Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines

Abstract

Motivation: In addition to alternative splicing, alternative polyadenylation has also been identified as a critical and prevalent regulatory mechanism in human gene expression. However, the mechanism of alternative polyadenylation selection and the involved factors is still largely unknown.

Results: We use the ENCODE data to scan DNA functional elements, including chromatin accessibility and histone modification, around transcript cleavage sites. Our results demonstrate that polyadenylation sites tend to be less sensitive to DNase I. However, these polyadenylation sites have preference in nucleosome-depleted regions, indicating the involvement of chromatin higher-order structure rather than nucleosomes in the resultant lower chromatin accessibility. More interestingly, for genes using two polyadenylation sites, the distal sites show even lower chromatin accessibility compared with the proximal sites or the unique sites of genes using only one polyadenylation site. We also observe that the histone modification mark, histone H3 lysine 36 tri-methylation (H3K36Me3), exhibits different patterns around the cleavage sites of genes using multiple polyadenylation sites from those of genes using a single polyadenylation site. Surprisingly, the H3K36Me3 levels are comparable among the alternative polyadenylation sites themselves. In summary, polyadenylation and alternative polyadenylation are closely related to functional elements on the DNA level.

Contact: liang.chen@usc.edu.

Fig. 1.

Chromatin accessibility differences among poly (A) sites. (A) DNase-seq signals around different positions in the K562 cell line. The lines show the average DNase-seq density around proximal poly (A) sites (1), distal poly (A) sites (2), unique poly (A) sites (3), random exonic sites (4), random exon ending sites (5), random positions in intergenic regions or pseudogenes (6). Position 0 represents the considered sites, and the 100 bp upstream and downstream regions are shown. The vertical lines represent the standard errors for each position. (B) Wilcoxon rank test results for DNase-seq signals around different sites in the six cell lines. Each rectangular block displays the results for the six cell lines shown in the top left block. Thus, each block is divided into six smaller rectangular regions. For each cell line, four different regions, including the −160 to −80 bp upstream, −80 to 0 bp upstream, 0–80 bp downstream and 80–160 bp downstream regions of the considered sites, were tested separately, and the results are shown from the left to the right in the smaller rectangles. Thus, each smaller rectangle is further divided into four segments. The colors were coded to demonstrate the significance level of the difference between the two groups. For the comparison between distal poly (A) sites and proximal poly (A) sites, Wilcoxon signed-rank tests were performed instead

Fig. 2.

Nucleosome distribution around poly (A) sites in the K562 cell line. Three lines represent the third quartile, the median and the first quartile of the MNase-seq values at each position. For all the three different poly (A) groups, the cleavage sites display fewer nucleosomes than randomly chosen exonic or exon ending positions

Fig. 3.

An example of H3K36me3 signals in the K562 cell line. The big arrows indicate the APA sites of DTNBP1 and the uniquely deployed poly (A) site of HCCS in the considered cell line. The APA sites tend to display higher H3K36me3 modification than the unique poly (A) site