Sucrose gradient chromatin enrichment for quantitative proteomics analysis in budding yeast

STAR Protocols - Tập 2 - Trang 100825 - 2021
Kiran Challa1, Jan Seebacher1, Susan M. Gasser1
1Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland

Tài liệu tham khảo

Challa, 2021, Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair, Mol. Cell, 81, 811, 10.1016/j.molcel.2020.12.021 Dungrawala, 2015, Purification of proteins on newly synthesized DNA using iPOND, Methods Mol. Biol., 1228, 123, 10.1007/978-1-4939-1680-1_10 Elias, 2010, Target-decoy search strategy for mass spectrometry-based proteomics, Methods Mol. Biol., 604, 55, 10.1007/978-1-60761-444-9_5 Hauer, 2017, Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates, Nat. Struct. Mol. Biol., 24, 99, 10.1038/nsmb.3347 Hurst, 2021, A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress, EMBO J., 40, 10.15252/embj.2021108439 Jones, 2020, Assessing budding yeast phosphoproteome dynamics in a time-resolved manner using TMT10plex mass tag labeling, STAR Protoc., 1, 100022, 10.1016/j.xpro.2020.100022 Koontz, 2014, TCA precipitation, Methods Enzymol., 541, 3, 10.1016/B978-0-12-420119-4.00001-X Kulak, 2014, Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells, Nat. Methods, 11, 319, 10.1038/nmeth.2834 Li, 2021, TMTpro-18plex: the expanded and complete set of TMTpro reagents for sample multiplexing, J. Proteome Res., 20, 2964, 10.1021/acs.jproteome.1c00168 Meister, 2010, Visualizing yeast chromosomes and nuclear architecture, Methods Enzymol., 470, 535, 10.1016/S0076-6879(10)70021-5 Nelson, 2006, Protocol for the fast chromatin immunoprecipitation (ChIP) method, Nat. Protoc., 1, 179, 10.1038/nprot.2006.27 Scott, 1980, Lyticase: endoglucanase and protease activities that act together in yeast cell lysis, J. Bacteriol., 142, 414, 10.1128/jb.142.2.414-423.1980 Touati, 2019, Cdc14 and PP2A phosphatases cooperate to shape phosphoproteome dynamics during mitotic exit, Cell Rep., 29, 2105, 10.1016/j.celrep.2019.10.041 Verdier, 1990, Preparation and characterization of yeast nuclear extracts for efficient RNA polymerase B (II)- dependent transcription in vitro, Nucleic Acids Res., 18, 7033, 10.1093/nar/18.23.7033 Yang, 2012, High pH reversed-phase chromatography with fraction concatenation as an alternative to strong-cation exchange chromatography for two-dimensional proteomic analysis, Expert Rev. Proteomics, 9, 129, 10.1586/epr.12.15 Zhang, 2019, Multiple layers of phospho-regulation coordinate metabolism and the cell cycle in budding yeast, Front. Cell Dev. Biol., 7, 338, 10.3389/fcell.2019.00338