The sequence structure of human nucleosome DNA

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The sequence structure of human nucleosome DNA
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The team

• Simon B. Kogan and Edward N. Trifonov University
  of Haifa (Israel)
• Megumi Kato, Yoshiaki Onishi and Ryoiti Kiyama
  National Institute of Advanced Industrial Science
  and Technology (Japan)
• Yuko Wada-Kiyama Nippon Medical School (Japan)
• Takashi Abe, Toshimichi Ikemura National
  Institute of Genetics (Japan)

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High-order chromatin

• Chromatin is protein-DNA complex from which
  eukaryotic chromosomes are comprised (Euchromatin
  and heterochromatin).
• Levels of chromatin organization 300-nm loops
  100-nm fiber ? 30-nm fiber nucleosomes.
• Models of 30-nm fiber solenoid zigzag sallow
  thorn.

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Electron Micrographs of Chromatin
Isolated metaphase chromosome
From the web site of Dr. Carol Heckman (Bowling
Green State University).
Modified from Bloom and Fawcett, A Textbook of
Histology, Chapman and Hall, 12th edition, Figure
1-14 (BioMEDIA web site)
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10-30 nm fibers and fibrils
Modified from Bloom and Fawcett, A Textbook of
Histology, Chapman and Hall, 12th edition, Figure
1-12 (BioMEDIA web site)
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Levels of chromatin structure
From The University of Edinburgh Faculty of
Medicine web site
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Nucleosome

• Nucleosome is the basic block (lowest level) of
  chromatin organization.
• Most of genomic DNA is confined in nucleosomes
  (one nucleosome per 200 base pairs on average).
• Nucleosome core particle consist of histone
  octamer (two molecules each of H2A, H2B, H3 and
  H4 histone proteins) and stretch of super-coiled
  double-stranded DNA 125-166 base pairs long.

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Nucleosome core particle

• Ribbon traces for the 146-bp DNA phosphodiester
  backbones (brown and turquoise) and eight histone
  protein main chains (blue H3 green H4 yellow
  H2A red H2B (Luger et al., 1997).

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Chromatin function

• Package of DNA into chromosomes and nucleus.
• Condense chromatin (heterochromatin) silences
  large chromosome DNA parts.
• Epigenetic regulation of gene expression.
• Low and high order chromatin structures are
  flexible and dynamic (i.e. chromatin remodeling).
  They regulate biological activity by hiding or
  exposure of DNA sites for protein binding.

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Nucleosome function

• Local higher-order chromatin structure depends on
  positions of individual nucleosomes.
• The level of DNA sequence exposure to variety of
  binding factors depends on whether the sequence
  is constrained in nucleosome core or belongs to
  linker DNA.
• Nucleosomes are positioned specifically in gene
  promoters and splice junctions. Thus, influence
  gene expression.

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Nucleosome positioning

• Nucleosome histones bind to DNA by means of
  electrostatic forces. However, the binding
  strength depends on specific DNA sequence. Thus,
  sequence can modulate nucleosome positioning
  preferences.
• The important positioning factors are thought to
  be sequences anisotropic flexibility and
  curvature. Both of them depend mostly on base
  pairs interactions in dinucleotides.
• The anisotropy can be achieved by periodical
  positioning of specific dinucleotides on the
  distance equal to DNA helix period in
  nucleosomes 10.4 bases.

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Positioning pattern

• Experimental identification of nucleosome
  positions is a cumbersome task and results are
  often imprecise and unreliable. Thus, the need
  for computational biology methods.
• Because of nucleosome abundance, the positioning
  signal is necessary weak or very diverse to allow
  overlapping of other DNA codes (i.e. amino-acid
  triplet code).
• However, several studies, observed weak AA(TT)
  dinucleotide periodicity (Trifonov and Sussman,
  1980). Consequently, AA(TT) positioning pattern
  was built (Ioshikhes et al., 1996). More general
  RR(YY) pattern was built even earlier
  (Mengeritsky and Trifonov, 1983).

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RR(YY) pattern in humans

• Nobody (to the best of our knowledge) found the
  10.4 periodicity in human genome. The presumed
  reason is the exceptional weakness of nucleosome
  preferential positioning in higher eukaryotes.
• Utilizing large database of human dinucleosome
  DNA obtained from laboratory of Prof. Kiyama, we
  manage to obtain RR(YY) nucleosome positional
  periodical pattern (Kato et al., 2003) and get
  additional confirmation of nucleosome steric
  exclusion rules described earlier (Ulanovsky and
  Trifonov, 1986).

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RR(YY) pattern

• A symmetrized sum of RR and YY distributions.
  The extrema corresponding to the 10.4n ladder
  are indicated by arrows. Nucleosome sequences
  were smoothed by running the average of three
  positions (Kato et al., 2003).

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GG(CC) pattern in humans

• Detailed investigation of database sequences
  revealed predominant usage of GG(CC)
  dinucleotides in humans.
• GG(CC) predominance is in contradiction with the
  current opinion that only AA(TT) and TA are
  important for nucleosome positioning.
• This finding points to possible species
  specificity of nucleosome positioning signal.
• The result was confirmed in independent study
  concerning the connection between nucleosome and
  splicing junction positions (Kogan and Trifonov,
  2005).

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GG(CC) pattern
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Weights of eight topmost periodical components of
splice junction dinucleotide profiles in four
species (Kogan and Trifonov, 2005)
Second line indicates amount of EI(IE) splice
junctions of the respective species in the data
set. For the purpose of comparison, the weights
are calculated as fitting sine amplitudes divided
by the sum of all 32 amplitudes, for each species
separately.
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Selected references

• Bolshoy, A. CC dinucleotides contribute to the
  bending of DNA in chromatin. Nat Struct Biol 2
  (1995) 446-8.
• Herzel, H., Weiss, O. and Trifonov, E.N. 10-11
  bp periodicities in complete genomes reflect
  protein structure and DNA folding. Bioinformatics
  15 (1999) 187-93.
• Ioshikhes, I., Bolshoy, A., Derenshteyn, K.,
  Borodovsky, M. and Trifonov, E.N. Nucleosome DNA
  sequence pattern revealed by multiple alignment
  of experimentally mapped sequences. J Mol Biol
  262 (1996) 129-39.
• Kato, M., Onishi, Y., Wada-Kiyama, Y., Abe, T.,
  Ikemura, T., Kogan, S., Bolshoy, A., Trifonov,
  E.N. and Kiyama, R. Dinucleosome DNA of human
  K562 cells experimental and computational
  characterizations. J Mol Biol 332 (2003) 111-25.
• Kogan, S. and Trifonov, E.N. Gene splice sites
  correlate with nucleosome positions. GENE, in
  press (2005).
• Mengeritsky, G. and Trifonov, E.N. Nucleotide
  sequence-directed mapping of the nucleosomes.
  Nucleic Acids Res 11 (1983) 3833-51.
• Thastrom, A., Lowary, P.T., Widlund, H.R., Cao,
  H., Kubista, M. and Widom, J. Sequence motifs
  and free energies of selected natural and
  non-natural nucleosome positioning DNA sequences.
  J Mol Biol 288 (1999) 213-29.
• Trifonov, E.N. and Sussman, J.L. The pitch of
  chromatin DNA is reflected in its nucleotide
  sequence. Proc Natl Acad Sci U S A 77 (1980)
  3816-20.