1. BB30055: Genes and genomes
Genomes - Dr. MV Hejmadi

2. Applications genome projects
BB30055: Genomes - MVH
3 broad areas
Genomes
Applications genome projects
(C) Genome evolution

3. Why sequence the genome?
3 main reasons
description of sequence of every gene valuable. Includes regulatory regions which help in understanding not only the molecular activities of the cell but also ways in which they are controlled.
identify & characterise important inheritable disease genes or bacterial genes (for industrial use)
Role of intergenic sequences e.g. satellites, intronic regions etc

4. History of Human Genome Project (HGP)
1953 – DNA structure (Watson & Crick)
1972 – Recombinant DNA (Paul Berg)
1977 – DNA sequencing (Maxam, Gilbert and Sanger)
1985 – PCR technology (Kary Mullis)
1986 – automated sequencing (Leroy Hood & Lloyd Smith
1988 – IHGSC established (NIH, DOE) Watson leads
1990 – IHGSC scaled up, BLAST published (Lipman+Myers)
1992 – Watson quits, Venter sets up TIGR
1993 – F Collins heads IHGSC, Sanger Centre (Sulston)
1995 – cDNA microarray
1998 – Celera genomics (J Craig Venter)
2001 – Working draft of human genome sequence published
2003 – Finished sequence announced

5. Human Genome Project (HGP)
Goal: Obtain the entire DNA sequence of human genome
Players:
International Human Genome Sequence Consortium (IHGSC)
- public funding, free access to all, started earlier
- used mapping overlapping clones method
(B) Celera Genomics
– private funding
- used whole genome shotgun strategy

6. Whose genome is it anyway?
International Human Genome Sequence Consortium (IHGSC)
- composite from several different people generated from primary samples taken from numerous anonymous donors across racial and ethnic groups
(B) Celera Genomics
– 5 different donors (one of whom was J Craig Venter himself !!!)

7. sequencing genomes
Mapping phase
Sequencing phase

8. Strategies for sequencing the human genome
IHGSC
Celera

9. Result….
~ ,000 protein-coding genes estimated based on known genes and predictions
IHGSC Celera
definite genes 24, ,383
possible genes ,000

10. Other genomes sequenced
Sept 2003
18,473
human orthologs
1997
4,200 genes
1998
19,099 genes
June 2006
Sept 2007
diploid genome
‘HuRef’
2002
38,000 genes
2002
36,000 genes
Science (26 Sep 2003)Vol301(5641)pp

11. Genomics: World's smallest genome
the smallest genome known is the DNA of a 'nucleomorph' of Bigelowiella natans, a single-celled algae of the group known as chlorarachniophytes.
373,000 base pairs and a mere 331 genes
The nucleomorph is an evolutionary vestige that was originally the nucleus of a eukaryotic cell. The eukaryotic cell swallowed a cyanobacterium to acquire a photosynthetic 'plastid' organelle, and that cell was in turn engulfed by another cell to produce B. natans as we know it. Now, most of the nucleomorph's genome is concerned with its own maintenance, and just 17 of its genes still exert any control over the plastid. Its small size suggests it is heading for evolutionary oblivion.
Proc. Natl Acad. Sci. USA 103, 9566–9571 (2006) by G McFadden, University of Melbourne, Australia

12. Organisation of human genome
Mitochondrial genome
Nuclear genome (3.2 Gbp)
24 types of chromosomes
Y- 51Mb and chr1 -279Mbp

13. General organisation of human genome

14. Basic structure of a gene
Figure 21.11
Fig

15. Polypeptide-coding regions

16. Gene organisation
Rare bicistronic transcription units E.g. UBA52 transcription generates ubiquitin and a ribosomal protein S27a

17. Non polypeptide–coding: RNA encoding
rRNA and 497 tRNA genes

18. Class of RNA
Example types
Function
Ribosomal RNA
16,23,18,28S
Ribosomal subunits
Transfer RNA
22 mitochondrial 49 cytoplasmic
mRNA binding
Small nuclear RNA(snRNA)
U1,U2,U4,U5 etc
RNA splicing
Small nucleolar RNA (snoRNA)
U3,U8 etc
rRNA modification and processing
microRNA (miRNA)
>200 types
Regulatory RNA
XIST RNA
Inactivation of X chromosome
Imprinting associated RNA
H19 RNA
Genomic imprinting
Antisense RNA
>1500 types
Suppression of gene expression
Telomerase RNA
Telomere formation

19. General organisation of human genome

20. Pseudogenes () non functional copies of an active gene. May be either
a) Nonprocessed pseudogenes
May contain exons, introns & promoters but are inactive due to inappropriate termination codons
Arise by gene duplication events usually in gene clusters (e.g. a and b–globin gene clusters)

21. Pseudogenes in globin gene cluster

22. Gene fragments or truncated genes
Gene fragments: small segments of a gene (e.g. single exon from a multiexon gene)
Truncated genes:
Short components of functional genes (e.g. 5’ or 3’ end)
Thought to arise due to unequal crossover or exchange

23. b) processed pseudogenes -
Thought to arise by genomic insertion of a cDNA as a result of retrotransposition
Contributes to overall repetitive elements (<1%)
Retrogene – functional copy - testis

24. processed pseudogenes -
Retrogene – functional copy - testis

25. General organisation of human genome

26. Unique or low copy number sequences
Non –coding, non repetitive and single copy sequences of no known function or significance

27. General organisation of human genome

28. Repetitive elements Main classes based on origin Tandem repeats
Interspersed repeats
Segmental duplications

29. References Chapter 9 pp 265-268 Chapter 10: pp 351-366
HMG 3 by Strachan and Read
Chapter 10: pp
Genetics from genes to genomes by Hartwell et al (3/e)
Nature (2001) 409: pp