Rosalind Elsie Franklin Biophysicist and
crystallographer X-ray diffraction
images of DNA Tobacco mosaic
and polio viruses 1920-1958
(source: wikipedia)
A Structural Split in the Human Genome
Clara S. M. Tang and Richard J. EpsteinPLoS One (2007) 7:e603
February 13, 2007I. Elizabeth Cha
Introduction PCIs
Promoter-associated CpG islands Mediate methylation-dependent gene
silencing Co-locate to transcriptionally active
genes 60% of human genes contains PCIs
CpG Islands Genomic regions containing high
frequency of CG dinucleotides CpG
cytidine-phosphodiester-guanosine Formal definition
At least 200bp GC percentage >50% CpG ratio >60%
DNA Methylation
Materials and Methods Sequence data and annotations Determination of CpG island overlapping
transcription start site Housekeeping genes and paralogs of
pseudogenes Bimodal distribution of GC content Gene expression data Evolutionary rate determination Principal component analysis
Sequence Data and Annotations UCSC genomic assemblies, RefSeq
dataset, Emsembl gene dataset Human (hg18, 3/2006) Mouse (mm6, 3/2006) Fugu (fr1, 8/2002) Fruit fly (dm2, 4/2004) Worm (ce2, 3/2004)
Data Preprocessing RepeatMask – Alu Discard sequences
Not commencing with ATG codons Not terminating with canonical stop
codons Retain the longest genomic
sequences containing identical exonic sequences
Determination of CpG Island Overlapping Transcription Start Site Download CpG islands annotation
(cpgIslandExt) from UCSC Identify CpG islands overlapping with
promoter regions Map with RefGene annotation (200bp
upstream and 500bp downstream)
Data and Tools 502 Housekeeping genes 1220 pseudogene paralogs
NOCOM program SAGEmap Homologue data XSTAT
Results – PCI+ Genes Housekeeping gene
higher GC contentlower intron length/number
Pseudogene paraloglower GC contenthigher intron length/number
Functional distinguishable
Table 1
Results – PCI- Genes Higher evolutionary rate Narrower expression breadth than
PCI+ genes More frequent tissue-specific
inactivation
Figure 1 Biphasic GC/AT Distribution of PCI+ Genes
A. Distribution of GC content among different regions of genes
3’ UTR
5’ UTR
coding region
intronic
Figure 1 Biphasic GC/AT Distribution of PCI+ Genes (cont’d)
With ‘start’ CpG islands (CGI+)
Without ‘start’ CpG islands (CGI+)
B&C Proportion of genes among different GC groups.
Figure 2 GC Content of Promoter vs. Non-promoter CpG Island Overlapping Genes
All genes Genes with medium total intron size (10-50kb)
Intronless genes
Genes with short total intron size (<10kb) and long intron size (>50kb)
PCI+: solid line; PCI-: dash line
Figure 3 Distribution of Coding GC% of RefGenes with PCIs
pseudogenes House-keeping genes
Figure 4 Quantitative Comparison of Gene Subsets
L: low, GC<40%; H: high, GC>65%; double dark, <0.001; single dark, <0.01; open, < 0.05
Figure 4 Quantitative Comparison of Gene Subsets (cont’d)
L: low, GC<40%; H: high, GC>65%; double dark, <0.001; single dark, <0.01; open, < 0.05
Figure 4 Quantitative Comparison of Gene Subsets (cont’d)
L: low, GC<40%; H: high, GC>65%; double dark, <0.001; single dark, <0.01; open, < 0.05
Figure 6 Model of human genomic evolution
Conclusions PCIs
Transcriptional regulators Evolutionary accelerators to facilitate
intron insertion Mthylated PCIs on transcription and
chromatin accelerate adaptive evolution towards biological complexity
Conclusions Adaptive evolution of human genome
Declining transcription of a subset of PCI+ genes
Predisposing to both CpGTpA mutation and intron insertion
Biological complexity model Environmentally selected gains/losses of
PCI methylation (+/-) Polarizing PCI+ gene structures arounda
genomic core of ancestral PCI- genes
Discussion AT-rich, PCI+ gene vs. GC-rich PCI+
housekeeping gene Lower transcriptional activity Higher intron number Higher evolutionary rate
Loss of negative selection pressure
Discussion (cont’d) PCI- genes vs. PCI+ genes
Higher evolutionary rate Lower expression breadth
Intron number relates more directly to PCI positivity
Figure 5 Principal component analysis (PCA)
A. PCA analysis using six variables at either 53% (left) or 59% (right) variance
Figure 5 Principal component analysis (PCA) (cont’d)
B. 2D dot plots C. 3D dot plots
GC-rich, blue; GC-poor, red