Study on the Relationship between Histone Modifications and Gene Expression Levels in the Human H1 cell line
Wen-Xia Su, Qian-Zhong Li*
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
E-mail: qzli@inu.edu.cn
*Corresponding author
Key words: histone modification; gene expression
Motivation and Aim: It is well known that histone modifications can control gene expression. In this study, we chose embryonic stem cells to learn the profiles of histone modifications and the relationships between histone modifications and gene expression.
Methods and Algorithms: we separated the human genes into two groups, the high and the low expression genes, according to reads per kilobase of exon model per million mapped reads (RPKM). The distributions of 16 kinds of histone modifications were obtained in promoter, 5’UTR, exon, intron, 3’UTR, and particularly TSS±2kb regions of high and low expression genes separately. Heatmaps were gotten by R program based on the Spearman rank correlations of the 16 kinds of histone modifications to evaluate the pairwise correlations of these modifications. The Pearson correlation coefficients between histone modification signals and the gene expression levels were calculated to measure the relationship between histone modifications and gene expression levels quantitatively.
Results: The major conclusions of this study are that different histone modifications locate in different functional regions; different histone modifications are related to gene activity or gene silencing separately, for example we gotten that H3K9ac has the highest positive correlation, while H3K27me3 has the highest negative correlation with gene expression; and histone modifications which have the same relationship to gene expression have the tendency to have high correlation with each other.