RESUMO
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.
Assuntos
Montagem e Desmontagem da Cromatina , Cromatina/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , DNA/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Histonas/metabolismo , Animais , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/química , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Cromatina/química , Cromatina/genética , Proteínas Cromossômicas não Histona/química , Proteínas Cromossômicas não Histona/genética , Simulação por Computador , DNA/química , DNA/genética , DNA de Plantas/química , DNA de Plantas/genética , DNA de Plantas/metabolismo , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Histonas/química , Histonas/genética , Humanos , Modelos Biológicos , Conformação de Ácido Nucleico , Conformação Proteica , Relação Estrutura-Atividade , Transcrição GênicaRESUMO
Chromosome conformation capture assays have been established, modified, and enhanced for over a decade with the purpose of studying nuclear organization. A recently published method uses in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) to enrich the overall yield of significant genome-wide interactions mediated by a specific protein. Here we applied a modified version of the HiChIP protocol to retrieve the significant contacts mediated by architectural protein CP190 in D. melanogaster cells.