Histone Purification Combined with High‐Resolution Mass Spectrometry to Examine Histone Post‐Translational Modifications and Histone Variants in Caenorhabditis elegans

Abstract

Histones are the major proteinaceous component of chromatin in eukaryotic cells and an important part of the epigenome, affecting most DNA‐related events, including transcription, DNA replication, and chromosome segregation. The properties of histones are greatly influenced by their post‐translational modifications (PTMs), over 200 of which are known today. Given this large number, researchers need sophisticated methods to study histone PTMs comprehensively. In particular, mass spectrometry (MS)−based approaches have gained popularity, allowing for the quantification of dozens of histone PTMs at once. Using these approaches, even the study of co‐occurring PTMs and the discovery of novel PTMs become feasible. The success of MS‐based approaches relies substantially on obtaining pure and well‐preserved histones for analysis, which can be difficult depending on the source material. Caenorhabditis elegans has been a popular model organism to study the epigenome, but isolation of pure histones from these animals has been challenging. Here, we address this issue, presenting a method for efficient isolation of pure histone proteins from C. elegans at good yield. Further, we describe an MS pipeline optimized for accurate relative quantification of histone PTMs from C. elegans . We alkylate and tryptically digest the histones, analyze them by bottom‐up MS, and then evaluate the resulting data by a C. elegans −adapted version of the software EpiProfile 2.0. Finally, we show the utility of this pipeline by determining differences in histone PTMs between C. elegans strains that age at different rates and thereby achieve very different lifespans. © 2020 The Authors. Basic Protocol 1 : Large‐scale growth and harvesting of synchronized C. elegans Basic Protocol 2 : Nuclear preparation, histone extraction, and histone purification Basic Protocol 3 : Bottom‐up mass spectrometry analysis of histone PTMs and histone variants

SIN-3 acts in distinct complexes to regulate the germline transcriptional program in Caenorhabditis elegans

“…Histones from wild-type and sin-3(tm1276) young adult worms were purified following ‘Basic protocol 2’ published by Millan-Ariño et al (2020) . MS was then performed according to ‘Basic Protocol 3’ and histone peptides were analyzed as described in the same article by bottom-up MS with a C. elegans -adapted version of EpiProfile 2.0 software ( Yuan et al, 2018 ).…”

Mouse primary T cell phosphotyrosine proteomics enabled by BOOST

“…With increased interest in using proteomics to study rare or specific posttranslational modifications 20,51,52 and the proteomes of single-cells, 41,49,53 reliable methods to increase multiplexing capabilities, 54 posttranslational modification selection, 55 and quantitation 21,22,56 are desired. These experimental techniques will come with a wave of computational methods to further improve quantitation, 30,57,58 which will require stringent testing for both experimental-computational method compatibility and to understand the range of biological processes that these methods can work with.…”

SIN3 acts in distinct complexes to regulate the germline transcriptional program inC. elegans

“…Histones from wildtype and sin-3(tm1276) young adult worms were purified following Basic protocol 2 published by Millan-Ariño et al (Millan-Ariño et al, 2020). Mass spectrometry was then performed according to Basic Protocol 3 and histone peptides were analyzed as described in the same manuscript by bottom-up MS with a C. elegans−adapted version of the software EpiProfile 2.0 (Yuan et al, 2018) for upregulated genes in sin-3(syb2172) and hda-3(ok1991) mutants.…”