Related Experiment Video
Updated: Apr 6, 2026
08:12
Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue
Published on: May 5, 2022
4.6K
Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria
Lijuan Yang1, Xinlei Lian1, Wanling Zhang1
1Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou 510632, China.
Journal of Proteome Research
|July 24, 2015
Summary
Epigenetic modifications in human cells can stimulate silenced genes, aiding the discovery of missing proteins. This approach successfully identified previously undetected proteins involved in development and spermatogenesis.
Area of Science:
- Proteomics
- Epigenetics
- Human Proteome Project
Background:
- The Chromosome-centric Human Proteome Project (C-HPP) faces challenges in identifying missing proteins, particularly those specific to developmental stages.
- Limited availability of developmental stage-specific samples hinders the discovery of these proteins.
Purpose of the Study:
- To investigate the potential of epigenetic modifications to induce the expression of silenced genes in adult cells.
- To enhance the discovery of missing proteins by creating in vitro human cell models with modified histone acetylation, demethylation, and methylation.
Main Methods:
- Established in vitro human cell models with controlled epigenetic modifications (histone acetylation, demethylation, methylation).
- Utilized mRNA sequencing (mRNA-seq) to analyze gene expression changes.
- Employed mass spectrometry (MaxQuant and Mascot) for protein identification and quantification, followed by stringent manual spectrum inspection.
Main Results:
- Epigenetic modifications led to a general increase in gene expression across chromosomes.
- Identified a significant number of PE2-4 and PE5 proteins, with 19 PE2-4 and 3 PE5 proteins passing stringent FDR < 1% criteria at both peptide and protein levels.
- Gene ontology analysis indicated that identified PE2-4 proteins are significantly involved in development and spermatogenesis.
Conclusions:
- Epigenetically manipulated cell models are a valuable tool for the Chromosome-centric Human Proteome Project to discover missing proteins.
- The study provides a novel strategy to overcome limitations in sample availability for proteomic research.
- Mass spectrometry data are publicly available in the iProx database (IPX00020200).
