BB30055: Genes and genomesGenomes - Dr. MV Hejmadi (bssmvh@bath.ac.uk)

BB30055: Genomes - MVH3 broad areas

(A) Genomes

(B)Applications genome projects

(C) Genome evolution

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

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

Smith1988 – IHGSC established (NIH, DOE) Watson leads1990 – IHGSC scaled up, BLAST published

(Lipman+Myers)1992 – Watson quits, Venter sets up TIGR1993 – F Collins heads IHGSC, Sanger Centre (Sulston)1995 – cDNA microarray1998 – Celera genomics (J Craig Venter)2001 – Working draft of human genome sequence

published2003 – Finished sequence announced

Human Genome Project (HGP)

Goal: Obtain the entire DNA sequence of human genome

Players:(A) International Human Genome Sequence

Consortium (IHGSC)- public funding, free access to all, started

earlier- used mapping overlapping clones method

(B) Celera Genomics – private funding, pay to view- started in 1998- used whole genome shotgun strategy

Whose genome is it anyway?

(A) International Human Genome Sequence Consortium (IHGSC)- composite from several different people generated from 10-20 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 !!!)

sequencing genomes

Mapping phase

Sequencing phase

Strategies for sequencing the human genome

IHGSC Celera

Result….

~30 - 40,000 protein-coding genes estimated based on known genes and predictions

IHGSC Celeradefinite genes 24,500 26,383 possible genes 5000 12,000

Other genomes sequenced

200236,000 genes

Sept 200318,473human orthologs

19974,200 genes

199819,099 genes

200238,000 genes

Science (26 Sep 2003)Vol301(5641)pp1854-1855

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

Organisation of human genome

Nuclear genome (3.2 Gbp) 24 types of chromosomes Y- 51Mb and chr1 -279Mbp

Mitochondrial genome

http://www.ncbi.nlm.nih.gov/Genomes/

General organisation of human genome

Basic structure of a gene

Fig. 21.11

Polypeptide-coding regions

Gene organisation

Rare bicistronic transcription units E.g. UBA52 transcription generates ubiquitin

and a ribosomal protein S27a

Non polypeptide–coding: RNA encoding

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

General organisation of human genome

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. and –globin gene

clusters)

Pseudogenes in globin gene cluster

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

b) processed pseudogenes -

Thought to arise by genomic insertion of a cDNA as a result of retrotransposition

Contributes to overall repetitive elements (<1%)

processed pseudogenes -

General organisation of human genome

Unique or low copy number sequences

Non –coding, non repetitive and single copy sequences of no known function or significance

General organisation of human genome

Repetitive elements

Main classes based on origin

Tandem repeats

Interspersed repeats

Segmental duplications

References

1) Chapter 9 pp 265-268 HMG 3 by Strachan and

Read

2) Chapter 10: pp 339-348Genetics from genes to genomes by Hartwell et al (2/e)

3) Nature (2001) 409: pp 879-891

http://www.ncbi.nlm.nih.gov/Genomes/