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E-GEOD-43751 - Transcription dependent dynamic supercoiling in Raji human B cells in vivo

Status
Released on 16 February 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (24)
Array (1)
Protocols (11)
Description
Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation. Raji cells: untreated and treated with DRB, CPT and BLAP. Three biological replicates per treatment, each hybridized to new array. Total: 12 samples (4 treatments x 3 replicates).
Experiment type
comparative genomic hybridization by array 
Contacts
Ashutosh Gupta, Damian Wojtowicz, David Levens, Fedor Kouzine, Juhong Liu, Khadija Ben-Aissa, Laura Baranello, Teresa M Przytycka
MIAME
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