Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending

This repository contains the DNA affinity purification sequencing (DAP-seq) data, for two biological replicates, as used in the following manuscript:Yimin Hu, Samuel Schwab, Silvia Deiss, Pedro Escudeiro, Joe D. Joiner, Marcus D. Hartmann, Andrei N. Lupas, Birte Hernandez Alvarez, Vikram Alva, and Remus T. Dame. 'Bacterial Histone HBb from Bdellovibrio Bacteriovorus Compacts DNA by Bending'. bioRxiv, 27 September 2023. https://doi.org/10.1101/2023.02.26.530074.There are four types of data in this repository: Paired-end FASTQ files, containing the raw Illumina reads (raw_reads folder). Raw read QC reports, generated by the nf-core/chipseq pipeline (fastqc folder). BAM files, generated by the nf-core/chipseq pipeline (bam folder). bigWig files, generated by the nf-core/chipseq pipeline (bigwig folder). Abstract:Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have recently been identified in bacteria, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. We also elucidate the crystal structure of the HBb dimer at 1.06 Å resolution and employ various biophysico-chemical approaches to show its ability to bind and compact DNA in a sequence-independent manner. This binding induces DNA bending, similar to that observed with bacterial HU/IHF family proteins. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These unique DNA-binding properties of bacterial histones, distinct from their archaeal and eukaryotic counterparts, highlight the diverse roles that histones can play in DNA organization across the domains of life.To whom correspondence should be addressed (E-mail):birte.hernandez@tuebingen.mpg.de, or vikram.alva@tuebingen.mpg.de, or rtdame@chem.leidenuniv.nl