A high-resolution map of human evolutionary constraints using 29 mammals Kerstin Lindblad-Toh et...
-
Upload
douglas-blair -
Category
Documents
-
view
212 -
download
0
description
Transcript of A high-resolution map of human evolutionary constraints using 29 mammals Kerstin Lindblad-Toh et...
A high-resolution map of human evolutionary constraints using 29 mammalsKerstin Lindblad-Toh et al. 2011
Presentation by Robert Lewis and Kaylee Wells
What is Evolutionary Constraint?
• Restrictions that conserve non-deleterious alleles!
• Explains why something didn’t (or doesn’t) evolve.
• Aspect of an organism that has not changed over time
Phylogeny and constrained elements from the 29 genome sequences
• Compared with the HMRD
• Looked at 100 bp sites • 4.2 substitutions per site vs 0.68 HMRD
• Low probability of a non purifying sequence remaining fixed with 29 species!
• Therefore, better constraint detection
Shotgun Sequencing
Method for Detecting Constraint
• Generated 2X coverage Shotgun Sequence
• Contigs were 2.8kb
• Scaffolds were 51.8kb
Depth (Coverage) = N x (L/G)• N = # Reads• G = Genome Length• L = Read Length
Sequencing Assembly and Alignment!
With 29 mammalian species they were able to find:
• 3.6 million elements spanning 4.2% of the human genome
• Length of elements significantly smaller 36 bp vs 123 bp in the HMRD comparison
• PhastCons – How well individual bases are conserved
• SiPhy – Indicates bases under selection
HMRD vs 29 Mammals
HMRD 1 Element
29 Mammals 4 elements for NRSF binding
• ~1.5% of the genome is Protein coding
• 5% undergoing purifying selection
• Of the 5%, 3.5% are regulatory elements
Genome Wide Association Studies Rely on Non-Coding Sequences
Exons and protein coding regions
• 3,788 candidate exons. (2% increase)
• Stop codon read through to subsequent stop codon in 4 genes (regulatory)
• >10,000 synonymous constrained elements in 25% of genes
• Regions with very low synonymous substitution rate (No change in AA) HIGHLY CONSTRAINED
HoxA2 (2 sites with SCE)Synonymous rate = base change but not AA change
PhyloP = Nucleotide ConservationScale from -14 to 3(+) = More Conserved(-) = Faster Evolution (changing)
dN/dS indicates selective pressureX > 1 = Change in phenotype
These sites are known enhancers and drive expression in other Hox
RNA structures and structural elements!
Look at RNA sequences Determine secondary structure
Found 37,381 possible elements
Important b/c structure indicates function! (Look at structure and find likely target)
Promoters!Again, Structure = Function!
Organized into 3 categories• High Constraint
• Development• Intermittent constrain
• Basic Cell Functions• Low Constraint
• Immunity & Reproduction
Regulatory Motifs
• HMRD already created catalog of motifs conserved across genome Not good for finding new motifs!
• 29 Mammals revealed 688 regulatory motifs associated with 345 transcription factors
• 2.7 million conserved instances form regulatory network
• 375 motif targets with 21 regulators per target gene
Chromatin Signatures
Indicate possible functions for 37.5% of unexplained conserved elements
Functions of elements outside coding regions, UTRs, proximal promoters.
Accounting for constrained elements
~30% constrained elements overlap were associated with protein-coding transcripts~27% overlap specific enriched chromatin states~1.5% novel RNA structures~3% conserved regulatory motifs
~60% of constrained elements overlap with any of those features
Implications for interpreting disease associated variants
SNPs associated with human disease are 1.37-fold enriched for constrained regions.
Only a small portion of SNPs are likely to be causative.
HOXB1 and HOXB2 associated with tooth development phenotypes
Implications for Disease associated variance
Look at SNPs for HOXB1
• Helps resolve which SNPs disrupt function
• Rs8073963 disrupts Forkhead-family motif in an enhancer
Codon specific selectionLooked at 6.05 million codons
• 84.2% Purifying (Negative) selection sites• 2.4% Positive selection sites
4,431 Proteins with 15,383 positive selections sites
• Distributed positively selected sites for: immune response, taste perception, meiotic chromosome segregation and transcription regulation
• Localized positive selection sites for: microtubule based movement, topological change, telomere maintenance
Exaptation of mobile elements• Elements can move and be retained where advantageous in the
genome• 280,000 mobile elements exaptations common to mammalian
genomes• Of the ~1.1 million constrained elements from 90 million years of
divergence between marsupials and eutherians we can trace 19% to mobile elements
• 11% of mobile elements constrained
Accelerated evolution in the primate linage
564 human-accelerated regions (HARs) • Previously 202 known577 primate-accelerated regions (PARs)
In these regions constrained elements for brain and limb development
Influence genes harboring or neighboring are enriched for extracellular signaling, receptor activity, immunity, axon guidance, cartilage development, and embryonic pattern formation
Why are we different from our primate linage?
Main Points and Key Techniques
• Analysis of 29 mammalian genomes showed a map of >3.5 million constrained elements.
• ~4% of the human genome
• The function of ~60% of these constrained sequences can be identified.
• Protein coding sequences• RNA structures• Promoters and transcriptional regulators• Chromatin signatures
• This article shows the importance of constrained elements in the evolution of the mammalian lineage as well as their role in diseases.
Further Reading• Identifying novel constrained elements by exploiting baised substitution
patterns Manuel Garber, Mitchell Guttman, Michele Clamp, Michael C. Zody,Nir Friedman, and Xiaohui Xie Bioinformatics (2009) 25 (12): i54-I 62 doi:10.1093/bioinformatics/btp190
• Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304,1321–1325 (2004).
• Cooper, G. M., Brudno, M., Green, E. D., Batzoglou, S. & Sidow, A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13, 813–820 (2003)
Acknowledgments
Lindblad-Toh et al., (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478,476–482.
Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304,1321–1325 (2004).