Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation

Abstract Background Chromatin insulators shield promoters and chromatin domains from neighboring enhancers or chromatin regions with opposing activities. Insulator-binding proteins and their cofactors mediate the boundary function. In general, covalent modification of proteins by the small ubiquitin-like modifier (SUMO) is an important mechanism to control the interaction of proteins within complexes. Results Here we addressed the impact of dSUMO in respect of insulator function, chromatin binding of insulator factors and formation of insulator speckles in Drosophila. SUMOylation augments the enhancer blocking function of four different insulator sequences and increases the genome-wide binding of the insulator cofactor CP190. Conclusions These results indicate that enhanced chromatin binding of SUMOylated CP190 causes fusion of insulator speckles, which may allow for more efficient insulation

MOESM3 of Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation

Additional file 3: Table S1. All primer sequences are listed

MOESM4 of Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation

Additional file 4: Table S2. Flag-SUMO and CP190 staining after luc or after Smt3 knockdown. Analyses of CP190 intensity maxima as well as determination of FLAG-dSUMO signal intensity were performed with Fiji, the image processing package of ImageJ. FLAG-dSUMO signal intensity measured by integrated density was background-corrected

MOESM1 of Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation

Additional file 1: Figure S1. dCTCF and CP190 peaks co-localize with previously identified dCTCF and CP190 binding sites. Peaks for dCTCF and CP190 were identified using MACS2 based on publicly available (GSE41354) ChIP-seq profiles published in Ong et al. [42] (PMID 24055367). Average binding of dCTCF as well as CP190 before and after expression of FLAG-dSUMO is shown across the known dCTCF (left) and CP190 (right) binding sites

Genotyping circulating tumor DNA of pediatric Hodgkin lymphoma

We used hybrid capture-targeted next-generation sequencing of circulating cell-free DNA (ccfDNA) of pediatric Hodgkin lymphoma (PHL) patients to determine pathogenic mechanisms and assess the clinical utility of this method. Hodgkin-Reed/Sternberg (HRS) cell-derived single nucleotide variants, insertions/deletions, translocations and VH-DH-JH rearrangements were detected in pretherapy ccfDNA of 72 of 96 patients. Number of variants per patient ranged from 1 to 21 with allele frequencies from 0.6 to 42%. Nine translocation breakpoints were detected. Genes involved in JAK/STAT, NFkB and PI3K signaling and antigen presentation were most frequently affected. SOCS1 variants, mainly deletions, were found in most circulating tumor (ct) DNAs, and seven of the nine translocation breakpoints involved SOCS1. Analysis of VH-DH-JH rearrangements revealed an origin of PHL HRS cells from partially selected germinal center B cells. Amounts of pretherapy ctDNA were correlated with metabolic tumor volumes. Furthermore, in all ccfDNA samples of 43 patients with early response assessment quantitative qPET 3, indicative of an unfavorable clinical course, ctDNA remained detectable. ccfDNA analysis of PHL is thus a suitable approach to determine pathogenic mechanisms and monitor therapy response