Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing

Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.

Location decision-making of 'creative' industries: the media and computer games sectors in Dublin, Ireland

There has been significant research undertaken examining the “creative class” thesis within the context of the locational preferences of creative workers. However, relatively little attention has been given to the locational preferences of creative companies within the same context. This paper reports on research conducted to qualitatively analyse the location decision making of companies in two creative sectors: media and computer games. We address the role of the so-called “hard” and “soft” factors in company location decision making within the context of the creative class thesis, which suggests that company location is primarily determined by “soft” factors rather than “hard” factors. The study focuses upon “core” creative industries in the media and computer game sectors and utilises interview data with company managers and key elite actors in the sector to investigate the foregoing questions. The results show that “hard” factors are of primary importance for the location decision making in the sectors analysed, but that “soft” factors play quite an important role when “hard” factors are satisfactory in more than one competing city-region.