Histone Methylation Analysis Service

MtoZ Biolabs provides dedicated Histone Methylation Analysis Service using high-resolution LC-MS/MS to identify, localize, and quantify histone lysine and arginine methylation across core histones and key variants. Our workflow is built for chromatin-rich biology and delivers site-specific methylation states, including mono-, di-, and tri-methylation, with options for global profiling or targeted quantification panels.

 

Overview

Histones are highly basic, chromatin-bound proteins enriched in Lys and Arg residues, and their modification patterns often exist as closely related proteoforms with co-occurring PTMs. Compared with general protein methylation analysis, histone methylation studies typically require chromatin-aware enrichment, histone-specific extraction, and chemistry that standardizes digestion for Lys-rich sequences to enable confident site localization and reproducible quantification.

 

 

Fallah, M. S. et al. Front Genet. 2021.

Figure1. Histone Methylation Regulates Gene Expression

 

Histone Methylation Analysis Service at MtoZ Biolabs

MtoZ Biolabs supports both discovery and hypothesis-driven histone methylation studies by combining histone-optimized sample processing with high-resolution LC-MS/MS and PTM-aware bioinformatics. Depending on your study goals, we offer global profiling, targeted quantification, and variant-aware strategies to resolve methylation states and site localization.

●  Global Histone Methylation Profiling

Site-level identification and relative quantification of Lys and Arg methylation, including me1, me2, and me3, across core histones and selected variants.

●  Targeted Methylation Quantification

PRM-style panels for defined marks such as H3K4me3 and H3K27me3, designed for precise cross-condition comparisons and subtle effect sizes.

●  Variant-Aware and Multi-PTM Context

Methods and reporting that address closely related histone sequences and co-occurring PTMs when they impact interpretation.

 

Workflow of Histone Methylation Analysis Service

1. Study design and sample intake aligned to your biological question and quantification needs

2. Nuclei or chromatin enrichment to improve histone coverage and reduce background

3. Histone extraction and cleanup, commonly using acid extraction

4. Derivatization and controlled digestion, often propionylation-based, to generate informative peptides

5. High-resolution LC-MS/MS acquisition and PTM-aware identification, localization, and quantification

6. Standardized reporting with QC summaries and study-aligned interpretation

 

Applications of Histone Methylation Analysis Service

·  Comparing histone methylation patterns across treatments, perturbations, or time courses

·  Epigenetic profiling in cancer, inflammation, and differentiation models

·  Evaluating chromatin regulation in gene knockout or overexpression studies

·  Supporting target validation and mechanism studies in epigenetic drug discovery

·  Monitoring histone methylation shifts during process changes in cell-based workflows

 

Start Your Project with MtoZ Biolabs

Send us your organism, sample type, and experimental groups, and we will recommend an efficient study design for global profiling, targeted quantification, or a combined strategy that matches your biological question.

 

FAQ

Q1: What types of samples are suitable?

This service is compatible with common chromatin-related inputs and can be tailored to your study design. Typical sample types include:

·  Cell pellets from cultured cells

·  Fresh-frozen tissues with clear provenance and consistent handling

·  Purified nuclei or chromatin fractions prepared in-house

·  Pre-extracted histone preparations for direct downstream processing

 

Q2: How should I prepare my samples?

·  Rapid processing and snap-freezing, with storage at -80°C

·  Minimized thaw time and avoidance of repeated freeze-thaw cycles

·  Clear labeling of groups, replicates, and treatment conditions in a sample sheet

·  Sufficient material per condition and inclusion of biological replicates whenever possible
·  If you already have nuclei, chromatin, or histone extracts, we can advise on buffer compatibility and cleanup needs prior to shipment. 

For more information, please refer to Sample Submission Guidelines for Proteomics.

 

Q3: What is the service general workflow?

 

 

Q4: What data formats are provided?

·  Raw LC-MS/MS files (.raw)

·  Histone methylation site and state tables in Excel or CSV

·  Summary reports in PDF format, including analytical methods, quality control results, and key findings

·  Figures and chromatograms in high-resolution image formats (TIFF or PNG)

Additional file formats or data structures can be provided upon request to meet specific research or publication requirements.

 

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