In vivo and in vitro footprinting analyses of URRs of CREI-target genes. The Trichoderma reesei wild-type strain QM6a and Rut-C30 were pre-grown on glycerol and then incubated on D-glucose for 3 hours followed by DMS-induced in vivo methylation. An URR bearing functional CREI sites (underlined in red) of the cbh1 (a), cbh2 (b), and xyr1 (c) genes was investigated, and methylated, naked DNA was used as the reference. Numbers indicate the position of the base upstream from ATG. Analysis of data and visualization was performed using ivFAST (in vivo footprinting analysis software tool) . Only signals that are statistically different are considered. Protected bases are highlighted in red shades and hypersensitive bases are highlighted in blue shades. The three colour intensities each correspond to stronger differences between compared conditions; increasing colour intensity means more than 1.4-, 1.6-, and 1.8-fold difference in cbh1 and cbh2 (a, b), and more than 2.4-, 2.6-, and 2.8-fold difference in xyr1 (c).