Transcript slides

A Genomic Code for Nucleosome
Positioning
Authors: Segal E., Fondufe-Mittendorfe Y., Chen L., Thastrom A.,
Field Y., Moore I. K., Wang J.-P. Z., Widom J.
Presented by Apostol Gramada
DNA organization – Chromatin
Taken from: http://sgi.bls.umkc.edu/waterborg/chromat/chroma09.html
Nucleosome organization
Nucleosome organization
• An octamer of 8 histone chains, 2 of each of the following: H2A,
H2B, H3, H4.
• H3, H4 highly conserved in
eukaryots.
• 147 bp per nucleosome
• DNA sharply bent and tightly wrapped in
approx 1.7 turns around the histone core.
• DNA bends discontinuously with the
periodicity of the helical repeat.
• Bending is facilitated by certain
dinucleotides placed at the right positions.
Nucleosome organization
• DNA in nucleosomes is far more sharply bent than in unstressed
naked DNA => significant free energy cost needed for stability.
• Particular DNA sequence could reduce this cost by
• either having an inherent bendedness
• being more easily bendable (more flexible).
• The later seems to be more supported by evidence.
• The ~10 bp periodicity of AA/TT, TA, GC seems to be an
especially flexible sequence motif.
Nucleosome positioning
• DNA sequences differ in their ability to bend sharply. This affects
the DNA binding affinity of the histone octamer.
• In vitro studies show a wide range of affinities with respect to
sequence variability (approx 1000-fold). Some sequences highly
preferred.
• Is this mechanism used to control the access to specific binding
sites?
• The positions of the nucleosomes may have important inhibitory
or facilitatory roles in regulating gene expression.
Nucleosome positioning – current
views
• Sequence preferences is over-ridden by nucleosome remodeling
complexes which move them to new locations whenever needed.
• Opposing view: the remodeling complexes only enable the
nucleosomes to sample rapidly alternative positions and therefore
compete efficiently with DNA binding proteins. They do not
determine their destination however. Then, the genome would
encode a nucleosome organization intrinsic to the DNA sequence
alone, comprising sequences with both regions of low and high
affinity for nucleosomes.
• The high affinity regions will be occupied in vivo and the detailed
distribution of nucleosome positions will significantly influence
the chromosome functions genome-wide.
Validating a nucleosome-DNA
interaction model
• The data: 199 mono-nucleosome DNA sequences (142-152
bp) from yeast.
• Used to construct a probabilistic model measuring the
sequence preferences of yeast nucleosome:
• Generate distribution functions at each site on the nucleosome for all
dinucloetides, from the population of the 199 sequences.
• A probability can then be assigned to each sequence of 147 bp.
• Derive a thermodynamic model for predicting the nucleosome
positions genome-wide from all legal configurations of nucleosomes
(no overlap, at least 10 bp away).
Validating a
nucleosome-DNA
interaction model
Validating a nucleosome-DNA
interaction model
Validating a nucleosome-DNA
interaction model
Validating a nucleosome-DNA
interaction model
Predicting nucleosome organization
in genomic DNA sequence
Resulting intrinsic nucleosome organizations: mutually exclusive organization
dominate, a single organization dominate, none dominates => may reveal
potential regulatory role of nucleosomes.
Predicted nucleosome
organization reflects in vivo data
• Orange Data in
vivo.
• 54% within 35
bp (only 39% by
chance).
Predicted nucleosome
organization reflects in vivo data
• Comparison to three genome-wide measurements reveals:
• significant correspondence between predicted and experimental
nucleosome-depleted coding and intergenic regions: 68% of 57
depleted coding regions and 76% of 294 depleted intergenic
regions.
• strong correspondence with a higher resolution nucleosome
map: 45% within 35bp distance (32% by chance).
Predicted nucleosome
organization reflects in vivo data
• Compared
prediction of yeast model with one using only nucleosomebound sequence from chicken
Predicted nucleosome organization
reflects in vivo data
Global features of intrinsic
nucleosome organization in yeast
• From ~ 11 mil
positions => ~15800
stable ncls. => cover
20% of genome. 
array?
• Fig d shows the
distribution of
pairwise distances
between stable ncls.
=> periodicity of ~
177 bp extending over
~ six positions 
higher level chromatin
organization?
Nucleosome organization varies
by type of genomic region
• Centromer function requires
enhanced stability => max
occupancy
• Highly expressed Ribosomal
RNA and transfer RNA => low
predicted occupancy
• Genes that very their expression
levels (Ribosomal protein) in
different conditions requires other
mechanisms.
Nucleosomes facilitate their own
remodeling
• Analyzing ~1900 genes from a gene annotation database and
various studies shows significance association with either high or
low predicted occupancy
• In particular, the chromatin remodeling complex RSC is
associated with low occupancy => genomes facilitate their own
remodeling
Low nucleosome occupancy
encoded at functional binding sites
• Stable ncls. over non-functional sites => decrease
accessibility to transcription factors.
• Tests showed: for 37% (out of 46) occupancy was
lower over functional sites than for non-functional
sites.
Low nucleosome occupancy
encoded at transcription start sites
Conclusions
• Nucleosome organization is encoded in eukaryotic genome
• The limited predictive power (~50% of in vivo nucleosome
organization) is explained by a too crude model yet:
• a more accurate nucleosome-DNA interaction model
• no account for favorable interactions and for steric
hindrances implied by the 3D ncls structure
• no account for competition with binding proteins.
Math
Wc[S] = statistical weight of sequence S with nucleosome configuration c.
“Legal” nucleosome configuration
Math