Lecture 10

Genes, genomes and chromosomes

Repeated and transposable elements

t

i

ii ppk

S

1

ln

1 2 3 4 5 1 2 3 4 5 1 2 3 4 5

S = maxS = min

n

lattice position

Show this!

WkS ln

p – probabilities of states

What if microstates are occupied unequally? How to write the entropy?

E. coli 4.5 Mb 1 circular chromosomeS. cerevisiae 16 Mb 16 (haploid set)C. elegans 100 Mb 6A. thaliana 125 Mb 5D. melanogaster 180 Mb 4M. musculus 3200 Mb 20H. sapiens 3300 Mb 23

Caryotype of H. sapiens

Chapter 6

Chromosomal organization

Genomes of many organisms contain large amount of ‘nonfunctional’ DNA

E. coli 4.5 Mb 1Yeast 12 Mbases/haploid set 16 chromosomesFruit fly 180 4Chicken 1300 39Human 3300 23

Tulips ~30000 Mbases

Amoeba ~660,000 Mbases/nucleus

The DNA contents does not reflect the complexity of the organism!

Related and structurally similar species may have variation in the amount of their total DNA by a factor of 100

In humans: ~5% of DNA is transcribed and 1.5% represents coding regions (exons). The rest is made of repeats with no obvious function.

Human Genome is ‘over-inflated’

What is gene?

Not only the coding sequence, a bit more …

- the entire nucleic acid sequence that is necessary for the synthesis of a functional gene product, polypeptide or RNA, both the coding and control sequences

5’ cap – 7-methylguanilate attached to mRNA

3’ Poly(A) site – allows cleavage by endonuclease and attachment of a poly(A) string (100-250 bases) by Poly(A) polymerase

Cap site = region coding for “5’-cap structure” making ribosome-binding site, close to the starting AUG codon

Poly(A) site – signals 3’ polyadenilation of mRNA

Splice sites

What mutations can do?

Control regions, shared exons or alternate parts can be hit. Mutations d and e will complement each other, despite being in the same gene. Mutation c in the common exon will not complement any of the mutations.

Density of coding regions varies in different species

Genes can be SOLITARY (occur once per haploid genome)

or form FAMILIES of DUPLICATED genes

How does exon or gene duplication occur?

Clusters of genes: transcription factors, kinases, GPCRs, immunoglobulins, …

Duplication also generates pseudo genes (non-functional sequences resembling genes)

Duplication then can be followed by a sequence drift; divergence is driven by beneficial mutations resulting in functional refinement, as in -globins (A and G genes code for embryonic versions having higher affinity to O2)

L1 – homologous non-coding regions interspersed throughout the genome

L1 – homologous non-coding regions interspersed throughout the genome

Tandemly repeated genes encode rRNAs, tRNAs and histones, the components utilized by cells in huge quantities

Up to 250 RNA polymerase complexes can be transcribing one gene simultaneously

Human Genome is ‘over-inflated’

Repetitious DNA

Simple-sequence (satellite) DNA is typically represented by 14-500 bp repeats in tandems of 20-100 kb. Often occurs near centromeres or in telomeres.

Microsatellite: 1-13 bp repeats (usually 1-4), tandems are less than 150 bp(sometimes occur within transcription units, causing diseases)

Microsatellite is thought to have originated from back-slippage of the daughter strand on its template strand during DNA replication

Chromosome 16 stained by a fluorescent probe in-situ hybridized with a simple sequence locus

Simple sequence DNA is localized near telomeres in mouse chromosomes

What’s the use of variable repeats? DNA fingerprinting

Minisatellite: 15-100 bp repeats making 20-50 repeat units (1-5 kb regions)These regions are used in DNA fingerprinting

Southern blot of DNA taken from three individuals, cut with a restriction enzyme and hybridized with three different minisatellites as probes

Why does the length of minisatellite repeats vary?

Mobile DNA = Transposable elements

Present in both eukaryotes and prokaryotes

Considered to be endosymbiotic, selfish DNA, with no specific function for the host

When transposition/duplication occurs in the germ line, it is inherited

In somatic sells transposition may inactivate a tumor-suppressor gene causing cancer.

Interspersed repeats (moderately repeated DNA) make up 45% of entire human DNA!

Transposons were discovered in maze by Barbara McClintock in the 1940s.

Two types of transposons

Bacterial DNA transposons = IS elements (insertion sequences)

About 20 different IS elements in E. coli

Transposition is a rare event ~10-5 to 10-7/generation, the rate is finely tuned by evolution

One or two enzymes are coded (Transposase)

IS elements can insert into plasmids or lysogenic phages and thus can be transferred to other cells