@article{VučićevićGehreDhamijaetal.2016, author = {Vučićević, Dubravka and Gehre, Maja and Dhamija, Sonam and Friis-Hansen, Lennart and Meierhofer, David and Sauer, Sascha and {\O}rom, Ulf Andersson}, title = {The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation}, series = {Oncotarget}, volume = {7}, journal = {Oncotarget}, number = {23}, doi = {10.18632/oncotarget.8985}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166519}, pages = {33934-33947}, year = {2016}, abstract = {Long non-coding RNAs are important regulators of gene expression and signaling pathways. The expression of long ncRNAs is dysregulated in cancer and other diseases. The identification and characterization of long ncRNAs is often challenging due to their low expression level and localization to chromatin. Here, we identify a functional long ncRNA, PARROT (Proliferation Associated RNA and Regulator Of Translation) transcribed by RNA polymerase II and expressed at a relatively high level in a number of cell lines. The PARROT long ncRNA is associated with proliferation in both transformed and normal cell lines. We characterize the long ncRNA PARROT as an upstream regulator of c-Myc affecting cellular proliferation and translation using RNA sequencing and mass spectrometry following depletion of the long ncRNA. PARROT is repressed during senescence of human mammary epithelial cells and overexpressed in some cancers, suggesting an important association with proliferation through regulation of c-Myc. With this study, we add to the knowledge of cytoplasmic functional long ncRNAs and extent the long ncRNA-Myc regulatory network in transformed and normal cells.}, language = {en} } @article{ConradAlbrechtRodriguesdeMeloCostaetal.2016, author = {Conrad, Thomas and Albrecht, Anne-Susann and Rodrigues de Melo Costa, Veronica and Sauer, Sascha and Meierhofer, David and Andersson {\O}rom, Ulf}, title = {Serial interactome capture of the human cell nucleus}, series = {Nature Communications}, volume = {7}, journal = {Nature Communications}, number = {11212}, doi = {10.1038/ncomms11212}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166172}, year = {2016}, abstract = {Novel RNA-guided cellular functions are paralleled by an increasing number of RNA-binding proteins (RBPs). Here we present 'serial RNA interactome capture' (serIC), a multiple purification procedure of ultraviolet-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with high specificity. We apply serIC to the nuclei of proliferating K562 cells to obtain the first human nuclear RNA interactome. The domain composition of the 382 identified nuclear RBPs markedly differs from previous IC experiments, including few factors without known RNA-binding domains that are in good agreement with computationally predicted RNA binding. serIC extends the number of DNA-RNA-binding proteins (DRBPs), and reveals a network of RBPs involved in p53 signalling and double-strand break repair. serIC is an effective tool to couple global RBP capture with additional selection or labelling steps for specific detection of highly purified RBPs.}, language = {en} } @article{CuiSchlesingerSchoenhalsetal.2016, author = {Cui, Huanhuan and Schlesinger, Jenny and Schoenhals, Sophia and Tonjes, Martje and Dunkel, Ilona and Meierhofer, David and Cano, Elena and Schulz, Kerstin and Berger, Michael F. and Haack, Timm and Abdelilah-Seyfried, Salim and Bulyk, Martha L. and Sauer, Sascha and Sperling, Silke R.}, title = {Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA}, series = {Nucleic Acids Research}, volume = {44}, journal = {Nucleic Acids Research}, number = {6}, doi = {10.1093/nar/gkv1244}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166391}, pages = {2538-2553}, year = {2016}, abstract = {DPF3 (BAF45c) is a member of the BAF chromatin remodeling complex. Two isoforms have been described, namely DPF3a and DPF3b. The latter binds to acetylated and methylated lysine residues of histones. Here, we elaborate on the role of DPF3a and describe a novel pathway of cardiac gene transcription leading to pathological cardiac hypertrophy. Upon hypertrophic stimuli, casein kinase 2 phosphorylates DPF3a at serine 348. This initiates the interaction of DPF3a with the transcriptional repressors HEY, followed by the release of HEY from the DNA. Moreover, BRG1 is bound by DPF3a, and is thus recruited to HEY genomic targets upon interaction of the two components. Consequently, the transcription of downstream targets such as NPPA and GATA4 is initiated and pathological cardiac hypertrophy is established. In human, DPF3a is significantly up-regulated in hypertrophic hearts of patients with hypertrophic cardiomyopathy or aortic stenosis. Taken together, we show that activation of DPF3a upon hypertrophic stimuli switches cardiac fetal gene expression from being silenced by HEY to being activated by BRG1. Thus, we present a novel pathway for pathological cardiac hypertrophy, whose inhibition is a long-term therapeutic goal for the treatment of the course of heart failure.}, language = {en} } @article{TeloracPrykhozhijSchoeneetal.2016, author = {Telorac, Jonas and Prykhozhij, Sergey V. and Sch{\"o}ne, Stefanie and Meierhofer, David and Sauer, Sascha and Thomas-Chollier, Morgane and Meijsing, Sebastiaan H.}, title = {Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements}, series = {Nucleic Acids Research}, volume = {44}, journal = {Nucleic Acids Research}, number = {13}, doi = {10.1093/nar/gkw203}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166330}, pages = {6142-6156}, year = {2016}, abstract = {Out of the myriad of potential DNA binding sites of the glucocorticoid receptor (GR) found in the human genome, only a cell-type specific minority is actually bound, indicating that the presence of a recognition sequence alone is insufficient to specify where GR binds. Cooperative interactions with other transcription factors (TFs) are known to contribute to binding specificity. Here, we reasoned that sequence signals preventing GR recruitment to certain loci provide an alternative means to confer specificity. Motif analyses uncovered candidate Negative Regulatory Sequences (NRSs) that interfere with genomic GR binding. Subsequent functional analyses demonstrated that NRSs indeed prevent GR binding to nearby response elements. We show that NRS activity is conserved across species, found in most tissues and that they also interfere with the genomic binding of other TFs. Interestingly, the effects of NRSs appear not to be a simple consequence of changes in chromatin accessibility. Instead, we find that NRSs interact with proteins found at sub-nuclear structures called paraspeckles and that these proteins might mediate the repressive effects of NRSs. Together, our studies suggest that the joint influence of positive and negative sequence signals partition the genome into regions where GR can bind and those where it cannot.}, language = {en} }