Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elegans

Abstract By measuring prevailing distances between YY, YR, RR, and RY dinucleotides in the large database of the nucleosome DNA fragments from C. elegans, the consensus sequence structure of the nucleosome DNA repeat of C. elegans was reconstructed: (YYYYYRRRRR)n. An actual period was estimated to be 10.4 bases. The pattern is fully consistent with the nucleosome DNA patterns of other eukaryotes, as established earlier, and, thus, the YYYYYRRRRR repeat can be considered as consensus nucleosome DNA sequence repeat across eukaryotic species. Similar distance analysis for [A, T] dinucleotides suggested the related pattern (TTTYTARAAA)n where the TT and AA dinucleotides display rather out of phase behavior, contrary to the “AA or TT” in-phase periodicity, considered in some publications. A weak 5-base periodicity in the distribution of TA dinucleotides was detected.

[1]  Steven M. Johnson,et al.  Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. , 2006, Genome research.

[2]  E. Trifonov.  Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. , 1987, Journal of molecular biology.

[3]  E. Trifonov,et al.  Nucleotide sequence-directed mapping of the nucleosomes. , 1983, Nucleic acids research.

[4]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[5]  Stephan C. Schuster,et al.  Nucleosome organization in the Drosophila genome , 2008, Nature.

[6]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[7]  M. Borodovsky,et al.  Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. , 1996, Journal of molecular biology.

[8]  Ryoiti Kiyama,et al.  Dinucleosome DNA of human K562 cells: experimental and computational characterizations. , 2003, Journal of molecular biology.

[9]  A. Palleschi,et al.  The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning. , 1991, Biophysical chemistry.

[10]  Yechezkel Kashi,et al.  Three Sequence Rules for Chromatin , 2006, Journal of biomolecular structure & dynamics.

[11]  Steven Henikoff,et al.  Nucleosome destabilization in the epigenetic regulation of gene expression , 2008, Nature Reviews Genetics.

[12]  M. Q. Zhang,et al.  Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[13]  V. Zhurkin,et al.  Anisotropic flexibility of DNA and the nucleosomal structure. , 1979, Nucleic acids research.

[14]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[15]  V. Zhurkin,et al.  Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine—pyrimidine and pyrimidine—purine dimers , 1983, FEBS letters.

[16]  Yechezkel Kashi,et al.  Yeast Nucleosome DNA Pattern: Deconvolution from Genome Sequences of S. cerevisiae , 2005, Journal of biomolecular structure & dynamics.

[17]  E. Trifonov,et al.  Sequence-directed Mapping of Nucleosome Positions , 2007, Journal of biomolecular structure & dynamics.

[18]  Ryoiti Kiyama,et al.  Sequence Structure of Human Nucleosome DNA , 2006, Journal of biomolecular structure & dynamics.

[19]  J. Widom.  Short-range order in two eukaryotic genomes: relation to chromosome structure. , 1996, Journal of molecular biology.

[20]  J. Widom,et al.  Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. , 2000, Journal of molecular biology.

[21]  E. Trifonov,et al.  Epigenetic Nucleosomes: Alu Sequences and CG as Nucleosome Positioning Element , 2008, Journal of biomolecular structure & dynamics.