1. BB30055: Genes and genomes
Major insights from the HGP

2. Major insights from the HGP
Gene size, content and distribution
Proteome content
SNP identification
Distribution of GC content
CpG islands
Recombination rates
Repeat content
Nature (2001) 15th Feb Vol 409 special issue; pgs 814 &

3. 1) Gene size

4. Gene content…. More genes: Twice as many as drosophila / C.elegans
Uneven gene distribution: Gene-rich and gene-poor regions
More paralogs: some gene families have extended the number of paralogs e.g. olfactory gene family has 1000 genes
More alternative transcripts: Increased RNA splice variants produced thereby expanding the primary proteins by 5 fold (e.g. neurexin genes)

5. Gene distribution Genes generally dispersed (~1 gene per 100kb)
Class III complex at HLA 6p21.3
Overlapping genes (transcribed from 2 DNA strands) - Rare
Genes- within genes E.g. NF1 gene
HMG3 Fig 9.8

6. Uneven gene distribution
Gene-rich
E.g. MHC on chromosome 6 has 60 genes with a GC content of 54%
Gene-poor regions
82 gene deserts identified
? Large or unidentified genes
What is the functional significance of these variations?

7. 2) Proteome content proteome more complex than invertebrates
Protein Domains (sections with identifiable shape/function)
Domain arrangements in humans
largest total number of domains is 130
largest number of domain types per protein is 9
Mostly identical arrangement of domains A A B B B C C C C C
Protein X

8. Proteome more complex than invertebrates……
no huge difference in domain number in humans
BUT, frequency of domain sharing very high in human proteins (structural proteins and proteins involved in signal transduction and immune function)
However, only 3 cases where a combination of 3 domain types shared by human & yeast proteins.
e.g carbomyl-phosphate synthase (involved in the first 3 steps of de novo pyrimidine biosynthesis) has 7 domain types, which occurs once in human and yeast but twice in drosophila

9. 3) SNPs (single nucleotide polymorphisms)
Sites that result from point mutations in individual base pairs
biallelic
~60,000 SNPs lie within exons and untranslated regions (85% of exons lie within 5kb of a SNP)
May or may not affect the ORF
Most SNPs may be regulatory
More than 1.4million SNPs identified
One every 1.9kb length on average
Densities vary over regions and chromosomes
e.g. HLA region has a high SNP density, reflecting maintenance of diverse haplotypes over many MYears
Nature (2001) 15th Feb Vol 409 special issue; pgs & 928

10. How does one distinguish sequence errors from polymorphisms?
Each piece of genome sequenced at least 10 times to reduce error rate (0.01%)
Polymorphisms
Sequence variation between individuals is 0.1%
To be defined as a polymorphism, the altered sequence must be present in a significant population
Rate of polymorphisms in diploid human genome is about 1 in 500 bp
Nature (2001) 15th Feb Vol 409 special issue; pgs & 928

11. SNPs and disease

12. SNPs……and risk of disease
N(291)S

13. SNPs……and pharmacogenomics

14. 4) Distribution of GC content
Genome wide average of 41%
Huge regional variations exist
E.g.distal 48Mb of chromosome 1p-47% but chromosome 13 has only 36%
Confirms cytogenetic staining with G-bands (Giemsa)
dark G-bands – low GC content (37%)
light G-bands – high GC content (45%)
Nature (2001) 15th Feb Vol 409 special issue; pg

15. CpG islands show no methylation
TpG
Methyl CpG
Deamination
methylated at C
CpG islands show no methylation
Significance of CpG islands
Non-methylated CpG islands associated with the 5’ ends of genes
Usually overlap the promoter region
Aberrant methylation of CpG islands linked to pathologies like cancer or epigenetic diseases like Rhett’s syndrome

16. Inheritance of CpG methylation

17. Epigenetic disease – Rett Syndrome
Characterised by neurodevelopmental problems after birth
mutations in a gene on the X chromosome, MECP2 (methyl CpG-binding protein 2), whose protein normally binds to methylated CpG and represses gene expression
RS symptoms associated with the failure of mutated MECP2 to regulate transcription of a specific gene, DLX5, one allele of which is normally imprinted. Without the MeCP2 protein, production of the Dlx5 protein is increased, which influence production of the neurotransmitter GABA in the brain
DLX5
DLX5

18. CpG islands Greatly under-represented in human genome
~28,890 in number (5 times less than expected)
~ 56% of human genes and 47% of the mouse genes have CpG islands
Variable density
e.g. Y – 2.9/Mb but
16,17 & 22 have 19-22/Mb
Average is 10.5/Mb
Nature (2001) 15th Feb Vol 409 special issue; pg

19. 6) Recombination rates 2 main observations
Recombination rate increases with decreasing arm length
Recombination rate suppressed near the centromeres and increases towards the distal 20-35Mb

20. 7) Repeat content Age distribution Comparison with other genomes
Variation in distribution of repeats
Distribution by GC content
Y chromosome
Nature (2001) 409: pp

21. Repeat content…….
a) Age distribution
Most interspersed repeats predate eutherian radiation (confirms the slow rate of clearance of nonfunctional sequence from vertebrate genomes)
LINEs and SINEs have extremely long lives
2 major peaks of transposon activity
No DNA transposition in the past 50MYr
LTR retroposons teetering on the brink of extinction
Most IR predate eutherian radiation (confirms the slow rate of clearance of nonfunctional sequence from vertebrate genomes)
LINEs and SINE have extremely long lives
2 major peaks of transposon activity
No DNA transposition in the past 50MYr
LTR teetering on the brink of extinction

22. a) Age distribution
overall decline in interspersed repeat activity in hominid lineage in the past 35-40MYr
compared to mouse genome, which shows a younger and more dynamic genome
Most IR predate eutherian radiation (confirms the slow rate of clearance of nonfunctional sequence from vertebrate genomes)
LINEs and SINE have extremely long lives
2 major peaks of transposon activity
No DNA transposition in the past 50MYr
LTR teetering on the brink of extinction

23. b) Comparison with other genomes
Higher density of transposable elements in euchromatic portion of genome
Higher abundance of ancient transposons
60% of IR made up of LINE1 and Alu repeats
whereas DNA transposons represent only 6%
(a few human genes appear likely to have resulted from horizontal transfer from bacteria!!)

24. c) Variation in distribution of repeats
Some regions show either
High repeat density
e.g. chromosome Xp11 – a 525kb region shows 89% repeat density
Low repeat density
e.g. HOX homeobox gene cluster (<2% repeats)
(indicative of regulatory elements which have low tolerance for insertions)

25. d) Distribution by GC content
High GC – gene rich ; High AT – gene poor
LINEs abundant in AT-rich regions
SINEs lower in AT-rich regions
Alu repeats in particular retained in actively transcribed GC rich regions E.g. chromosme 19 has 5% Alus compared to Y chromosome

26. e) The Y chromosome !
Unusually young genome (high tolerance to gaining insertions)
Mutation rate is 2.1X higher in male germline
Possibly due to cell division rates or different repair mechanisms

27. Working draft published – Feb 2001
Finished sequence – April 2003
Annotation of genes going on
(refer: International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 21 October 2004 (doi: /nature03001)

28. References Chapter 9 pp 265-268 Chapter 10: pp 339-348
HMG 3 by Strachan and Read
Chapter 10: pp
Genetics from genes to genomes by Hartwell et al (2/e)
Nature (2001) 409: pp