This repository contains the run scripts for this publication. Complete data download http://resources-molpara.vetmed.lmu.de/Kraus_et_al_2019_sequencing_analysis.tar.gz Contents of the tar.gz archive: upload_sequencing/ ├── bin/ │ ├── scripts necessary to run the pipeline ├── input/ │ ├── input files ├── output/ │ ├── output files for ChIP and RNA-seq └── output2/ └── output files for ATAC-seq Abstract Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histone or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in Trypanosoma brucei, we identify 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we find TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription.

We thank all current and former members of the Siegel and Janzen laboratories for valuable discussions and for assistance with experiments. We thank Joana Correia-Faria for sharing protocols for the isolation of the chromatin-associated protein fractions. We thank Felix Müller-Planitz, Stan Gorski, Kirsty McWilliam and Raúl Cosentino for critically reading the manuscript. We thank Konrad U. Förstner and Raúl O. Cosentino for suggestions regarding data analysis and the Core Unit Systems Medicine of the University of Würzburg for the high-throughput sequencing. We acknowledge the support and resources from the Bioinformatics Core Facility at the Biomedical Center Munich. We thank Beate Vogt and Christiane Winkler for their help in sample preparation for FIPQuant. This work was funded by the Young Investigator Program of the Research Center for Infectious Diseases (ZINF) at the University of Würzburg, Germany, a grant from the German Research Foundation (SI 1610/2-1) and an ERC Starting Grant (3D_Tryps 715466).