Genome-wide analysis of SU(VAR)3-9 distribution in chromosomes of Drosophila melanogaster
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Histone modifications represent one of the key factors contributing to proper genome regulation. One of histone modifications involved in gene silencing is methylation of H3K9 residue. Present in the chromosomes across different eukaryotes, this epigenetic mark is controlled by SU(VAR)3-9 and its orthologs. Despite SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern. To fill in this gap, we used DamID-seq approach and obtained high-resolution genome-wide profiles for SU(VAR)3-9 in two somatic (salivary glands and brain ganglia) and two germline (ovarian nurse cells and testes) tissues of Drosophila melanogaster. Analysis of tissue and developmental expression of SU(VAR)3-9-bound genes indicates that in the somatic tissues tested, as well as in the ovarian nurse cells, SU(VAR)3-9 tends to associate with transcriptionally silent genes. In contrast, in the testes, SU(VAR)3-9 shows preferential association with testis-specific genes, and its binding appears dynamic during spermatogenesis. In somatic cells, the mere presence/absence of SU(VAR)3-9 binding correlates with lower/higher expression. No such correlation is found in the male germline. Interestingly, transcription units in piRNA clusters (particularly flanks thereof) are frequently targeted by SU(VAR)3-9, and Su(var)3-9 mutation affects the expression of select piRNA species. Our analyses suggest a context-dependent role of SU(VAR)3-9. In euchromatin, SU(VAR)3-9 may serve to fine-tune the expression of individual genes, whereas in heterochromatin, chromosome 4, and piRNA clusters, it may act more broadly over large chromatin domains.
KeywordsDrosophila SU(VAR)3-9 SETDB1 piRNA Transcription Spermatogenesis
brain tissue of female larvae
brain tissue of male larvae
larval salivary glands (female)
larval salivary glands (male)
ovarian nurse cells
testes from aly mutants
testes from can mutants
testes from bam mutants
The authors are grateful to Dr. A. Gorchakov for useful comments and translating manuscript. DNA sequencing was performed by the “Molecular and cellular biology” facility at IMCB SB RAS.
This work was supported by the grants from the Russian Foundation for Basic Research (12-04-00160 and 15-04-02264) and from the Russian Programme for Basic Research (0310-2016-0005). Bioinformatic analysis of the sequencing data of the testes samples was supported by the grant from the Russian Science Foundation (14-14-00641).
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Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
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