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Updated: Jul 16, 2026
Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue
Published on: May 5, 2022
An Energy Model Based on Molecular Structure for Predicting Histone Modification Levels at lncRNA Promoter Regions in
Menglan Li1, Yingli Chen1,2, Qianzhong Li1,2
1Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
Abstract:
In hepatocellular carcinoma (HepG2), aberrant histone modifications are closely linked to long non-coding RNA (lncRNA) expression. However, existing computational models lack physical interpretability at specific promoter coordinates. To address this, we developed a position-specific statistical scoring model based on adjacent and next-adjacent nucleotide frequencies. We trained two independent, position-specific matrices representing increased and decreased modification states across 600 bp promoter windows centered on the true signal summits. Finally, ten-fold cross-validation revealed that significant energy differences between sequences with increased and decreased histone signals enable excellent classification performance. These results indicted a strong correlation between the total energy of local DNA structures and histone modification signal.
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