The large fraction of heterochromatin in Drosophila neurons is simultaneously bound by B-type lamin and HP1a
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ABSTRACT:
PROVIDER: PRJNA431214 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6491420.fastq.gz | Fastqsanger.gz | |||
| SRR6491430.fastq.gz | Fastqsanger.gz | |||
| SRR6491440.fastq.gz | Fastqsanger.gz | |||
| SRR6491450.fastq.gz | Fastqsanger.gz | |||
| SRR6491421.fastq.gz | Fastqsanger.gz |
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Project description:In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin as observed by both microscopy observations and DamID mapping of lamina-associated domains (LADs), enriched in dimethylated Lys9 of histone H3 (H3K9me2). In Drosophila Kc167 cell culture, where LADs were only mapped to the moment, they are neither H3K9me2-enriched, nor overlap with the domains of Heterochromatin Protein 1a (HP1a). Here, using a cell type-specific DamID approach we mapped genome-wide LADs, HP1a and Pc domains from the central brain, Repo-positive glia, Elav-positive neurons and the fat body of Drosophila third instar larvae. Silent or weakly-expressed genes occupy LADs, HP1a and Pc domains, with genes residing in the HP1a-bound LADs expressed at the lowest level. However, a fraction of HP1a domains contain actively expressed genes. The inter-LAD regions that are shared by all cell types are populated by ubiquitously expressed genes, whereas the conserved LADs are less abundant than in mammals. Importantly, in the central brain and in neurons we found strong overlap of HP1a domains with LADs both in the chromosome arms and in pericentromeric regions. In the glia and fat bodies, this overlap was less frequent. Consistent with these results, centromeres appear to reside closer to nuclear lamina in neurons than in Kc167 cells. The discovery of Drosophila peripheral chromatin bound by both HP1a and B-type lamin implies that mechanisms of heterochromatin compaction and attachment to nuclear lamina may be similar in Drosophila and mammals.
2018-10-31 | GSE109495 | GEO
Project description:BackgroundIn most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin, as evidenced by microscopy observations and DamID mapping of lamina-associated domains (LADs) enriched in dimethylated Lys9 of histone H3 (H3K9me2). However, in Kc167 cell culture, the only Drosophilla cell type where LADs have previously been mapped, they are neither H3K9me2-enriched nor overlapped with the domains of heterochromatin protein 1a (HP1a).ResultsHere, using cell type-specific DamID we mapped genome-wide LADs, HP1a and Polycomb (Pc) domains from the central brain, Repo-positive glia, Elav-positive neurons and the fat body of Drosophila third instar larvae. Strikingly, contrary to Kc167 cells of embryonic origin, in neurons and, to a lesser extent, in glia and the fat body, HP1a domains appear to overlap strongly with LADs in both the chromosome arms and pericentromeric regions. Accordingly, centromeres reside closer to the nuclear lamina in neurons than in Kc167 cells. As expected, active gene promoters are mostly not present in LADs, HP1a and Pc domains. These domains are occupied by silent or weakly expressed genes with genes residing in the HP1a-bound LADs expressed at the lowest level.ConclusionsIn various differentiated Drosophila cell types, we discovered the existence of peripheral heterochromatin, similar to that observed in mammals. Our findings support the model that peripheral heterochromatin matures enhancing the repression of unwanted genes as cells terminally differentiate.
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Project description:Identification of transcripts simultaneously bound by Mmi1 and Mei2
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Project description:We determined the repertoire of transcripts simultaneously bound by Mmi1 and Mei2 through sequential immunoprecipitations followed by high-throughput sequencing of associated RNAs (seqRIP-seq)
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Project description:Heterochromatin is enriched for characteristic epigenetic factors, including Heterochromatin Protein 1a (HP1a) and is essential for many organismal functions. However, how this nuclear domain is organized and functions is unclear. We extensively investigated heterochromatin protein compostion by biochemically purifying Drosophila melanogaster HP1a interactors.
2016-08-18 | PXD003780 | Pride
Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites.
2012-12-21 | GSE38366 | GEO
Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites. In total 44 samples; 2 replicates for each genotype and for each ChIP (HP1a, H3K9me2 and H3K9me3)
2012-12-21 | E-GEOD-38366 | biostudies-arrayexpress
Project description:influence of lamin B rereceptor knockout and lamin A/C knockout on gene expression in cultured myoblast cells and in striated muscle tissue knockout samples are obtained by mating of heterozygous animals. Homozygous KO and wt animals of one litter are compared. Two boilogical replicates of KO samples are processed in parallel. wt samples are used as controls. One wt sample is processed per KO litter. Where appropriate two wt samples are used as biological replicates.
2013-01-28 | E-GEOD-37076 | biostudies-arrayexpress
Project description:Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs. Total RNA obtained from ASCs and ASCs depleted of LMNA (LMNA-KD) and processed for microarray hybridization.
2013-07-14 | E-GEOD-42523 | biostudies-arrayexpress
Project description:Heterochromatin protein 1a (HP1a) is a well-known component of pericentromeric and telomeric heterochromatin in Drosophila. However, its role and the mechanisms of its binding in the chromosome arms (ChAs) remain largely unclear. Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamIDseq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. Although HP1a domains cover only 13% of ChAs, they non-randomly associate with 42% of TE insertions. Furthermore, HP1a propagates from TE insertions at distances up to 10-kb. These data confirm the role of TEs in formation of HP1a islands in ChAs. However, only 18% of HP1a domains have adjacent TEs, indicating the existence of other mechanisms of HP1a domain formation besides spreading from TEs. In particular, many TE-independent HP1a domains correspond to the regions attached to the nuclear pore complexes (NPCs), or contain active gene promoters. Surprisingly, HP1a occupancy on the promoters of these genes does not lead to their repression. However, the steady-state transcript level of many genes located outside of HP1a domains was altered upon HP1a knockdown in the somatic cells of ovaries, thus pointing to the strong indirect effect of HP1a depletion. Collectively, our results support an existence of at least three different mechanisms of HP1a domain emergence in ChAs: spreading from TE insertions, interaction with the chromatin located near NPCs and targeting to the promoters of moderately expressed genes.
2020-05-26 | GSE132756 | GEO