Figure 1

Validation of data sets. A. Genome browser view (Artemis [56]) showing genome coverage for a section of chromosome 4, with the gene model indicated in the top. Genes located on the forward and the reverse strands are indicated in yellow and orange, respectively. Sequencing of genomic DNA resulted in an even distribution of reads across intergenic and coding regions. Sequence read coverage for MAINE-Seq [18], Sonication ChIP-Seq and MNase ChIP-Seq was similar and showed increased coverage of coding region as compared to intergenic regions, while opposite results were observed for FAIRE-Seq [18]. B. DNA yields of immunoprecipitations using a non-specific antibody, an antibody directed against histone H3 (Abcam ab1971) and an antibody directed against histone H4 (Millipore 05-858). These data show a reduced amount of DNA obtained from trophozoite samples, despite using the same amount of input material for each immunoprecipitation. Since low amounts of DNA were obtained using the anti-H4 antibody, we concluded that this antibody was not well suited for ChIP-Seq experiments and was therefore not used for further analysis. C. Total spectral counts for all histone proteins (left) and all annotated RNA polymerase II proteins (right) obtained by mass spectrometry analysis of nuclear fractions from ring, trophozoite and schizont stage parasites [24]. Abundance levels of histones decreased during the trophozoite stage, while the amount of RNA polymerase II increased, consistent with high transcriptional activity in this stage, but not the ring or schizont stages. Spectral count data were obtained from PlasmoDB (http://www.plasmodb.org).