Chromatin poises miRNA- and protein-coding genes for expression

Abstract

Chromatin modifications have been implicated in the regulation of gene expression. While association of certain modifications with expressed or silent genes has been established, it remains unclear how changes in chromatin environment relate to changes in gene expression. In this article, we used ChIP-seq (chromatin immunoprecipitation with massively parallel sequencing) to analyze the genome-wide changes in chromatin modifications during activation of total human CD4(+) T cells by T-cell receptor (TCR) signaling. Surprisingly, we found that the chromatin modification patterns at many induced and silenced genes are relatively stable during the short-term activation of resting T cells. Active chromatin modifications were already in place for a majority of inducible protein-coding genes, even while the genes were silent in resting cells. Similarly, genes that were silenced upon T-cell activation retained positive chromatin modifications even after being silenced. To investigate if these observations are also valid for miRNA-coding genes, we systematically identified promoters for known miRNA genes using epigenetic marks and profiled their expression patterns using deep sequencing. We found that chromatin modifications can poise miRNA-coding genes as well. Our data suggest that miRNA- and protein-coding genes share similar mechanisms of regulation by chromatin modifications, which poise inducible genes for activation in response to environmental stimuli.

Figure 1.

E2F1 and NKTR genes do not change their chromatin status upon induction or silencing, respectively. The chromatin modification patterns of the E2F1 gene (A) and the NKTR gene (B) are shown in resting (top panel) and activated (bottom panel) T cells.

Figure 2.

A majority of the genes do not change their chromatin status upon induction or silencing. Average ChIP-seq tag density for the four gene sets are shown in resting (top panel) and activated (bottom panel) CD4⁺ T cells. The four gene sets: S→E (silent in resting and expressed in activated T cells), red dashed line in density plot and light red in box plot; E→S, blue dashed line and light blue; E→E, red line and red; S→S, blue line and blue. The average tag density values for resting and activated cells are not directly comparable as they have not been normalized across samples. Box plot summarizes the distribution of the number of tags in the region of interest (highlighted in yellow) for each gene set. Box plot captures the median, the middle 50% of the data points, and the outliers. The data points for each gene set are divided into quartiles, and the interquartile range (IQR) is calculated as the difference between the first and the third quartiles. The filled box denotes the middle 50% of the data points, with the horizontal line in-between and the notch representing the median and confidence intervals, respectively. Data points more than 1.5 times IQR lower or higher than first or third quartiles, respectively, represent outliers and are shown as dots. The horizontal line connected by vertical dashed lines above and below the filled box (whiskers) represents the largest and the smallest nonoutlier data points. The cluster of horizontal red and black lines below each box plot signifies whether or not the difference between the medians of two gene sets are statistically significant, respectively (P < 0.01; two-tailed Wilcoxon rank-sum test). (A) H3K4me3, (B) H3K27me3, (C) Pol II, and (D) H3K79me2. Profiles for other modifications are presented in Supplemental Figures S3 and S4.

Figure 3.

Inducible genes are poised for expression. (A–C) A majority of inducible genes have H3K4me3 (A), H2A.Z (B), and Pol II (C) at their promoters. The percentage of genes that have significant (P-value < 10⁻³) number of tags at the promoter for each set of genes is shown in resting (top panel) and activated (bottom panel) T cells. (D,E) Silent genes associated with cell cycle and metabolism, but not muscle or organ function and development, are poised in T cells. H3K4me3 (D) and Pol II (E) tag density profiles for silent genes taking part in specific biological processes.

Figure 4.

miRNA promoters have chromatin modification patterns similar to that of protein-coding genes. Chromatin modification patterns in the region surrounding the intergenic MIRLET7 miRNA cluster (A), and intragenic MIR98 and MIRLET7F2 (B), and MIR491 (C) are shown. Putative promoters are marked by H3K4me3, H2A.Z, and Pol II peaks. The green bars extend from the predicted transcription start site to the 3′ end of the pre-miRNA. H3K27me1, H3K9me1, H3K79me2, and H3K36me3 modifications, typically found within gene bodies of protein-coding genes, are seen within the putative miRNA coding transcript.

Figure 5.

Promoter-reporter assay. Predicted miRNA promoters or control sequences were cloned into pGL3 enhancer vector containing SV40 enhancer, but no promoter. Plasmids were transfected into Jurkat cells together with Renilla luciferase control. Luciferase activity was measured after two days. Ratio of firefly and Renilla luciferase signal + SD (n = 3) is shown. *P-value < 0.005 in Student t-tests vs. both controls 1 and 2.

Figure 6.

Inducible miRNA genes are poised for expression. The chromatin modification patterns at the intragenic MIR877 (A) and intergenic MIR301B (B) genes that are induced upon T-cell activation.