Establishment and evolution of heterochromatin

Abstract

The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein-coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic "dark matter" in the context of topologically associated domains and phase-separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever-changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.

Keywords: chromatin conformation; heterochromatin; histone modifications; sex chromosomes.

Figure 1

The concept of heterochromatin has been evolving since its first description in 1928 by Emil Heitz. Shown is an incomplete list of events that led to changes in the concept of heterochromatin during research developments from the cytogenetic era until very recently in the 3D genomics era. The characterization of proteins (e.g., HP1) regulating constitutive heterochromatin was largely attributed to the genetic screens in Drosophila for mutants affecting the position‐effect variegation (PEV) phenotype. The studies into facultative heterochromatin were first marked by the discovery of the Barr body, that is, the female‐specific inactivated X chromosome. After the discovery of nucleosome structure as the chromatin unit for gene regulation, many PEV‐related genes were found to be the reader or writer of histone modifications within the chromatin unit. With the development of chromatin immunoprecipitation (ChIP) technology targeting these histone modifications, combined with either microarray (ChIP‐chip) or sequencing analyses (ChIP‐seq), it became clear that heterochromatin is usually associated with highly repetitive regions and the histone methylation marks H3K9me2/3 and H3K27me3. This facilitated the definition of the heterochromatin region at the base pair resolution in the genomic and epigenomic era. Recently, it has been shown in Drosophila and humans that heterochromatin forms within phase‐separated droplets of HP1 protein and forms distinct topologically associated domains from those of euchromatin, as detected by Hi‐C technology.

Figure 2

Establishment of heterochromatin during Drosophila embryogenesis. After fertilization, Drosophila embryos undergo 13 rapid cleavage divisions (cycles 2–13) with little zygotic transcription, as transcripts and proteins (e.g., EGG and PcG proteins) and histone modifications (e.g., H3K27me3) are mainly maternally inherited. During these early embryonic stages, both the state and topology of chromatin remain in a naive state, and there are more mobile HP1 proteins than immobile ones observed in the embryos. The establishment of the heterochromatin marker H3K9me2/3 has been recently shown to involve the histone methyltransferase EGG. At the onset of zygotic transcription at mitotic cycle 14, H3K9me2/3 can be detected by immunostaining, and there are significantly more structured TADs than in previous stages. Once the constitutive heterochromatin and chromatin topology are established, they remain largely stable across later developmental stages. The dynamics of mobile and immobile HP1a are adopted from Strom et al.110

Figure 3

Transitions from euchromatin to heterochromatin. Three proposed models of euchromatin to heterochromatin transition. Heterochromatin is usually distributed close to the nuclear periphery and tethered to the lamina or around the nucleoli, while euchromatin is located in the nuclear interior. (A) The de novo formation of heterochromatin domains induced by TE insertions. A TE insertion into the euchromatic region may trigger heterochromatin formation mediated by small RNA pathways. This may further impact the expression of nearby genes by the spreading effect of newly formed heterochromatin domains. (B) Change in euchromatin/heterochromatin balance. The expansion of heterochromatin or ectopic formation of heterochromatin can be caused by upregulation of heterochromatin‐associated proteins (e.g., histone methyltransferase SU(VAR)3‐9, shown as dark blue circles) or downregulation of euchromatin‐associated proteins (red circles). This has been demonstrated in Drosophila and yeast. Such chromatin boundaries form without the participation of boundary elements, such as CTCF proteins, and are thus called negotiable borders. (C) Mutations of TAD boundary sequences (green bars between the two TADs) between euchromatin and heterochromatin domains. The TAD boundary sequences are usually CTCF binding sites or transcriptionally active genes or TEs. Removal or inversion of such boundary sequences may lead to the expansion of heterochromatin domains into euchromatin. The newly formed heterochromatin domains through the TE insertions, A, or expanded heterochromatin domains through B or C will convergently interact with other preexisting heterochromatin domains at the lamina through fusions of phase‐separated droplets. Such interactions may impact the nearby genes or genes on a different chromosome by reshaping the genome‐wide folding. Het, heterochromatin; Eu, euchromatin; TE, transposable element.