Constitutive heterochromatin formation and transcription in mammals

Abstract

Constitutive heterochromatin, mainly formed at the gene-poor regions of pericentromeres, is believed to ensure a condensed and transcriptionally inert chromatin conformation. Pericentromeres consist of repetitive tandem satellite repeats and are crucial chromosomal elements that are responsible for accurate chromosome segregation in mitosis. The repeat sequences are not conserved and can greatly vary between different organisms, suggesting that pericentromeric functions might be controlled epigenetically. In this review, we will discuss how constitutive heterochromatin is formed and maintained at pericentromeres in order to ensure their integrity. We will describe the biogenesis and the function of main epigenetic pathways that are involved and how they are interconnected. Interestingly, recent findings suggest that alternative pathways could substitute for well-established pathways when disrupted, suggesting that constitutive heterochromatin harbors much more plasticity than previously assumed. In addition, despite of the heterochromatic nature of pericentromeres, there is increasing evidence for active and regulated transcription at these loci, in a multitude of organisms and under various biological contexts. Thus, in the second part of this review, we will address this relatively new aspect and discuss putative functions of pericentromeric expression.

Keywords: epigenetic factors; heterochromatin; histone modifying enzymes; pericentromere; transcription.

Figure 1

Organization of constitutive heterochromatin. (A) Constitutive heterochromatin is found at pericentromeric, telomeric, and ribosomal regions, as well as at different loci along the chromosome (B) Centromeres and pericentromeres consist of predominantly repetitive DNA sequences, including simple repeats, DNA transposons, LTR-endogenous retroviral elements, non-LTR autonomous retrotransposons including long interspersed elements and short interspersed elements. The approximate length of the different repetitive elements is indicated. In mice, centromeres consist mainly of minor satellites and pericentromeres of major satellites. In human beings, centromeres consist mainly of alpha satellites and pericentromeres of chromosome specific satellite repeats, including satellites I, II and III. (C) Chromocenters in differentiated cells are smaller, more numerous and more condensed than chromocenters in undifferentiated pluripotent cells, which are probably more dynamic. CT, centromere; DR, direct repeat; IR, inverted repeats; LINE, long interspersed element; MEF, mouse embryonic fibroblasts; mESC, mouse embryonic stem cells; PCT, pericentromere; SINE, short interspersed element; TSDR, target site direct repeat.

Figure 2

Schematic representation of constitutive heterochromatin formation in mammals. SUV39H is the responsible HTMase for H3K9me3 on pericentromeres, a histone mark recognized by HP1 proteins. HP1 proteins interact and recruit SUV420H and DNMTs, leading to H4K20me3 and DNA methylation, respectively. These epigenetic marks function also as docking sites, like H4K20me3 for ORC (origin of replication complex) proteins and CpGme for MBDs (factors with a methyl-binding domain). An alternative for DNMT recruitment might be through UHRF1 that directly interacts with DNMT1 and might read the H3K9me3 mark. In general, proteins involved in various pathways are required for heterochromatin formation and maintenance, and are listed in this panel.

Figure 3

Schematic representation of constitutive heterochromatin formation in fission yeast. Sir2 is responsible for deacetylation of histone tails. Clr4 methylates histone H3 on lysine 9 (H3K9me3), which is an anchor for the HP1 homolog Swi6. RNA Polymerase II (RNAPII) transcribes pericentromeric noncoding repeats in single strand RNA. Rdp1, a component of the RNA-dependent RNA polymerase, can generate a double-strand RNA, which is digested by Dicer to produce short interfering RNAs (siRNAs). The siRNAs associate with the RITS (RNA-induced initiation of transcriptional silencing) complex, which is responsible for further recruitment of Clr4, and therefore stimulates further H3K9me3 and maintains local heterochromatin.

Figure 4

Different biological contexts of pericentromeric satellite expression. Physiological expression of pericentromeric satellite repeats has been reported during cell cycle, aging cellular senescence, differentiation and development. Expression levels are detectible but low. Pathological expression has been reported upon cellular stress and in cancer, and expression levels are often aberrantly overexpressed. The size and orientation of the transcripts are indicated when known. In addition, putative functions of the noncoding transcripts in different biological contexts are mentioned and discussed in the text.