Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA594174 | ENA |
REPOSITORIES: ENA
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Project description:Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appears to be present at all centromeres, and none of which is found only at centromeres. Although centromere sequences from a minichromosome have been identified and candidate centromere sequences have been proposed, the DNA sequences at native Drosophila centromeres remain unknown. Here we use native chromatin immunoprecipitation to identify the centromeric sequences bound by the foundational kinetochore protein cenH3, known in vertebrates as CENP-A. In D. melanogaster, these sequences include a few families of 5-bp and 10-bp repeats, but in closely related D. simulans, a partially overlapping set of short repeats and more complex repeats comprise the centromeres. The results suggest that a recent expansion of short repeats is replacing more complex centromeric repeats in the melanogaster subgroup of Drosophila.
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Project description:Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. Regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. We investigated the contribution of pericentromeric genome organization and heterochromatic factors in orchestrating heterochromatic gene expression. Using 5C-seq, we characterized the pericentromeric TADs in Drosophila melanogaster. Het TAD borders are enriched in nuclear matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs, indicating transcriptional co-regulation. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. A subset of active heterochromatic genes has been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Consequently, knock-down of dMES-4 (H3K36 methyl transferase) downregulates expression of the heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, is likely to regulate the heterochromatic gene expression in the presence of HP1a or H3K9me3 marks. Therefore, our findings provide mechanistic insights into the interplay of chromatin interactions and the combination of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) in regulating heterochromatic gene expression.
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Project description:Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. Regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. We investigated the contribution of pericentromeric genome organization and heterochromatic factors in orchestrating heterochromatic gene expression. Using 5C-seq, we characterized the pericentromeric TADs in Drosophila melanogaster. Het TAD borders are enriched in nuclear matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs, indicating transcriptional co-regulation. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. A subset of active heterochromatic genes has been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Consequently, knock-down of dMES-4 (H3K36 methyl transferase) downregulates expression of the heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, is likely to regulate the heterochromatic gene expression in the presence of HP1a or H3K9me3 marks. Therefore, our findings provide mechanistic insights into the interplay of chromatin interactions and the combination of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) in regulating heterochromatic gene expression.
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