“Anticipated” nucleosome positioning pattern in prokaryotes

Rapoport, Alexandra E.; Trifonov, Edward N.

doi:10.1016/j.gene.2011.08.002

Cited by 11 publications

(10 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…When compared with eukaryotic genomes, archaeal (and bacterial) genomes are very small, and many different proteins have been described that participate both in gene expression and prokaryotic genome compaction [15]. The first histone may have evolved as a protein that bound preferentially to sequences that encoded amphipathic peptide helices [61] with this sequence-directed binding participating in gene regulation. But, given that the histone fold mechanism of DNA binding results in DNA wrapping, this would have also inherently resulted in DNA compaction.…”

Section: Discussionmentioning

confidence: 99%

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

Nalabothula

Bhattacharyya

et al. 2013

BMC Genomics

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

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

Nalabothula

Bhattacharyya

et al. 2013

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…The prebiotic evolutionary interest of the G:C system was pointed out [49,50]. The reconstruction of molecular events leading to emergence of the triplet code [49,50] suggests that the first genes were formed on the basis of expanding (GCC)*(GGC)n duplexes.…”

Section: Discussion and Evolutionary Implicationsmentioning

confidence: 99%

“…The reconstruction of molecular events leading to emergence of the triplet code [49,50] suggests that the first genes were formed on the basis of expanding (GCC)*(GGC)n duplexes. The consecutive transesterifications described in the Tetrahymena pre-rRNA and cyclization of the excised IVS [3] are a series of chemically homogeneous reactions guided by programmed RNA structures.…”

Section: Discussion and Evolutionary Implicationsmentioning

confidence: 99%

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

Pino

Costanzo

Giorgi

et al. 2013

Entropy

View full text Add to dashboard Cite

3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3′ terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA.

show abstract

“…Interestingly, the Shannon extension also revealed that vocabularies of prokaryotic sequences indicate that this alternating pattern is characteristic of prokaryotic genomes as well, although in lesser degree as compared to eukaryotes [15]. It appears that in this case the periodicity is due to presence in proteins of appreciable amount of amphipathic alpha-helices.…”

Section: Shannon K-tuple Extensionmentioning

confidence: 93%

Weak Signal Carried by Chromatin DNA Sequences: Zooming In and Sobering Surprises

Trifonov¹

2016

2016 Second International Symposium on Stochastic Models in Reliability Engineering, Life Science and Operations Management (SM

View full text Add to dashboard Cite

The 35 year long story of the chromatin signal (code) started with discovery of a very weak 10-11 base sequence periodicity of AA and TT dinucleotides, detected by distance analysis (equivalent of autocorrelation in time series). It soon became clear that this is counter-phase oscillation of AA and TT, or rather of RR and YY -by a version of multiple alignment ("synchronous detection" in signal processing). The campaign incrementally agonized through reconstruction of signal from its parts, N-gram Shannon extension and strong nucleosomes (SNs) with visible sequence periodicity to (RRRRRYYYYY) n pattern, and culminated in this form, with small changes suggested by consensuses from strong nucleosomes. 10-11 base YR dinucleotide periodicity (first suggested by Zhurkin) is a part of the above consensus. The periodically repeating YR elements form long tracks of hundreds to thousands basepairs indicating that the chromatin consists of columnar structures, rather than of solitary nucleosomes. In particular, the classical SV40 minichromosome appears to form one continuous column.

show abstract

“Anticipated” nucleosome positioning pattern in prokaryotes

Cited by 11 publications

References 28 publications

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

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

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

Weak Signal Carried by Chromatin DNA Sequences: Zooming In and Sobering Surprises

Contact Info

Product

Resources

About