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PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information

Antonia Lock, Kim Rutherford, Midori A Harris, Jacqueline Hayles, Stephen G Oliver, Jürg Bähler, Valerie Wood
2018 Nucleic Acids Research  
An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genomescale datasets.  ...  PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service  ...  ACKNOWLEDGEMENTS PomBase thanks the fission yeast community for dataset and literature curation contributions, valuable feedback on the website and their continued support.  ... 
doi:10.1093/nar/gky961 pmid:30321395 fatcat:5na6ieqhfjfaxjoysutm3x2kmq

Human Sulfotransferase Assays With PAPS Production in situ

Yanan Sun, Lukas Corbinian Harps, Matthias Bureik, Maria Kristina Parr
2022 Frontiers in Molecular Biosciences  
In the present study, we developed and optimized a new approach that combines SULT-dependent biotransformation using recombinant and permeabilized fission yeast cells (enzyme bags) with PAPS production  ...  The concomitant degradation of some sulfoconjugates was investigated, and further optimization of the reaction conditions was performed in order to reduce product loss.  ...  PomBase 2018: User-Driven Reimplementation of the Fission Yeast Database Provides Rapid and Intuitive Access to Diverse, Interconnected Information.  ... 
doi:10.3389/fmolb.2022.827638 pmid:35281274 pmcid:PMC8914157 fatcat:xxwfggjlubdwvc2yu4h2e4u5me

Nucleosome-constrained loop extrusion model for the origin of topologically associating domains [article]

Mary Lou P. Bailey, Ivan Surovtsev, Jessica F. Williams, Hao Yan, Simon G. J. Mochrie, Megan C. King
2020 bioRxiv   pre-print
Overall, this work reveals new tenets for the origins of TADs in eukaryotes, driven by transcription-coupled nucleosome remodeling.  ...  Here, we combine experimental measurements of chromatin dynamics in vivo with simulations to further develop the LEF model.  ...  We also thank the Yeast Genome Resource Center at Osaka University and the many investigators who have deposited strains at this resource. This work was supported by an NSF EFRI CEE  ... 
doi:10.1101/2020.02.29.969683 fatcat:l3cyzw74fzam7bnbdkopbtj66a

Reconstitution of Microtubule Nucleation In Vitro Reveals Novel Roles for Mzt1

Su Ling Leong, Eric M. Lynch, Juan Zou, Ye Dee Tay, Weronika E. Borek, Maarten W. Tuijtel, Juri Rappsilber, Kenneth E. Sawin
2019 Current Biology  
Many insights into γ-TuC regulators have come from in vivo analysis in fission yeast Schizosaccharomyces pombe.  ...  The S. pombe CM1 protein Mto1 recruits the γ-TuC to microtubule-organizing centers (MTOCs) [14, 20-22], and analysis of Mto1[bonsai], a truncated version of Mto1 that cannot localize to MTOCs, has shown  ...  The authors declare no competing interests.  ... 
doi:10.1016/j.cub.2019.05.058 pmid:31287970 pmcid:PMC6616311 fatcat:5e2whpuhprbm7a4b4bi6jbr7pq

An analysis of intrinsic base substitution patterns in diverse species reveals connections to cancer and metabolism [article]

Kin Chan, Kassidy N Doherty, Salma Alasmar
2019 bioRxiv   pre-print
Signature 5 is ubiquitous in cancers and normal human cells, suggesting that the similar patterns of mutation across many species are likely due to conserved biochemical processes.  ...  nucleotide polymorphisms (SNPs) in 41 species from the NCBI SNP database (>603 million SNPs).  ...  Bähler, V. 29 Wood, PomBase 2018: user-driven reimplementation of the fission yeast da-30 tabase provides rapid and intuitive access to diverse, interconnected infor-31 mation.  ... 
doi:10.1101/758540 fatcat:xewx6nizrvajhcnivw72p2e7cm

Size-independent mRNA synthesis and chromatin-based partitioning mechanisms generate and maintain constant amounts of protein per cell [article]

Matthew P Swaffer, Devon Chandler-Brown, Maurice Langhinrichs, Georgi Marinov, William Greenleaf, Anshul Kundaje, Kurt M Schmoller, Jan M Skotheim
2020 bioRxiv   pre-print
As an exception, the budding yeast cell-cycle inhibitor Whi5 is synthesized in a constant amount per cell cycle, so that it is diluted in large cells to trigger division.  ...  A screen for similar genes identified histones as the major class of size-independent transcripts during the cell cycle, consistent with histone synthesis being coupled to genome content rather than cell  ...  We would like to thank Bruce Futcher and Yuping Chen for invaluable advice on 530 centrifugal elutriation, members of the Skotheim laboratory for constructive feedback, Gabriel Neurohr  ... 
doi:10.1101/2020.08.28.272690 fatcat:yvicphmlufgdli2olbgtuzxd4m

Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes [article]

Alberto Elias-Villalobos, Damien Toullec, Celine Faux, Martial Seveno, Dom Helmlinger
2019 bioRxiv   pre-print
Using fission yeast, which contain two functionally non-redundant paralogs of the shared Tra1 subunit, we demonstrate that Tra1 contributes to scaffolding the entire NuA4 complex.  ...  Overall, our work brings mechanistic insights into the de novo assembly of transcriptional complexes through ordered pathways and reveals the contribution of dedicated chaperones to this process.  ...  Biol. , Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J & Wood V (2018) PomBase 26 2018: user-driven reimplementation of the fission yeast database provides rapid and 27 intuitive access to diverse  ... 
doi:10.1101/524959 fatcat:zp3lijrgt5gm3ae5u55t4dcrbe

Referee report. For: SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast [version 1; peer review: 2 approved]

Sophie Martin
2020
PubMed Abstract | Publisher Full Text | Free Full Text Lock A, Rutherford K, Harris MA, et al.: PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access  ...  to diverse, interconnected information.  ...  We thank members of the Allshire lab for valuable discussions.  ... 
doi:10.21956/wellcomeopenres.18048.r41573 fatcat:vhugpnh7nnh6bfl3r34g6ocj6u