosche. Cell type-specific complement expression from healthy and diseased retinae. bioRxiv. https://doi.org/10.1101/413088
  • Angerilli A, Smialowski P, Rupp RA. The Xenopus animal cap transcriptome: building a mucociliary epithelium. The Xenopus animal cap transcriptome: building a mucociliary epithelium. Nucleic Acids Res. 2018 Aug 27. https://doi.org/10.1093/nar/gky771
  • Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA. 2018 Sep;24(9):1195-1213. https://doi.org/10.1261/rna.065524.118
  • Riedemann T, Straub T, Sutor B. Two types of somatostatin-expressing GABAergic interneurons in the superficial layers of the mouse cingulate cortex. PLoS One. 2018 Jul 12;13(7):e0200567. https://doi.org/10.1371/journal.pone.0200567
  • Salvermoser J, van Blijswijk J, Papaioannou NE, Rambichler S, Pasztoi M, Pakalniškytė D, Rogers NC, Keppler SJ, Straub T, Reis E Sousa C, Schraml BU. Clec9a-Mediated Ablation of Conventional Dendritic Cells Suggests a Lymphoid Path to Generating Dendritic Cells In Vivo. Front Immunol. 2018 Apr 16;9:699. https://doi.org/10.3389/fimmu.2018.00699
  • Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker. CHRAC/ACF Contribute to the Repressive Ground State of Chromatin. Life Science Alliance. Published 9 February 2018. https://doi.org/10.26508/lsa.201800024 

2017

  • Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker. CHRAC/ACF Contribute to the Repressive Ground State of Chromatin. bioRxiv. https://doi.org/10.1101/218768
  • Krendl C, Shaposhnikov D, Rishko V, Ori C, Ziegenhain C, Sass S, Simon L, Müller NS, Straub T, Brooks KE, Chavez SL, Enard W, Theis FJ, Drukker M. GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency. Proc Natl Acad Sci U S A. http://doi.org/10.1073/pnas.1708341114
  • Follwaczny P, Schieweck R, Riedemann T, Demleitner A, Straub T, Klemm AH, Bilban M, Sutor B, Popper B, Kiebler MA. Pumilio2 deficient mice show a predisposition for epilepsy.  Dis Model Mech. http://doi.org/10.1242/dmm.029678
  • Pünzeler S, Link S, Wagner G, Keilhauer EC, Kronbeck N, Spitzer RM, Leidescher S, Markaki Y, Mentele E, Regnard C, Schneider K, Takahashi D, Kusakabe M, Vardabasso C, Zink LM, Straub T, Bernstein E, Harata M, Leonhardt H, Mann M, Rupp RA, Hake SB. Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation. EMBO J. http://doi.org/10.15252/embj.201695757
  • Dillinger S, Straub T, Németh A. Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation. PLoS One http://doi.org/10.1371/journal.pone.0178821
  • Wagner G, Singhal N, Nicetto D, Straub T, Kremmer E, Rupp RAW. Brg1 chromatin remodeling ATPase balances germ layer patterning by amplifying the transcriptional burst at midblastula transition. PLoS Genet. doi: 10.1371/journal.pgen.1006757
  • Barthels C, Ogrinc A, Steyer V, Meier S, Simon F, Wimmer M, Blutke A, Straub T, Zimber-Strobl U, Lutgens E, Marconi P, Ohnmacht C, Garzetti D, Stecher B, Brocker T. CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis. Nat Commun. http://doi:10.1038/ncomms14715
  • Gerland, T. A., Sun, B., Smialowski, P., Lukacs, A., Thomae, A. W., & Imhof, A. The Drosophila speciation factor HMR localizes to genomic insulator sites. PloS One. http://doi.org/10.1371/journal.pone.0171798

2016

  • Jain, D.S., Baldi, S., Zabel, A., Straub, T., Becker P.B. Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF. bioRxiv. http://dx.doi.org/10.1101/093666
  • Villa R, Schauer T, Smialowski P, Straub T, Becker PB. PionX sites mark the X chromosome for dosage compensation. Nature. http://dx.doi.org/10.1038/nature19338
  • Dillinger S, Straub T, Németh A. Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation. bioRxiv. http://dx.doi.org/10.1101/054908
  • Kammerl IE, Dann A, Mossina A, Brech D, Lukas C, Vosyka O, Nathan P, Conlon TM, Wagner DE, Overkleeft HS, Prasse A, Rosas IO, Straub T, Krauss-Etschmann S, Königshoff M, Preissler G, Winter H, Lindner M, Hatz R, Behr J, Heinzelmann K, Yildirim AÖ, Noessner E, Eickelberg O, Meiners S. Impairment of Immunoproteasome Function by Cigarette Smoke and in COPD. American Journal of Respiratory and Critical Care Medicine. http://doi.org/10.1164/rccm.201506-1122OC
  • Peleg S, Feller C, Forne I, Schiller E, Sévin DC, Schauer T, Regnard C, Straub T, Prestel M, Klima C, Schmitt Nogueira M, Becker L, Klopstock T, Sauer U, Becker PB, Imhof A, Ladurner AG. Life span extension by targeting a link between metabolism and histone acetylation in Drosophila. EMBO Reports. http://doi.org/10.15252/embr.201541132
  • Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D. Heptad-Specific Phosphorylation of RNA Polymerase II CTD. Molecular Cell. http://doi.org/10.1016/j.molcel.2015.12.003

2015

  • Heiseke AF, Jeuk BH, Markota A, Straub T, Lehr HA, Reindl W, Krug AB. IRAK1 Drives Intestinal Inflammation by Promoting the Generation of Effector Th Cells with Optimal Gut-Homing Capacity. Journal of Immunology (Baltimore, Md. : 1950). http://doi.org/10.4049/jimmunol.1501874
  • Jain D, Baldi S, Zabel A, Straub T, Becker PB. Active promoters give rise to false positive “Phantom Peaks” in ChIP-seq experiments. Nucleic Acids Research. http://doi.org/10.1093/nar/gkv637
  • Pataskar A, Jung J, Smialowski P, Noack F, Calegari F, Straub T, Tiwari VK. NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. The EMBO Journal. http://doi.org/10.15252/embj.201591206
  • Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Chung CY, Yao JL, Singh R, Segura MF, Fontanals-Cirera B, Verma A, Mann M, Hernando E, Hake SB, Bernstein E. Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. Molecular Cell. http://doi.org/10.1016/j.molcel.2015.05.009

2013

  • Nicetto, D., Hahn, M., Jung, J., Schneider, T. D., Straub, T., David, R., et al. (2013). Suv4-20h histone methyltransferases promote neuroectodermal differentiation by silencing the pluripotency-associated oct-25 gene. PLoS Genetics, 9(1), e1003188. http://doi.org/10.1371/journal.pgen.1003188
  • Straub, T., & Becker, P. B. (2013). Comment on “Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters.” Science (New York, NY), 340(6130), 273. http://doi.org/10.1126/science.1231895
  • Taverna, M., Straub, T., Hampel, H., Rujescu, D., & Lichtenthaler, S. F. (2013). A New Sandwich Immunoassay for Detection of the α-Secretase Cleaved, Soluble Amyloid-β Protein Precursor in Cerebrospinal Fluid and Serum. Journal of Alzheimer's Disease : JAD. http://doi.org/10.3233/JAD-130509

2012

  • Eckey, M., Kuphal, S., Straub, T., Rümmele, P., Kremmer, E., Bosserhoff, A. K., & Becker, P. B. (2012). Nucleosome remodeler SNF2L suppresses cell proliferation and migration and attenuates Wnt signaling. Molecular and Cellular Biology. http://doi.org/10.1128/MCB.06619-11
  • Feller, C., Prestel, M., Hartmann, H., Straub, T., Soeding, J., & Becker, P. B. (2012). The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Research, 40(4), 1509–1522. http://doi.org/10.1093/nar/gkr869
  • Gilfillan, G. D., Hughes, T., Sheng, Y., Hjorthaug, H. S., Straub, T., Gervin, K., et al. (2012). Limitations and possibilities of low cell number ChIP-seq. BMC Genomics, 13, 645. http://doi.org/10.1186/1471-2164-13-645
  • Straub, T., Zabel, A., Gilfillan, G. D., Feller, C., & Becker, P. B. (2012). Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq. Genome Research. http://doi.org/10.1101/gr.146407.112
  • Villa, R., Forné, I., Müller, M., Imhof, A., Straub, T., & Becker, P. B. (2012). MSL2 Combines Sensor and Effector Functions in Homeostatic Control of the Drosophila Dosage Compensation Machinery. Molecular Cell. http://doi.org/10.1016/j.molcel.2012.09.012

before 2012

  • Bartkuhn, M., Straub, T., Herold, M., Herrmann, M., Rathke, C., Saumweber, H., et al. (2009). Active promoters and insulators are marked by the centrosomal protein 190. The EMBO Journal, 28(7), 877–888. http://doi.org/10.1038/emboj.2009.34
  • Bonaldi, T., Straub, T., Cox, J., Kumar, C., Becker, P. B., & Mann, M. (2008). Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular Cell, 31(5), 762–772. http://doi.org/10.1016/j.molcel.2008.07.018
  • Gilfillan, G. D., Straub, T., de Wit, E., Greil, F., Lamm, R., van Steensel, B., & Becker, P. B. (2006). Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. Genes & Development, 20(7), 858–870. http://doi.org/10.1101/gad.1399406
  • Lantermann, A. B., Straub, T., Strålfors, A., Yuan, G.-C., Ekwall, K., & Korber, P. (2010). Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nature Structural & Molecular Biology, 17(2), 251–257. http://doi.org/10.1038/nsmb.1741
  • Linder, B., Mentele, E., Mansperger, K., Straub, T., Kremmer, E., & Rupp, R. A. W. (2007). CHD4/Mi-2beta activity is required for the positioning of the mesoderm/neuroectoderm boundary in Xenopus. Genes & Development, 21(8), 973–983. http://doi.org/10.1101/gad.409507
  • Prestel, M., Feller, C., Straub, T., Mitlöhner, H., & Becker, P. B. (2010). The activation potential of MOF is constrained for dosage compensation. Molecular Cell, 38(6), 815–826. http://doi.org/10.1016/j.molcel.2010.05.022
  • Regnard, C., Straub, T., Mitterweger, A., Dahlsveen, I. K., Fabian, V., & Becker, P. B. (2011). Global analysis of the relationship between JIL-1 kinase and transcription. PLoS Genetics, 7(3), e1001327. http://doi.org/10.1371/journal.pgen.1001327
  • Straub, T., Gilfillan, G. D., Maier, V. K., & Becker, P. B. (2005a). The Drosophila MSL complex activates the transcription of target genes. Genes & Development, 19(19), 2284–2288. http://doi.org/10.1101/gad.1343105
  • Straub, T., Grimaud, C., Gilfillan, G. D., Mitterweger, A., & Becker, P. B. (2008). The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex. PLoS Genetics, 4(12), e1000302. http://doi.org/10.1371/journal.pgen.1000302
  • Wiedemann, S. M., Mildner, S. N., Boenisch, C., Israel, L., Maiser, A., Matheisl, S., et al. (2010). Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. The Journal of Cell Biology, 190(5), 777–791. http://doi.org/10.1083/jcb.201002043