DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

Abstract

Transposable element (TE)-derived sequences comprise half of the human genome and DNA methylome and are presumed to be densely methylated and inactive. Examination of genome-wide DNA methylation status within 928 TE subfamilies in human embryonic and adult tissues identified unexpected tissue-specific and subfamily-specific hypomethylation signatures. Genes proximal to tissue-specific hypomethylated TE sequences were enriched for functions important for the relevant tissue type, and their expression correlated strongly with hypomethylation within the TEs. When hypomethylated, these TE sequences gained tissue-specific enhancer marks, including monomethylation of histone H3 at lysine 4 (H3K4me1) and occupancy by p300, and a majority exhibited enhancer activity in reporter gene assays. Many such TEs also harbored binding sites for transcription factors that are important for tissue-specific functions and showed evidence of evolutionary selection. These data suggest that sequences derived from TEs may be responsible for wiring tissue type-specific regulatory networks and may have acquired tissue-specific epigenetic regulation.

Figure 1. Clustering of TE families based on their DNA methylation profile reveals tissue specificity

TE families (rows) were clustered based on their MeDIP-seq (a) or MRE-seq (b) enrichment values across 29 samples (see Online Methods). The samples (columns) were clustered into four major groups, which were consistent with their tissue types: ESC H1 (gray), Brain (orange), Breast (blue), and Blood (purple). The vertical bar on the right side of the heat-map represents TE classes: LTR (blue), DNA transposon (purple), SINE (orange), and LINE (black). The corresponding methylation enrichment values are represented as horizontal bar with varying color gradients at the bottom of each panel.

Figure 2. Tissue-specific enhancer signatures of LTR77 and LFSINE

LTR77 (a-d) and LFSINE (e-h) are specifically hypomethylated in blood samples and brain samples, respectively. (a) Boxplots of MeDIP-seq and MRE-seq enrichment scores of LTR77 in multiple cell/tissue types. (b) Histone modification signatures of LTR77 in CD8+ Naïve cells. (c) Comparison of H3K4me1 signal of LTR77 between fetal brain sample and CD8+ Naïve cells. (d) p300 binding signal on LTR77 in four cell lines. (e) Boxplots of MeDIP-seq and MRE-seq enrichment scores of LFSINE in multiple cell/tissue types. (f) Histone modification signatures of LFSINE in fetal brain sample. (g) Comparison of H3K4me1 signal of LFSINE between fetal brain sample and CD8+ Naïve cells. (h) p300 binding signal on LFSINE in four cell lines. Signals of different histone modification or p300 binding for each genomic copy of the TE family including 3kb upstream and downstream flanking regions were averaged in 5bp tiling windows. Error bar represents 1 standard deviation.

Figure 3. Tissue-specific hypomethylated TEs correlate with gene expression

(a) Genome Browser view of an LTR77 element upstream of the ERAP1 gene. Displayed tracks include: DNA methylation (MeDIP-seq) for human ESC H1, breast, brain and blood samples; histone modification (H3K4me1 and H3K4me3) tracks for a CD8 naïve sample and a fetal brain cell sample; transcription factor binding tracks (ENCODE) for NFkB, Pol2, and TCF12 in three cell lines; gene annotation and RepeatMasker. (b) Bisulfite sequencing validation of DNA methylation status of the LTR77 element (5 CpG sites) in human ESC H1, breast, brain and blood samples. Black circle represents methylated CpG sites and white circle represents unmethylated CpG sites. (c) Boxplots of expression levels of ERAP1 in 4 different tissues. (d) Genome Browser view of an LFSINE element upstream of the GFRA1 gene. Displayed tracks include: DNA methylation (MeDIP-seq) for human ESC H1, breast, brain, and blood samples; histone modification (H3K4me3 and H3K4me1) tracks for a fetal brain sample and a CD8+ naïve cell sample; gene annotation and RepeatMasker. (e) Bisulfite sequencing validation of DNA methylation status of the LFSINE element (4 CpG sites) in human ESC H1, breast, brain, and blood samples. (f) Boxplots of expression levels of GFRA1 in 4 different tissues.

Figure 4. Correlation between cell type-specific enhancer marks, binding of transcription factors, and sequence motifs

Histone modification, transcription factor binding, and sequence motif prediction data were displayed for individual genomic copies of LTR77 and LFSINE. Each row represents one element. Data were obtained from UCSC ENCODE portal. For H3K4me1 histone modification and p300 ChIP-seq data, RPKM values at 50bp resolution were plotted for a 10kb region centered on the TE copy. For transcription factor binding data, a red tick indicates that the TE copy overlaps with a peak predicted using ChIP-seq data of the given transcription factor in the given cell type. For sequence motif data, each TE copy was scored using position specific weight matrix of the given transcription factor. A blue tick indicates log-transformed e-value of observing a sequence motif by chance.