README.md

Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

Robert K. Louder ¹, Giho Park ², Ziyang Ye ¹†, Justin S. Cha ³, Anne M. Gardner ³, Qin Lei ¹, Anand Ranjan ¹, Eva Höllmüller ^4,5,6, Florian Stengel ^5,6, B. Franklin Pugh ³, Carl Wu ^1,7

¹Department of Biology, Johns Hopkins University, USA
²Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins School of Medicine, USA
³Department of Molecular Biology and Genetics, Cornell University, USA
⁴Department of Chemistry, University of Konstanz, Germany
⁵Department of Biology, University of Konstanz, Germany
⁶Konstanz Research School Chemical Biology, University of Konstanz, Germany
⁷Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, USA
†Present Address: Department of Biology, Massachusetts Institute of Technology, USA

Correspondence: wuc@jhu.edu

PMID : XXXXXXXX

GEO ID : GSE275429

Abstract

The SWR1 chromatin remodeling complex (SRCAP in humans) is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here we use cryo-EM to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical structure-function roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α -helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1 promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 towards the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

Table of Contents

data

Stores BAM, BigWig, Fastq, BED, and Occupancy composite files.

bin

Stores scripts and executables that are not run directly but called by other scripts. In order to run other scripts, you must download ScriptManager with:

cd bin
./download_scriptmanager.sh

00_Download_and_Preprocessing

To download data and calculate normalization factors:

cd 00_Download_and_Preprocessing
./1_download_data.sh
mkdir norm_logs
sbatch 3_calculate_scaling_factors.slurm

02_Bulk_Processing

To process data:

cd 02_Bulk_Processing
mkdir pileup_logs
sbatch bulk_tagpileup.slurm

plot_composites.ipynb contains the code for creating composite plot svgs in 03_Composite_Results.

03_Composite_Results

Stores composite svg plots.