The transcription factor Sp2 is essential for early mouse development and for proliferation of mouse embryonic fibroblasts in culture. Yet its mechanisms of action and its target genes are largely unknown. In this study, we have combined RNA interference, in vitro DNA binding, chromatin immunoprecipitation sequencing and global gene-expression profiling to investigate the role of Sp2 for cellular functions, to define target sites and to identify genes regulated by Sp2. We show that Sp2 is import ...[more]
Project description:Mouse embyronic fibroblasts (MEFs) were depleted for transcription factor Specificity Factor 2 (Sp2) via Cre-Recombinase, harvested either 7 days or several weeks post infection and their expression profile compared to mock-infected MEFs.
Project description:We investigated the genomic binding profiles of the transcription factors Pbx1, Prep1, and Sp2 in mouse embryonic fibroblasts using ChIPseq and ChIPexo. Refer to E-MTAB-2970 and E-MTAB-994 for KO and IgG Controls.
Project description:Investigation of the binding behaviour of Sp1, Sp2, Sp3 and NF-ya, NF-yb and NF-yc in mouse embryonic fibroblasts and of Sp1, Sp2 and Sp3 in HEK-293 cells reveals distinct binding of the seemingly similar transcription factors Sp1/3 and Sp2.
Project description:We describe a method that permits the identification of proteins that are modified by both SUMOylation and ubiquitylation to better understand the role of this crosstalk. The procedure requires 3 days when starting from cell pellets and can yield more than 8000 SUMO sites and 3500 ubiquitin sites from 16 mg of cell extract.
Project description:Loss of nutrient supply elicits alterations of the SUMO proteome and sumoylation is crucial to various cellular processes including transcription. However, the physiological significance of sumoylation of transcriptional regulators is unclear. To begin clarifying this, we mapped the SUMO proteome under nitrogen-limiting conditions in Saccharomyces cerevisiae. Interestingly, several RNA polymerase III (RNAPIII) components are major SUMO targets under normal growth conditions, including Rpc53, Rpc82, and Ret1, and nutrient starvation results in rapid desumoylation of these proteins. These findings are supported by ChIP-seq experiments that show that SUMO is highly enriched at tDNA genes. Furthermore, RNA-seq experiments revealed that preventing sumoylation results in significantly decreased tRNA transcription. TORC1 inhibition resulted in the same effect, and our data indicate that the SUMO and TORC1 pathways are both required for robust tDNA expression. Importantly, tRNA transcription was strongly reduced in cells expressing a non-sumoylatable Rpc82-4KR mutant, which correlated with a misassembled RNAPIII transcriptional complex. Our data suggest that in addition to TORC1 activity, sumoylation of RNAPIII is key to reaching full translational capacity under optimal growth conditions.
Project description:Myc was depleted in HeLa cells (ATCC CRL-1934) with an shRNA and the resulting expression profile changes mapped via microarrays. This study is the equivalent of E-MTAB-1524 . E-MTAB-1524 has been replaced by E-MTAB-1886.
Project description:B-ALL Xenograft Histone Modification at BIM locus<br>The cells used are human B- acute lymphoblastic leukaemia cells that have been propagated in<br>NOD/SCID mice. B-ALL2 and B-ALL3 are cells from two different patients.<br><br>Normalized data files containing chromosome 2 data are available on the FTP site for this experiment in the E-MEXP-2814.additional.zip archive.
Project description:T-ALL Xenograft Histone Modification at ERG locus: The cells used are human T-acute lymphoblastic leukaemia cells that have been propagated in NOD/SCID mice. T-ALL8,T-ALL16, T-ALL27, T-ALL29, T-ALL30 and T-ALL31 are cells from six different patients. Normalized data files containing chromosome 21 data are available on the FTP site for this experiment in the E-MTAB-431.additional.zip archive.
Project description:micro RNA expression during adipogenesis of human mesenchynal stem cells. Cells transfected with wildtype human C/EBP-alpha (in expression vector pcDNA3.1) and overexpression of C/EBP-alpha for 48 hours were compared to control cells transfected with the empty vector.