4 Works

Data from: Genome dynamics of hybrid Saccharomyces cerevisiae during vegetative and meiotic divisions

Abhishek Dutta, , Ajith V. Pankajam, Parijat Chakraborty, Nahush Bhat, Lars M. Steinmetz & Nishant K. Thazath
Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid...

Data from: Nuclear microenvironments modulate transcription from low-affinity enhancers

Albert Tsai, Anand K. Muthusamy, Mariana R. P. Alves, Luke D. Lavis, Robert H. Singer, David L. Stern, Justin Crocker & Mariana RP Alves
Transcription factors bind low-affinity DNA sequences for only short durations. It is not clear how brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) utilizes low-affinity binding sites in the Drosophila melanogaster shavenbaby (svb) locus and related enhancers in nuclear microenvironments of high Ubx concentrations. Related enhancers colocalize to the same microenvironments independently of their chromosomal location, suggesting that microenvironments are highly differentiated transcription domains. Manipulating the affinity...

Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding

Manuel Alonso Y. Adell, Simona M. Migliano, Srigokul Upadhyayula, Yury S. Bykov, Simon Sprenger, Mehrshad Pakdel, Georg F. Vogel, Gloria Jih, Wesley Skillern, Reza Behrouzi, Markus Babst, Oliver Schmidt, Michael W. Hess, John A.G. Briggs, Tomas Kirchhausen, David Teis & John AG Briggs
The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3-45 second lifetimes, the ESCRT-III assemblies accumulated 75-200 Snf7 and 15-50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady...

Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Ramasubramanian Sundaramoorthy, Amanda L. Hughes, Vijender Singh, Nicola Wiechens, Daniel P. Ryan, Hassane El-Mkami, Maxim Petoukhov, Dmitri I. Svergun, Barbara Treutlein, Salina Quack, Monika Fischer, Jens Michaelis, Bettina Böttcher, David G. Norman & Tom Owen-Hughes
The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this...

Registration Year

  • 2017
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  • Dataset
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Affiliations

  • European Molecular Biology Laboratory
    4
  • European Molecular Biology Laboratory
    2
  • Howard Hughes Medical Institute
    1
  • Stanford University
    1
  • University of St Andrews
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  • University of Ulm
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  • University of Dundee
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  • University of Utah
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  • Harvard Medical School
    1
  • Max Planck Institute of Biochemistry
    1