DNA-bridging by an archaeal histone variant via a unique tetramerisation interface

Abstract

In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into ‘hypernucleosome’ particles of varying sizes with each dimer wrapping 30 bp of DNA. These are composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension enabling homotetramerisation. The 1.9 Å X-ray structure of a dimeric MJ1647 species, structural modelling of the tetramer, and site-directed mutagenesis reveal that the C-terminal tetramerization module consists of two alpha helices in a handshake arrangement. Unlike canonical histones, MJ1647 tetramers can bridge two DNA molecules in vitro. Using single-molecule tethered particle motion and DNA binding assays, we show that MJ1647 tetramers bind ~60 bp DNA and compact DNA in a highly cooperative manner. We furthermore show that MJ1647 effectively competes with the transcription machinery to block access to the promoter in vitro. To the best of our knowledge, MJ1647 is the first histone shown to have DNA bridging properties, which has important implications for genome structure and gene expression in archaea.

Archaeal histone-based chromatin structures regulate transcription elongation rates

“…Archaeal histones can form both homo- and hetero-dimers that protect ~30 bp of DNA and assemble into an extended, continuous super-helical structure. The geometry of the DNA bound within an archaeal chromatin superhelix nearly exactly matches that of the eukaryotic nucleosomal DNA arrangement 4 , 24 , 29 – 32 and the overall archaeal histone-based extended chromatin structure closely matches chromatin structures found on eukaryotic telomeres 33 . Both archaeal and eukaryotic histone-DNA interactions align to the same nucleosome positioning code and the specific protein-DNA contacts that stabilize chromatin are conserved 29 , 34 – 36 .…”

Dual dimeric interactions in the nucleic acid-binding protein Sac10b lead to multiple bridging of double-stranded DNA

“…In a 4 Å crystal structure of archaeal histone-DNA complex, the DNA winds three histone homodimers [ 9 ]. The histone paralogue MJ1647 forms homotetramers that are capable of cooperatively bridging DNA molecules [ 10 ].…”