Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs

Narasimharao Nalabothula,John N Reeve,Liqun Xi,Yvonne N Fondufe-Mittendorf,Ji-Ping Wang,Jonathan Widom,Sucharita Bhattacharyya,Thomas J Santangelo

doi:10.1186/1471-2164-14-391

Narasimharao Nalabothula, John N Reeve + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-14-391

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Abstract

BackgroundHistone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code.ResultsEukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription.ConclusionsThe results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.

Highlights

Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes
Sequencing DNA molecules selected from a large random population by repetitive selection (SELEX) and PCR-amplification, based on increased archaeal histoneDNA affinity, revealed that DNA molecules preferentially assembled into archaeal nucleosomes in vitro had sequences that conformed to the eukaryotic nucleosome positioning code [12]
Confirmed, that archaeal nucleosome positioning in vivo was directed by same sequence motifs in M. thermautotrophicus and T. kodakarensis and focused on T. kodakarensis, as the experimental system, for which genetic procedures and strains with histone genes deleted were available [13]

Summary

Introduction

Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. Sequencing DNA molecules selected from a large random population by repetitive selection (SELEX) and PCR-amplification, based on increased archaeal histoneDNA affinity, revealed that DNA molecules preferentially assembled into archaeal nucleosomes in vitro had sequences that conformed to the eukaryotic nucleosome positioning code [12]. With the advent of large-scale DNA sequencing technologies, such comparisons became possible, and here we document that archaeal nucleosome assembly in vivo is directed by the nucleosome positioning code in both Methanothermobacter thermautotrophicus and Thermococcus kodakarensis, and that this is reproduced in vitro with archaeal genomic DNA and purified archaeal or eukaryotic histones. We show that the histone deletions result in changes in the archaeal nucleosome profiles upstream of the genes that have increased or decreased transcription

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