Epigenetic regulation of gene expression in keratinocytes

Abstract

The nucleus is a complex and highly compartmentalized organelle, which undergoes major organization changes during cell differentiation, allowing cells to become specialized and fulfill their functions. During terminal differentiation of the epidermal keratinocytes, the nucleus undergoes a programmed transformation from active status, associated with execution of the genetic programs of cornification and epidermal barrier formation, to a fully inactive condition and becomes a part of the keratinized cells of the cornified layer. Tremendous progress achieved within the past two decades in understanding the biology of the nucleus and epigenetic mechanisms controlling gene expression allowed defining several levels in the regulation of cell differentiation-associated gene expression programs, including an accessibility of the gene regulatory regions to DNA-protein interactions, covalent DNA and histone modifications, and ATP-dependent chromatin remodeling, as well as higher-order chromatin remodeling and nuclear compartmentalization of the genes and transcription machinery. Here, we integrate our current knowledge of the mechanisms controlling gene expression during terminal keratinocyte differentiation with distinct levels of chromatin organization and remodeling. We also propose directions to further explore the role of epigenetic mechanisms and their interactions with other regulatory systems in the control of keratinocyte differentiation in normal and diseased skin.

Figure 1. Schematic structure of interphase nucleus

A - Nucleus is surrounded by nuclear envelope that consists of outer and inner membranes, nuclear pore complexes and lamina located beneath the inner nuclear membrane. Chromosomes occupy distinct territories, in which distinct chromatin domains are permeated by interchromatin channels connected with a network of larger channels and lacunas separating distinct chromosomes and harboring a number of nuclear bodies including speckles (inset). Nucleus also contains a number of nuclear bodies including nucleolus, PML bodies, speckles and Polycomb bodies. B: Images of nuclei of murine basal epidermal keratinocytes showing chromosome territory 11 (left image, large arrow) with keratin 15 gene (small arrow), as well as Epidermal Differentiation Complex locus (right image, red color) contacting SC-35-positive speckle (inset, green color, arrow).

Figure 2. Distinct levels of chromatin organization, characteristics of the active and inactive chromatin domains and epigenetic control of gene expression in the Epidermal Differentiation Complex locus

A – Levels of chromatin folding and size of the corresponding chromatin domains of the interphase chromosome. The lowest unit of chromatin organization is nucleosome, in which DNA form 1 and ¾ loops around the histone octamer core. Nucleosomes are connected by linker DNA and form the “beads on the string” structures, which are folded into 30 nm fiber followed by further folding into higher-order loop structures (modified from Felsenfeld and Groudine, 2003). B – Distribution of different epigenetic marks among the distinct regions of actively transcribed, paused and inactive genes. Actively transcribed genes are characterized by high levels of Polymerase II occupancy, low levels of DNA methylation, high levels of H3K4me3 and H3K9acetyl/H3K18acetyl at the transcription start site, as well as by high levels of H3K79me2/3 and H3K36me3 at the gene body region. Genes with paused transcription show high levels of Polymerase II occupancy, low levels of DNA methylation, high levels of H3K4me3 and H3K27me2/3 at the transcription start site. Inactive genes show lack of Polymerase II, high levels of DNA methylation and H3K9me2/3 at the transcription start site (modified from Wang et al., 2009). C – Epigenetic control of expression of terminal differentiation-associated genes in the Epidermal Differentiation Complex locus occupying about 3 Mb in mouse chromosome 3. Scheme of the locus shows chromosomal localization of the distinct genes and gene families. Genes activated during terminal keratinocyte differentiation constitute a central domain of the locus. Active transcription in the central domain is maintained by coordinated involvement of the regulators of local chromatin structure (ATP-dependent chromatin remodelers Brg1 and Mi-2β, histone demethylase JMJD3) and genome organizers Satb1 that support formation of specific higher-order chromatin folding in this region. Inhibition of transcription is associated with presence of DNA methyltransferase 1, HDAC1/2 and components of the Polycomb complexes Cbx4, Ezh1/2 and Bmi1, which promote formation of the repressive chromatin structure, as well as with lack of specific 3D-organization of the locus.

Figure 3. Model illustrating cross-talk between transcription factors and epigenetic regulators in the control of expression of tissue-specific genes in keratinocytes

In addition to direct regulation of tissue-specific genes, p63 and c-Myc transcription factors promote formation of the permissive chromatin structure in tissue-specific gene loci. p63 via regulation of genome organizer Satb1 support formation of specific higher-order organization of the tissue-specific EDC locus, whereas c-Myc via regulation of histone acetyltrasferase Gcn5 and histone methyltransferase Setd8 promotes formation of the transcription-friendly local chromatin structure. In turn, Setd8 is capable of positively influence p63 expression (based on data published (Driskell et al., 2011; Fessing et al., 2011; Knoepfler et al., 2006; Nascimento et al., 2011).