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首页> 外文期刊>BMC Genomics >Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs
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Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs

机译：体内和体外古细菌核小体的定位由一级序列基序指导

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Background 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. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. Results Eukaryotic 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. Conclusions The 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.
机译：背景技术组蛋白将DNA包裹成核小体的过程几乎可以肯定是在古细菌中发生的，并且早于真核生物。在真核生物中，核小体定位在调节基因表达中起着核心作用，并由一起形成核小体定位码的一级序列基序指导。进行了报道的实验以确定古细菌组蛋白装配是否符合核小体定位密码。结果AA / TT / AT / TA和CC / GG / CG / GC二核苷酸的分阶段螺旋重复有利和指导真核核小体的定位，而较长的富含AT的寡核苷酸不利于真核生物的定位。通过组装成古细菌核小体来保护免受微球菌核酸酶消化的基因组DNA的深度测序已确定，古细菌核小体的组装也受这些序列基序控制和定位，无论是在甲烷嗜热热菌，嗜热自养菌和柯达卡氏热球菌体内，还是在体外仅含有一种纯化产物的反应混合物中古细菌组蛋白和基因组DNA。古细菌核小体在体内和体外在相同的位置组装，在开放阅读框上游和整个核糖体rDNA操纵子的紧邻处，组装大大减少。为普通定位代码提供进一步的支持，古细菌组蛋白在真核DNA上组装成核小体，而真核生物组蛋白在古细菌DNA上组装成核小体。 T. kodakarensis有两个组蛋白，分别命名为HTkA和HTkB，并且两个组蛋白均被缺失但并非两个都缺失的菌株正常生长，但确实存在转录组差异。在没有HTkA或HTkB的情况下，在显示出增加或减少的转录的基因上游的基因间区域中，古细菌核小体概况的比较显示出实质性差异，但没有一致的变化模式，其直接与古细菌核小体定位抑制或刺激转录有关。结论获得的结果表明，古细菌组蛋白和基因组序列一起足以确定古细菌核小体在哪些地方优先组装以及在何处避免组装。我们证实，相同的核小体定位代码在古细菌中与真核生物中起作用，并且据推测因此是在真核生物发散之前，在古细菌谱系的早期与DNA结合和紧实的组蛋白折叠机制一起进化的。

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