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Series GSE155580 Query DataSets for GSE155580
Status Public on Aug 04, 2020
Title SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [RNA-seq]
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary Three distinct enzymes are known to be capable of methylating lysine 9 residue of the histone H3 in Drosophila melanogaster: Su(var)3-9, SetDB1, and G9a. Here, we explored functional specialization of the two of them: SetDB1 and Su(var)3-9. Using DamID approach, we generated the binding profile for SetDB1 in salivary gland chromosomes, and matched it to the previously published profile of Su(var)3-9. Unlike Su(var)3-9, SetDB1 is an euchromatic protein that is absent from repeated DNA compartment, and is largely restricted to TSSes and 5'UTRs of moderately active ubiquitously expressed genes. Significant SetDB1 association is also observed at or near insulator protein CP190 binding sites. Extensive, yet not exact colocalization SetDB1 with Su(var)3-9 occurs only along the chromosome 4. Importantly, SetDB1 and H3K9me2/3-enriched sites tend to display poor overlap. At the same time, SetDB1 has clear connection with the distribution of H3K27me3 mark. SetDB1 binds outside the domains possessing this modification, and about half of the borders of H3K27me3 domains are decorated by SetDB1 binding sites together with actively transcribed genes. Given that SetDB1 displays low correlation with H3K9 methylation and binds to the TSSes of active genes, that are usually nucleosome-poor, we speculate that in somatic cells, SetDB1 may contribute to the methylation of a broader set of chromosomal proteins than just H3K9. In addition, via association with insulator proteins and transcription machinery, SetDB1 can be expected to play a role in the establishment of chromatin functional domains.
Overall design Examination of expression of genes in salivary glands of oregon flies
Contributor(s) Kalashnikova DA, Romanov SE, Laktionov PP, Maksimov DA, Koryakov DE
Citation(s) 33288549
Submission date Aug 03, 2020
Last update date Jan 29, 2021
Contact name Daniil Maksimov
Organization name MCB NSC RAS
Lab Genomics lab
Street address Lavrentjeva ave., 8/2
City Novosibirsk
ZIP/Postal code 630090
Country Russia
Platforms (1)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
Samples (3)
GSM4707438 SG_oregon_wt-1
GSM4707439 SG_oregon_wt-2
GSM4707440 SG_oregon_wt-3
This SubSeries is part of SuperSeries:
GSE155581 SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster
BioProject PRJNA650401
SRA SRP275612

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Supplementary file Size Download File type/resource
GSE155580_SetDB1_SuVar_PE_summary_gene_id_Unstr_for_Deseq_FPKM.txt.gz 207.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
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