List derived from the BLAST analysis explained above. The presence of upstream t-, r- or

List derived from the BLAST analysis explained above. The presence of upstream t-, r- or snRNA genes was verified for internal start regions. The list of mapped transcription start regions is shown in Additional file 3: Table S5.Discrete Fourier analysis of dinucleotide frequenciesThe hygromycin resistance gene (Hygromycin-B 4-O-kinase; accession number V01499) as well as the neomycin resistance marker (aminoglycoside 3-phosphotransferase; accession number P00551) was indexed using Bowtie 2 with default settings, and the sequenced pairs for the BF HNI_VO2 aligned to the indexed sequences, allowing accordant alignments of sequence pairs resulting in fragment lengths of between 145 and 155 bp.Probability of sequence repeatsThe presence of strong 10-bp A dinucleotide periodicities was assessed from the Fourier magnitude of the distribution in specific regions using the program hp_fftw that utilizes the FFTW library (www.fftw.org).SoftwareNucleotide repeat sequences were identified in the T. brucei genome with polyA_genome_distribution. The occurrence of runs between specific genomic positions,All software was written in C++ (ISO/IEC 14882:2011) and compiled with the g++ version 4.8.2 64-bit compiler (gcc.gnu.org) using the mingw-w64 version 4.8.2 (mingww64.sourceforge.net) toolchain on a Windows version 8.1 operating system platform. The program hp_fftw was compiled with g++ version 4.8 on Linux openSUSE version 12.3 (www.opensuse.org). All plots were prepared with scripts using gnuplot version 4.6 (www.gnuplot.info). TheMaree et al. Epigenetics Chromatin (2017) 10:Page 19 ofsource code for software developed and used in this study is freely available (sourceforge.net/projects/nucpos/).Received: 14 March 2017 Accepted: 14 MarchAdditional filesAdditional file 1. Supplementary nucleosome dyad profiles, oligonu cleotide runs, (di)nucleotide occurrence and frequencies, megabase PP58 chemical information chromosome panels, and autocorrelation of nucleosome positions Additional file 2: Table S3. Genomic positions of equivalent sequences mapped as ORC1 sites in T. brucei strain 927 in T. brucei strain 427. Additional file 3: Table S5. Mapped transcription start regions from Tb927 to Tb427.Abbreviations LECA: last eukaryotic common ancestor; pol II: RNA polymerase II; TSS: tran scription start site; HAT: human African trypanosomiasis; BF: bloodstream form; PF: procyclic form; VSG: variant surface glycoprotein; ES: expression site; PTU: polycistronic transcription unit; SSR: strand switch region; Base J: dglucosyl hydroxymethyluracil; PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26024392 MNase: micrococcal nuclease; NDR: nucleosome depleted region; SAS: splice acceptor site; PAS: polyadenylation site; SL RNA: spliced leader RNA; PPT: polypyrimidine tract; RHS: retrotransposon hotspot protein; ESAG: expression siteassociated gene; LRRP: leucinerich repeat pro tein; FDR: false discovery rate; ORI: origins of replication; FCS: fetal calf serum. Authors’ contributions HGP conceived and coordinated the study; JPM performed the experimen tal work; MLP performed experimental work; GR provided the strains and facilities for the experimental work; DJC performed the DNA repair and pairedend sequencing; HGP wrote the software; HGP and JPM performed the analysis and drafted the manuscript. All authors read and approved the final manuscript. Author details Department of Biochemistry, Stellenbosch University, Matieland 7602, South Africa. 2 Department of Biology, Pennsylvania State University (Brandywine Campus), Media, PA 19063, USA. 3.