The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations

Drosophila grainyhead gene and its neural stem cell specific enhancers show epigenetic synchrony in the cells of the central nervous system

Enhancers are the epicentres of tissue-specific gene regulation. In this study, we have used the central nervous system (CNS) specific expression of the Drosophila grainyhead (grh) gene to make a case for deleting the enhancers in a sensitised background of other enhancer deletion, to functionally validate their role in tissue-specific gene regulation. We identified novel enhancers for grh and subsequently deleted two of them, to establish their collective importance in regulating grh expression in CNS. This showed that grh relies on multiple enhancers for its robust expression in neural stem cells (NSCs), with different combinations of enhancers playing a critical role in regulating its expression in various subset of these cells. We also found that these enhancers and the grh gene show epigenetic synchrony across the three cell types (NSCs, intermediate progenitors and neurons) of the developing CNS; and grh is not transcribed in intermediate progenitor cells, which inherits the Grh protein from the NSCs. We propose that this could be a general mechanism for regulating the expression of cell fate determinant protein in intermediate progenitor cells. Lastly, our results underline that enhancer redundancy results in phenotypic robustness in grh gene expression, which seems to be a consequence of the cumulative activity of multiple enhancers.

Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation

BACKGROUND

Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs), which represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored.

RESULTS

We report a survey of gene, lncRNA, and TE expression in four organs from mice with different combinations of gonadal and genetic sex. The data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in the liver. In contrast, the X-chromosome dosage alone had a modest influence on sex-biased transcription across organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y-chromosome influences TE, but not gene or lncRNA, expression in the liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside less than 100 kb from sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We test the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals finding no evidence to support it.

CONCLUSIONS

Our data show that sex-biased expression of TEs varies among organs with the highest numbers of sDETEs found in the liver following trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.

Moving epigenetic inheritance into the space age: Evidence that 3D genome organization is required for the establishment of epigenetic memory

In this issue, Fitz-James et al.1 use genetic manipulations to show that transient interchromosomal contacts between distant regulatory elements, mediated by the transcription factor GAF, can initiate transgenerational epigenetic inheritance in D. melanogaster.

Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila

Non-genetic information can be inherited across generations in a process known as transgenerational epigenetic inheritance (TEI). In Drosophila, hemizygosity of the Fab-7 regulatory element triggers inheritance of the histone mark H3K27me3 at a homologous locus on another chromosome, resulting in heritable epigenetic differences in eye color. Here, by mutating transcription factor binding sites within the Fab-7 element, we demonstrate the importance of the proteins pleiohomeotic and GAGA factor in the establishment and maintenance of TEI. We show that these proteins function by recruiting the polycomb repressive complex 2 and by mediating interchromosomal chromatin contacts between Fab-7 and its homologous locus, respectively. Using an in vivo synthetic biology system to induce them, we then show that chromatin contacts alone can establish TEI, providing a mechanism by which hemizygosity of one locus can establish epigenetic memory at another distant locus in trans through chromatin contacts.

Meiosis as a mechanism for epigenetic reprogramming and cellular rejuvenation

Meiosis is a hallmark of sexual reproduction because it represents the transition from one life cycle to the next and, in animals, meiosis produces gametes. Why meiosis evolved has been debated and most studies have focused on recombination of the parental alleles as the main function of meiosis. However, 40 years ago, Robin Holliday proposed that an essential function of meiosis is to oppose the consequence of successive mitoses that cause cellular aging. Cellular aging results from accumulated defective organelles and proteins and modifications of chromatin in the form of DNA methylation and histone modifications referred to collectively as epigenetic marks. Here, recent findings supporting the hypothesis that meiosis opposes cellular aging are reviewed and placed in the context of the diversity of the life cycles of eukaryotes, including animals, yeast, flowering plants and the bryophyte Marchantia.

Dynamic evolution of the heterochromatin sensing histone demethylase IBM1

Heterochromatin is critical for maintaining genome stability, especially in flowering plants, where it relies on a feedback loop involving the H3K9 methyltransferase, KRYPTONITE (KYP), and the DNA methyltransferase CHROMOMETHYLASE3 (CMT3). The H3K9 demethylase INCREASED IN BONSAI METHYLATION 1 (IBM1) counteracts the detrimental consequences of KYP-CMT3 activity in transcribed genes. IBM1 expression in Arabidopsis is uniquely regulated by methylation of the 7th intron, allowing it to monitor global H3K9me2 levels. We show the methylated intron is prevalent across flowering plants and its underlying sequence exhibits dynamic evolution. We also find extensive genetic and expression variations in KYP, CMT3, and IBM1 across flowering plants. We identify Arabidopsis accessions resembling weak ibm1 mutants and Brassicaceae species with reduced IBM1 expression or deletions. Evolution towards reduced IBM1 activity in some flowering plants could explain the frequent natural occurrence of diminished or lost CMT3 activity and loss of gene body DNA methylation, as cmt3 mutants in A. thaliana mitigate the deleterious effects of IBM1.

A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation

Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres, and the silent mating type locus in Schizosaccharomyces pombe. Using quantitative measures, iterative genetic screening, and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate domain-specific functions. For example, decreased mating type silencing was linked to mutations in heterochromatin maintenance genes, while compromised subtelomere silencing was associated with metabolic pathways. Furthermore, similar phenotypic profiles revealed shared functions for subunits within complexes. We also discovered that the uncharacterized protein Dhm2 plays a crucial role in maintaining constitutive and facultative heterochromatin, while its absence caused phenotypes akin to DNA replication-deficient mutants. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.