Genome Structural Variation in Human and Primate Evolution

1
Genome Structural Variation in Human and Primate
Evolution

• James M. Sikela, Ph.D.
• Professor, University of Colorado Denver School
  of Medicine
• Genomics Course Lecture, February 22, 2011

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Key Points

• All regions of the human genome are not created
  equal
• Gene duplication (copy number variation) is a
  (the?) major mechanism underlying genome
  evolution
• ArrayCGH can reconstruct the evolutionary history
  of gene duplication loss in the human/primate
  genome
• Lineage-specific gene duplications are candidates
  to underlie lineage-specific traits
• Selection of evolutionarily adaptive sequences
  also is a key driver of human disease
• Human lineage-specific amplification of DUF1220
  protein domains as a candidate underlying human
  brain evolution

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Primate Family Tree
Smithsonian Human Origins Program
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Human Characteristics

• Body shape and thorax
• Cranial properties (brain case and face)
• Small canine teeth
• Skull balanced upright on vertebral column
• Reduced hair cover
• Enhanced sweating
• Dimensions of the pelvis
• Elongated thumb and shortened fingers
• Relative limb length

• Neocortex expansion
• Enhanced language cognition
• Advanced tool making

modified from S. Carroll, Nature, 2005
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Reports of human-specific genes

• FOXP2
• Mutated in family with language disability
• Two human-specific amino acid changes
• ASPM/MCPH
• Mutated in individuals with microcephaly
• Under positive selection?
• HAR1F
• Encodes RNA (not protein) product
• Gene sequence highly changed in humans
• DUF1220 protein domains
• Highly increased in copy number in humans
• Copy number correlation with microcephaly/macrocep
  haly
• Expressed in important brain regions

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Molecular Mechanisms Underlying Genome Evolution

• Single nucleotide substitutions
• - change gene expression structure
• Genome rearrangements
• Gene duplication
• - copy number change gene dosage
• - redundancy as a facilitator of innovation

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Strategies to identify human lineage-specific
genomic changes

• Comparative genomic sequencing
• Chimp genome sequence 2005
• HAR1F, 2006
• Cross-species brain gene expression profiling
• Human, chimp, macaque
• Comparative genomic copy number studies gene
  duplication loss
• Fortna, et al, 2004 Human and great ape lineages

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Comparative analysis of primate genome WGS
sequences
Genome-wide comparison of inter-species gene copy
number and structural variation
Evolutionary studies of disease genes
associated with cognitive dysfunction e.g. MCPH
Genes and genomic changes underlying
human-specific cognitive capabilities
Comparative brain gene expression studies
Functional testing of candidate genes
Sikela, J.M., PLoS Genet. 2, e80, 2006
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Gene Duplication Evolutionary Change

• There is now ample evidence that gene
  duplication is the most important mechanism for
  generating new genes and new biochemical
  processes that have facilitated the evolution of
  complex organisms from primitive ones. - W.
  H. Li in Molecular Evolution, 1997
• Exceptional duplicated regions underlie
  exceptional biology - Evan Eichler, Genome
  Research 11653-656, 2001

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Interhominoid cDNA Array-Based Comparative
Genomic Hybridization (aCGH)
Fig 1. Measuring genomic DNA copy number
alteration using cDNA microarrays (array CGH).
Fluorescence ratios are depicted in a pseudocolor
scale, such that red indicates increased, and
green decreased, gene copy number in the test
(right) compared to reference sample (left).
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Experimental Design

• Carry out pairwise aCGH comparisons between human
  and other primate species
• Use a microarray containing gt41,000 human cDNAs
  representing gt24,000 human genes
• Hybridize human genomic DNA (reference sequence
  green) and other primate genomic DNAs (test
  sequence red) simultaneously to the microarray
• Visualize aCGH signals gene-by-gene along each
  chromosome across five species human (n5),
  bonobo (n3), chimpanzee (n4), gorilla (n3) and
  orangutan (n3)

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Whole Genome Caryoscope Image of Interhominoid
aCGH Data
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Human Great Ape Genes Showing Lineage-Specific
Copy Number Gain/Loss
Fortna, et al, PLoS Biol. 2004
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Clustering of hominoid lineage-specific genes
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H C G O
Value of Outgroup Comparisons Chimp vs Human
CNVs are not necessarily lineage-specific
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aCGH Caveats

• Functional status of extra copies unknown
• Small copy number changes in large, highly
  similar gene families difficult to detect
• Genes lost in human lineage will be missed
• Lineage-specific term needs better validation
• More individuals needed within each species
• More species need to be assayed to identify
  lineage-specific changes

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Conclusions from Fortna, et al

• First genome-wide first gene-based survey of
  gene duplication loss in human and great ape
  evolution
• Identified most of the major lineage-specific
  gene copy number changes that have occurred over
  the past 15 million years of human and great ape
  evolution
• Identified genes that potentially underlie many
  of the phenotypic characteristics that
  distinguish these species from one another

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• This (Fortna, et al, 2004) is the first time
  that copy number changes among apes have been
  assayed for the vast majority of human genes, and
  we can expect that the biological consequences of
  the 140 human-specific copy number changes
  identified in this study will be heavily
  investigated over the coming years.
• ---M. Hurles, PLoS Biol. 2004

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Human Great Ape Genes Showing Lineage-Specific
Copy Number Gain/Loss
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DUF1220 Repeat Unit
Popesco, et al, Science 2006
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InterPro-predicted DUF1220-containing proteins
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BLAT Estimation of the Number of DUF1220 Domains
Found in Different Species
A
B
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Copy Number of DUF1220 (Q8IX62/17-33) Sequences
in Primate Species
70
60
50
Q-PCR Predicted Copy Number
40
30
20
10
0
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BLAT-based DUF1220 copy number in sequenced
primates using IMAGE843276

• Full insert cDNA query (491 bp) encodes 3 DUF1220
  domains
• BLAT hits (gt200 score) in each species
• Species (Assembly) Copies (x3)
• Human (5/04) 51
• Human (3/06) 50
• Chimp (11/03) 6
• Chimp (3/06) 25
• Orangutan (7/07) 10
• Macaque (1/06) 3

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Summary of aCGH, Q-PCR and BLAT results

• DUF1220 domains are highly amplified in human,
  reduced in African great apes, further reduced in
  orangutan and Old World monkeys, single copy in
  non-primate mammals and absent in non-mammals

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Sequences encoding DUF1220 domains

• are virtually all primate specific
• are increasingly amplified generally as a
  function of a species evolutionary proximity to
  humans, where the greatest number of copies (218)
  is found
• show signs of positive selection
• are highly expressed in brain regions associated
  with higher cognitive function
• in brain show neuron-specific expression
  preferentially in cell bodies and dendrites

Popesco, et al, Science 2006
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Recent Relevant Publications

• Fortna, A., Kim, Y., MacLaren, E., Marshall, K.,
  Hahn, G., Meltesen, L., Brenton, M., Hink, R.,
  Burgers, S., Hernandez-Boussard, T.,
  Karimpour-Fard, A., Glueck, D., McGavran, L.,
  Berry, R., Pollack, J.R. and Sikela, J.M.
  Lineage-specific gene duplication and loss in
  human and great ape evolution. PLoS Biology,
  Jul2(7)E207, 2004.
• Sikela, J.M. The Jewels of Our Genome The
  Search for the Genomic Changes Underlying the
  Evolutionarily Unique Capacities of the Human
  Brain. PLoS Genet, May2(5)e80, 2006.
• Popesco, M., MacLaren, E., Hopkins, J., Dumas,
  L., Cox, M., Meltesen, L., McGavrin, L, Wyckoff,
  G., and Sikela, J.M. Human lineage-specific
  amplification, selection and neuronal expression
  of DUF1220 domains. Science, 3131304-1307, 2006.
  
• Dumas, L., Kim, Y., Karimpour-Fard, A., Cox, M.,
  Hopkins, J., Pollack, J., and Sikela, J.M. Gene
  copy number variation spanning 60 million years
  of human and primate evolution. Genome Research
  171266-1277, 2007.
• Dumas L. and Sikela, J.M. DUF1220 Domains,
  Cognitive Disease and Human Brain Evolution. Cold
  Spring Harb. Symp. Quant. Biol. E-published,
  October 22, 2009.