Heterochromatin: More than just an inert dense region
DNA contains all the genetic information necessary to build and maintain an organism. Inside the cell nucleus, DNA is wrapped around histone proteins to form chromatin fibers. Depending on the degree of compaction, the chromatin is classified as euchromatin (less condensed, gene-rich, and more accessible to transcription machinery) or heterochromatin (highly condensed, gene-poor, and transcriptionally silent; Huisinga et al., 2006; Figure 1A).
Heterochromatin had long been considered as genetically inert. However, it turned out to be crucial to the biology of cells and contributes, for example, to chromosome segregation during cell division. It is also important for silencing mobile genetic elements – segments of DNA that can move within the genome or jump into the genome of other cells. Mobile genetic elements can pose a real threat to the integrity of the genome, and consequently, several defence mechanisms have evolved to identify them and prevent them from multiplying.
Some heterochromatic loci, formed of remnants of mobile genetic elements, are at the center of these defence mechanisms. These parts of the genome, also known as piRNA clusters, are often compared to a ‘memory system’. Despite being heterochromatic and usually silent, they are transcribed and processed into small non-coding RNAs. These RNAs are called PIWI-interacting RNAs, or piRNAs for short, because they are loaded by proteins of the PIWI family (Figure 1B). They use sequence complementarity to recognize mobile genetic elements residing in other parts of the genome, and then silence them (Brennecke et al., 2007).
In many eukaryotes, the molecular feature defining heterochromatin is the enrichment of a specific histone mark called H3K9me3. This mark is recognized by proteins belonging to the HP1 (Heterochromatin Protein 1) family, which help to pack DNA into its condense structure (Bannister et al., 2001; Lachner et al., 2001). A member of this family, known as Rhino, facilitates the transcription of piRNA clusters in the germline of fruit flies. Although Rhino displays specific affinity for H3K9me3, it only binds to a subset of heterochromatin regions that contain this histone mark. So far, it was unclear how Rhino is guided to these specific parts of the genome (Mohn et al., 2014). Now, in eLife, Julius Brennecke and colleagues – including Lisa Baumgartner as first author – report the results of experiments that clarify this process (Baumgartner et al., 2022).
The team (who are based at the Vienna BioCenter and the Institute of Molecular Biotechnology of the Austrian Academy of Sciences) used a combination of genetic, genomic and imaging approaches to study Rhino in the germline of female fruit flies. The experiments revealed that Rhino interacts with a DNA-binding protein, which Baumgartner et al. named Kipferl. Indeed, a depletion of this protein in the ovaries of fruit flies leads to a broad redistribution and concentration of Rhino at the nuclear periphery in a form that evokes the shape of a Kipferl, an Austrian croissant.
They found that both Kipferl and Rhino are bound at many piRNA source loci, suggesting that Kipferl may act to identify the heterochromatin regions to which Rhino must bind. In the absence of Kipferl, Rhino is sequestered to another part of the genome and its binding to some piRNA clusters is lost, despite the presence of H3K9me3 marks. As a result, piRNA production in ovaries lacking Kipferl is reduced, several mobile elements are reactivated, and the females are less fertile than flies expressing Kipferl.
Kipferl is a DNA-binding protein that specifically binds to DNA sequences that are rich in the guanine nucleotide. This study suggests for the first time that such DNA sequences could help to attract Kipferl, which then recruits Rhino participate in defining piRNA clusters. However, while Kipferl guides and stabilizes Rhino to some chromatin domains enriched in H3K9me3 to convert them into piRNA clusters, some Rhino-dependent piRNA clusters do not need Kipferl (Figure 1B).
The study of Baumgartner et al. also suggests that additional factors help guide Rhino to piRNA clusters during early oogenesis, as Kipferl is not expressed during this developmental stage. Furthermore, piRNAs provided by the mothers may also help to recruit Rhino to specific heterochromatin regions in the embryo (Akkouche et al., 2017; Le Thomas et al., 2014). However, the relative contribution of maternally deposited piRNAs and Kipferl in recruiting Rhino to specify piRNA clusters during embryogenesis requires future investigations.
The study of Baumgartner et al. shows that the relationship between Rhino, Kipferl and DNA is complex, and their elegant dissection of the role of Kipferl provides substantial new insight into how piRNA clusters are defined in the genome.
References
Article and author information
Author details
Publication history
Copyright
© 2022, Akkouche and Brasset
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,420
- views
-
- 119
- downloads
-
- 1
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Chromosomes and Gene Expression
Cells evoke the DNA damage checkpoint (DDC) to inhibit mitosis in the presence of DNA double-strand breaks (DSBs) to allow more time for DNA repair. In budding yeast, a single irreparable DSB is sufficient to activate the DDC and induce cell cycle arrest prior to anaphase for about 12–15 hr, after which cells ‘adapt’ to the damage by extinguishing the DDC and resuming the cell cycle. While activation of the DNA damage-dependent cell cycle arrest is well understood, how it is maintained remains unclear. To address this, we conditionally depleted key DDC proteins after the DDC was fully activated and monitored changes in the maintenance of cell cycle arrest. Degradation of Ddc2ATRIP, Rad9, Rad24, or Rad53CHK2 results in premature resumption of the cell cycle, indicating that these DDC factors are required both to establish and maintain the arrest. Dun1 is required for the establishment, but not the maintenance, of arrest, whereas Chk1 is required for prolonged maintenance but not for initial establishment of the mitotic arrest. When the cells are challenged with two persistent DSBs, they remain permanently arrested. This permanent arrest is initially dependent on the continuous presence of Ddc2, Rad9, and Rad53; however, after 15 hr these proteins become dispensable. Instead, the continued mitotic arrest is sustained by spindle assembly checkpoint (SAC) proteins Mad1, Mad2, and Bub2 but not by Bub2’s binding partner Bfa1. These data suggest that prolonged cell cycle arrest in response to 2 DSBs is achieved by a handoff from the DDC to specific components of the SAC. Furthermore, the establishment and maintenance of DNA damage-induced cell cycle arrest require overlapping but different sets of factors.
-
- Chromosomes and Gene Expression
- Developmental Biology
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. Previous studies observed that different enhancers can achieve a wide range of transcriptional outputs through the same strategies of bursting control. For example, in Berrocal et al., 2020, we showed that despite responding to different transcription factors, all even-skipped enhancers increase transcription by upregulating burst frequency and amplitude while burst duration remains largely constant. These shared bursting strategies suggest that a unified molecular mechanism constraints how enhancers modulate transcriptional output. Alternatively, different enhancers could have converged on the same bursting control strategy because of natural selection favoring one of these particular strategies. To distinguish between these two scenarios, we compared transcriptional bursting between endogenous and ectopic gene expression patterns. Because enhancers act under different regulatory inputs in ectopic patterns, dissimilar bursting control strategies between endogenous and ectopic patterns would suggest that enhancers adapted their bursting strategies to their trans-regulatory environment. Here, we generated ectopic even-skipped transcription patterns in fruit fly embryos and discovered that bursting strategies remain consistent in endogenous and ectopic even-skipped expression. These results provide evidence for a unified molecular mechanism shaping even-skipped bursting strategies and serve as a starting point to uncover the realm of strategies employed by other enhancers.