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Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types

  • Yanmei Lin
  • Yan Li
  • Xingyong Zhu
  • Yuyao Huang
  • Yizhou LiEmail author
  • Menglong LiEmail author
Original research article
  • 84 Downloads

Abstract

Histone modifications play critical roles in mammalian development, regulating chromatin structure and gene expression. Dynamic histone modifications among cell types have been shown to associate with changes in mammalian development. However, how to quantitatively measure the histone modification alterations and how histone modifications vary across cell types under different genetic contexts remain largely unexplored and whether these changes are related to the primary DNA sequence remains limited. Here, we employed an entropy-based method to measure histone modification alterations in six definite genomic regions across five cell types and identified lineage-specific histone modification genes. We observed that histone modification alterations prefer to enrich in 5′-UTR exons, and also in 3′-UTR exons and its downstream. Then we built a model to predict the histone modification patterns from the primary DNA sequence. We found that the frequencies of k-mer sequence compositions are predictive of histone modification patterns, suggesting that the primary DNA sequence correlated with the histone modification alterations among cell types. Additionally, the lineage-specific histone modification genes display a higher conservation and lower GC-content. Together, we performed a systematic analysis for histone modification alterations and demonstrated how to identify genomic region-specific elements of epigenetic and genetic regulation and histone modification patterns across different cell types.

Keywords

Histone modification DNA primary sequence GC-content Conservation 

Notes

Acknowledgements

We would like to acknowledge the members of Center for Chemometrics and Bioinformatics at Sichuan University for valuable discussions and advices. National Natural Science Foundation of China (nos. 21775107, 21675114).

Compliance with Ethical Standards

Conflict of interest

No potential conflict of interest was reported by the authors.

Supplementary material

12539_2019_338_MOESM1_ESM.docx (479 kb)
Supplementary material 1 (DOCX 478 kb)

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Copyright information

© International Association of Scientists in the Interdisciplinary Areas 2019

Authors and Affiliations

  1. 1.College of ChemistrySichuan UniversityChengduChina
  2. 2.College of CybersecuritySichuan UniversityChengduChina

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