Use of the ND evidence code for Gene Ontology (GO) terms
Annotation inferences using phylogenetic trees
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Electronic Gene Ontology annotations created by ARBA machine learning models
Molecular analysis of Saccharomyces cerevisiae chromosome I. On the number of genes and the identification of essential genes using temperature-sensitive-lethal mutations.
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FUN19 was defined during the molecular analysis of chromosome I and shown to be non-essential; at the time its predicted product showed no significant homology to known proteins.
"FUN19 itself proved to be non-essential."
Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes.
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The SWIRM domain is a chromatin-associated module found in Swi3, Rsc8, Ada2 and LSD1; the Swi3 SWIRM binds DNA and nucleosomes and SWIRM domains are required for assembly and in vivo function of their complexes.
"The SWIRM domain is a module found in the Swi3 and Rsc8 subunits of SWI/SNF-family chromatin remodeling complexes, and the Ada2 and BHC110/LSD1 subunits of chromatin modification complexes."
The SAGA HAT module is tethered by its SWIRM domain and modulates activity of the SAGA DUB module.
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In S. cerevisiae Ada2, the SWIRM domain tethers the Ada2/Gcn5/Ada3/Sgf29 HAT module to the SAGA coactivator complex rather than acting as the acetyltransferase or an autonomous activation module.
"This depletion of just the HAT module proteins from the SAGA complex upon deletion of the Ada2 SWIRM domain indicates that the SWIRM domain plays a central role in tethering all four HAT module subunits to the rest of the SAGA complex."
OpenScientist hypothesis report for FUN19 Ada2/SAGA coactivation divergence
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A focused report argued that Fun19's retention of the SWIRM tethering domain is insufficient to retain Ada2-like positive coactivator activity after loss of the ZZ/SANT effector architecture and SAGA-type complex membership.
"Retaining the "docking" piece while losing the "business end" is not a conservative basis for inferring retained activation."
A multidimensional chromatography technology for in-depth phosphoproteome analysis.
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FUN19 is phosphorylated in vivo (Thr194, Ser207, Ser211) as detected by large-scale mass spectrometry, confirming the protein is expressed.
"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.
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FUN19 Ser207 was identified as a Cdk1-dependent phosphorylation site in a genome-wide analysis of Cdk1 substrates in budding yeast.
"we analyzed the position and conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase Cdk1 in the budding yeast Saccharomyces cerevisiae"
yeast/FUN19/FUN19-notes.md