Molecular targets of epigenetic regulation and effectors of environmental influences

Abstract

The true understanding of what we currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DNA methylation, chromatin modification, as well as on the expression of small non-coding RNAs (ncRNAs) have expanded the scope of research on the etiology of various diseases including cancer. The current review briefly discusses the molecular mechanisms of epigenetic regulation and expands the discussion with examples on the role of environment, such as the immediate environment during development, in inducing epigenetic changes and modulating gene expression.

Figure 1

The hierarchy of organization from chromosome to nucleosome. The histone octamer contains two molecules each of histones H2A, H2B, H3 and H4. The DNA wraps around the octamer in a left-handed supercoil in about 1.75 turns that encloses about 150 bp. Histone H1 is the linker histone. Linker histone and linker DNA physically connect adjacent nucleosome core particles. The nucleosomes (10 nm each) are condensed into 30 nm solenoid fiber structure, which are condensed into 300-nm filament; the 300-nm filaments are further condensed into the 700-nm chromosome. During cell division, when the chromosomes duplicate, a 1,400-nm metaphase chromosome is produced containing two chromatids, each chromatid being 700 nm.

Figure 2

Mechanism of transcriptional repression by MeCP2. MeCP2 selectively binds 5-methyl cytosine in symmetrically positioned CpG dinucleotides in mammalian genome, and methyl CpG-binding protein (MeCP2) is able to bind to a single methylated CpG pair. The methyl-CpG-binding domain (MBD) binds to 5-methyl cytosine, and the transcriptional repression domain (TRD) interacts with a corepressor complex containing histone deacetylases (HDACs) and the transcriptional repressor Sin3a. Recruitment of HDAC by MeCP2 causes deacetylation of histones, resulting in a more condensed chromatin conformation and transcriptional silencing.

Figure 3

In mouse Igf2 and H19 are on the same chromosome such that Igf2 is located ~80-kb upstream of H19. The imprint control region (ICE), located in between Igf2 and H19, contains an insulator. There are also a set of enhancers located downstream from H19, which are utilized by both Igf2 and H19 for their expression. On the maternal chromosome, the unmethylated ICE binds the vertebrate insulator protein CCCTC-binding factor (CTCF). ICE-CTCF insulator prevents the enhancer from acting upon Igf2, essentially silencing its expression. On the paternal chromosome, the ICE is methylated preventing CTCF binding. Methylation of ICE also leads to secondary methylation of the H19 promoter, and silencing of H19. Because the methylated paternal ICE lacks insulator activity, the enhancer can interact with paternal Igf2 promoter and enhance Igf2 expression.

Figure 4

Biogenesis and function of miRNA. The pri-miRNA transcript is processed in the nucleus by Drosha–DGCR8 complex to produce a 70–80 nt-long precursor miRNA (pre-miRNA). Pre-miRNA is transported to the cytoplasm by Exportin-5 and Ran-GTP. Some pri-miRNAs that are encoded by introns are processed by spliceosome (the mirtron pathway). Following spliceosome processing, the miRNA is released as lariat structure that first undergoes debranching followed by folding to form the pre-miRNA. In the cytoplasm, the 70–80 nt-long pre-miRNA is further processed into 22 nt-long duplex mature miRNA by Dicer, forming the miRNA/miRNA* duplex. From this duplex, only the guide strand is loaded onto the miRISC. The miRISC is targeted to the mRNA; the miRNA binds to the 3′-UTR of the mRNA and suppresses its translation.

Figure 5

Hepatic mRNA expression and enrichment of H3K4me2 around the Ugt2 and Ugt3 gene loci during development. (A) The ontogeny of Ugt2 and Ugt3 mRNAs in liver (from a sample size of n=5). The mRNA expression was determined by bDNA (branched DNA) assay. The average values were analyzed by a two-way hierachical clustering method (JMP v. 7.0) using Ward’s minimum variance and visualized by a dendrogram, which revealed adult-enriched expression patterns of these Ugts. Distances between genes reflect significance of associations. Blue color: low expression; red color: high expression. (B) and (C) H3K4me2 at the Ugt2 (B) and Ugt3 (C) gene loci during mouse liver development. ChIP-on-chip data were visualized by the Affymetrix Integrated Genome Browser (IGB) for H3K4me2 fold changes at day −2, 1, 5, and 45 of age. Solid lines through the signal enrichment peaks indicate the threshold value (4.0-fold compared to input background) for enriched intervals. Asterisks (*) indicate the peak center.

Figure 6

Distinct epigenetic signatures around the Mdr gene cluster in adult mouse liver (day 45 of age) (Mdr1a, 1b and 2). (A) H3K4me2, (B) H3K27Me3 and (C) DNA methylation (DNAme). ChIP-on-chip data were visualized by the Affymetrix Integrated Genome Browser (IGB) for H3K4me2, H3K27me3, and DNAme enrichment. Solid lines through the signal enrichment peaks indicate the threshold value (4.0-fold compared to input background for histone methylations, and 3.0-fold for DNAMe) for enriched intervals. Asterisks (*) indicate the peak center.