DNA-bound transcription factor complexes analysed by mass-spectrometry: binding of novel proteins to the human c-fos SRE and related sequences

Transcription factors control eukaryotic polymerase II function by influenc ing the recruitment of multiprotein complexes to promoters and their subseq uent integrated function. The complexity of the functional 'transcriptosome ' has necessitated biochemical fractionation and subsequent protein sequenc ing on a grand scale to identify individual components. As a consequence, m uch is now known of the basal transcription complex. In contrast, less is k nown about the complexes formed at distal promoter elements. The c-fos SRE, for example, is known to bind Serum Response Factor (SRF) and ternary comp lex factors such as Elk-1. Their interaction with other factors at the SRE is implied but, to date, none have been identified, Here we describe the us e of mass-spectrometric sequencing to identify six proteins, SRF, Elk-1 and four novel proteins, captured on SRE duplexes linked to magnetic beads. Th is approach is generally applicable to the characterisation of nucleic acid -bound protein complexes and the posttranslational modification of their co mponents.