Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes

Abstract

We analyzed the whole-genome experimental maps of nucleosomes in Drosophila melanogaster and classified genes by the expression level in S2 cells (RPKM value, reads per kilobase million) as well as the number of tissues in which a gene was expressed (breadth of expression, BoE). Chromatin in 5'-regions of genes we classified on four states according to the hidden Markov model (4HMM). Only the Aquamarine chromatin state we considered as Active, while the rest three states we defined as Non-Active. Surprisingly, about 20/40% of genes with 5'-regions mapped to Active/Non-Active chromatin possessed the minimal/at least modest RPKM and BoE. We found that regardless of RPKM/BoE the genes of Active chromatin possessed the regular nucleosome arrangement in 5'-regions, while genes of Non-Active chromatin did not show respective specificity. Only for genes of Active chromatin the RPKM/BoE positively correlates with the number of nucleosome sites upstream/around TSS and negatively with that downstream TSS. We propose that for genes of Active chromatin, regardless of RPKM value and BoE the nucleosome arrangement in 5'-regions potentiates transcription, while for genes of Non-Active chromatin, the transcription machinery does not require the substantial support from nucleosome arrangement to influence gene expression.

Keywords: 5′-regulatory region; breadth of expression; chromatin landscape; expression level; housekeeping and widely expressed genes; nucleosome arrangement; tissue-specific and silent genes.

Figure 1

Classification of genes according to expression level (RPKM, reads per kilobase million) and breadth of expression (BoE). BoE was computed for 29 tissues; RPKM values respected to S2 cells; panels (A,B) show “Active” and “Non-Active” genes, these classes respect to Aquamarine and Lazurite/Malachite/Ruby chromatin states according to 4HMM [23,30] (see Section 4).

Figure 2

Average numbers of mapped nucleosome sites for “Active” (A) and “Non-Active” (B) genes (see Section 4). Red/blue lines mark resistant/sensitive nucleosomes [21]. X axes denote the position relative to TSS. Y axes show the moving mean over a window of 3 nt for average number of nucleosome sites. The headers of columns/rows mean the classification of genes by BoE/RPKM. Ovals near X axes denote approximate positions of nucleosomes upstream (Nuc−2, Nuc−1) and downstream (Nuc+1) TSS.

Figure 3

Correlation coefficients (CC) between the expression level (RPKM) and the number of mapped nucleosomes. The top/bottom rows denote datasets of Active/Non-Active genes (see Section 4). The left, middle, and right columns mark intervals of the expression breadth (BoE). X axes show the position relative to TSS, Y axes denote the moving mean of CC over a window of three nt. Red/blue lines denote resistant/sensitive nucleosomes [21]. Dashed black lines mark the threshold of Bonferroni corrected p-value for CC (p < 0.05/500).