Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila.
Chromatin insulators are functionally conserved DNA-protein complexes situated throughout the genome that organize independent transcriptional domains. Previous work implicated RNA as an important cofactor in chromatin insulator activity, although the precise mechanisms are not yet understood. Here we identify the exosome, the highly conserved major cellular 3' to 5' RNA degradation machinery, as a physical interactor of CP190-dependent chromatin insulator complexes in Drosophila. Genome-wide profiling of exosome by ChIP-seq in two different embryonic cell lines reveals extensive and specific overlap with the CP190, BEAF-32 and CTCF insulator proteins. Colocalization occurs mainly at promoters but also boundary elements such as Mcp, Fab-8, scs and scs', which overlaps with a promoter. Surprisingly, exosome associates primarily with promoters but not gene bodies of active genes, arguing against simple cotranscriptional recruitment to RNA substrates. Similar to insulator proteins, exosome is also significantly enriched at divergently transcribed promoters. Directed ChIP of exosome in cell lines depleted of insulator proteins shows that CTCF is required specifically for exosome association at Mcp and Fab-8 but not other sites, suggesting that alternate mechanisms must also contribute to exosome chromatin recruitment. Taken together, our results reveal a novel positive relationship between exosome and chromatin insulators throughout the genome.
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
Su Jun
SJ
Lim
Patrick J
PJ
Boyle
Madoka
M
Chinen
Ryan K
RK
Dale
Elissa P
EP
Lei
D000818:Animals; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism*; D002874:Chromosome Mapping; D004268:DNA-Binding Proteins / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D004331:Drosophila melanogaster / Q000235:genetics*; D063326:Exosome Multienzyme Ribonuclease Complex / Q000378:metabolism; D055354:Exosomes / Q000235:genetics* / Q000378:metabolism; D005136:Eye Proteins / Q000378:metabolism; D005786:Gene Expression Regulation; D049750:Genome, Insect; D008869:Microtubule-Associated Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D010641:Phenotype; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D021122:Protein Subunits / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
C452919:BEAF-32 protein, Drosophila; D000076246:CCCTC-Binding Factor; C107964:CP190 protein, Drosophila; C524946:CTCF protein, Drosophila; D002843:Chromatin; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D005136:Eye Proteins; D008869:Microtubule-Associated Proteins; D009687:Nuclear Proteins; D021122:Protein Subunits; D012097:Repressor Proteins; C545895:Rrp6 protein, Drosophila; D063326:Exosome Multienzyme Ribonuclease Complex