Analysis of the abundance of CREI-96 in Rut-C30. (a) The Trichoderma reesei wild-type strain QM6a (green bars) and Rut-C30 (yellow bars) were pre-grown on glycerol and then transferred to media supplemented with D-glucose (G), sophorose (SO) or without carbon source (NC), respectively, and incubated for 3 hours. The transcript level analysis of cre1-96 was performed by qPCR using sar1 and act genes for data normalization. Levels refer to the wild-type strain incubated without carbon source. The values are means from measurements in triplicates and three biological experiments (cultivations). Error bars indicate standard deviations. (b-d) In vivo and in vitro footprinting analysis of URRs of CREI-target genes in Rut-C30, which was pre-grown on glycerol and then incubated on D-glucose (G) or sophorose (SO) for 3 hours followed by DMS-induced in vivo methylation. An URR bearing functional CREI sites (underlined in red) of the cbh1 (b), cbh2 (c), and xyr1 (d) genes each was investigated, and methylated, naked DNA (ND) was used as the reference. Numbers indicate the position of the base upstream from ATG. Analysis of data and visualization was performed using ivFAST . Colour codes are the same as in Figure 2.