Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry

Zheng, Yupeng; Huang, Xiaoxiao; Kelleher, Neil L.

doi:10.1016/j.cbpa.2016.06.007

Cited by 64 publications

(65 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, these methods require the prior knowledge of the potential modification and suffer from critical issues shared by all antibody-based techniques, such as antibody availability, batch-to-batch variability, cross-reactivity, dependence on the surrounding amino acid sequence, and/or protein structure. Thus, antibody-based immunopurifications do not allow for an unbiased interrogation of multiple histone PTMs at once, a solution for which is provided by mass spectrometry-based methods for comprehensive analysis of histone PTMs, which have been extensively described previously (Huang, Lin, Garcia, & Zhao, 2015; Zheng, Huang, & Kelleher, 2016). Briefly, for high-throughput, multihistone analyses, three analytical techniques, called Bottom Up, Middle Down, and Top Down, are established.…”

Section: Mass Spectrometry-based Methods Overviewmentioning

confidence: 99%

“…Bottom Up and Middle Down analyses require digestion of histones by proteolytic enzymes and subsequent analysis of the peptides by tandem mass spectrometry (MS/ MS). Top Down analysis uses no proteases and whole histone molecules with modification are detected by MS/MS (for an excellent recent review, see Zheng et al, 2016). …”

Section: Mass Spectrometry-based Methods Overviewmentioning

confidence: 99%

See 1 more Smart Citation

Mass Spectrometry-Based Methodology for Identification of Native Histone Variant Modifications From Mammalian Tissues and Solid Tumors

Nuccio¹,

Bui

Dalal

et al. 2017

Methods in Enzymology

View full text Add to dashboard Cite

Histone posttranslational modifications (PTMs) are key epigenetic marks involved in gene silencing or activation. Histone modifications impact chromatin organization and transcriptional processes through the changes in charge density between histones and DNA. They also serve as recognition and binding sites for specific binding proteins. Histone tails and globular cores contain many basic amino acid residues, which are subject to various dynamic modifications, making the modification repertoire extremely diverse. Consequently, determination of histone PTM identity and quantity has been a challenging task. In recent years, mass spectrometry-based methods have proven useful in histone PTM characterization. This chapter provides a brief overview of these methods and describes the approach to analyze the PTMs of the histone variant CENP-A, essential for the cell cycle progression, when present in minute amounts from tumor and mammalian tissues. Because this method does not rely on antibody-based immunopurification, we anticipate that these tools could be readily adaptable to the investigation to other histone variants in a range of mammalian tissues and solid tumors.

show abstract

Section: Mass Spectrometry-based Methods Overviewmentioning

confidence: 99%

Section: Mass Spectrometry-based Methods Overviewmentioning

confidence: 99%

Mass Spectrometry-Based Methodology for Identification of Native Histone Variant Modifications From Mammalian Tissues and Solid Tumors

Nuccio¹,

Bui

Dalal

et al. 2017

Methods in Enzymology

View full text Add to dashboard Cite

show abstract

“…Bottom-up MS has also intrinsic biases (discussed in [76]), mostly related to the ionization efficiency of the peptides, enzyme preference of cleavage of modified vs. unmodified sequences, peptide solubilization efficiency and also derivatization [26] when applied. Not all of them can be solved by using, e.g., internal standards.…”

Section: Expert Commentarymentioning

confidence: 99%

Middle-down proteomics: a still unexploited resource for chromatin biology

Sidoli

Garcia

2017

Expert Review of Proteomics

View full text Add to dashboard Cite

Introduction Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac. The traditional bottom-up MS strategy identifies and quantifies short (aa 4-20) tryptic peptides, and it is thus not suitable for the characterization of combinatorial PTMs. Areas covered Here, we review the advancement of the middle-down MS strategy applied to histones, which consists in the analysis of intact histone N-terminal tails (aa 50-60). Middle-down MS has reached sufficient robustness and reliability, and it is far less technically challenging than PTM quantification on intact histones (top-down). However, the very few chromatin biology studies applying middle-down MS resulting from PubMed searches indicate that it is still very scarcely exploited, potentially due to the apparent high complexity of method and analysis. Expert Opinion/Commentary We will discuss the state-of-the-art workflow and examples of existing studies, aiming to highlight its potential and feasibility for studies of cell biologists interested in chromatin and epigenetics.

show abstract

“…Although a number of PTM modification sites can be identified with bottom-up proteomics, it is difficult to identify the proteoforms involved. Top-down identification helps, 78 but locating PTM modification sites in the primary structure of a protein requires gas phase sequencing.…”

Section: Fractionation Of Structurally Similar Proteinsmentioning

confidence: 99%