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EVOLUSI GENOMOLEH :

ANDREIAN IMANUEL FIDHATAMIGENOMe EVOLUTION ?Evolusi genomChange of genome Why ?Kurang/bertambah/ hilangnya beberapa genBanyak Faktor Berkembang Its really happens ?IL2 interleukin 22ExampleHomeosisGen HoxManusia : kromosom 7 dan 17Tikus rumah : kromosom 6,9,11,5 ..Drosophila sp. : 3R.Rancangan dasar tubuh/ perkembangan pengaturan spesial organ-organ tubuh.the vertebrate ancestor hypothesis

Mutasi (Duplikasi) Kompleks hoxCd 4= sel ThCd8 = Sel T sittoksik (Tc)3Mekanisme Evolusi Genom (Symbiogenesis)Genom Prokaryote Transfer GenGenom Eukaryote MitokondriaChloroplas CyanobacteriumProteobacteriaCd 4= sel ThCd8 = Sel T sittoksik (Tc)4The Truth is Unkown .. But ... ?Genome ChloroplasGenom inti copies of mitochondrial DNAGenom MitokondriaSuperoxide dismutase(Chromosome 6) Cd 4= sel ThCd8 = Sel T sittoksik (Tc)52. Genome evolution - introductionIn the course of a human lifetime, the genome is used, damaged, repaired, copied and handed down to offspring cells dozens of times. In the process, the genome is changed. This change is called a mutation.

At first this involves just a single individual. If the change is has no phenotypic consequence, no selection acts against (or for) the mutation, and chance determines whether the individuals offspring will carry the mutation, and so on. The process by which the frequency of the mutation changes in the population is called (random) genetic drift.

Of all neutral mutations in a population of 2N haploid genomes, a fraction 1/2N will eventually spread through the entire population. The mutation is said to have gone to fixation. Mutations that have a beneficial effect have a (much) larger probability of getting fixed (once they reach a non-negligible population frequency), while deleterious mutations have almost no chance of going to fixation. Mutations that have become fixed in the population are called substitutions.

(Note: substitutions usually refer to single nucleotide substitutions, but the term indel substitution is also used.)

When comparing genomes from different species, what you see are all the fixed mutations (substitutions) that have occurred since the two species split. Mutations that are reside in either of the two individuals whose genomes were sequenced are called polymorphisms, and will also be included. Usually these form a small proportion and the distinction is ignored (but note that polymorphisms may well be deleterious, while substitutions rarely are).2. Genome evolution nucleotide substitutionsBasically two causes: damage, and copy errors during replication.

The two causes can be teased apart by comparing species with different generation times. More generations per unit of time mean more copying errors, while the rate of damage might stay relatively constant.

Errors are recognized and repaired by specific and highly efficient repair mechanisms.

Resulting error rate is low: about 3x10-8 per nucleotide per generation in humans.

The repair mechanism is extremely important: damage to this system increases the likelihood of getting cancer.

The rate of mutagenesis is higher in males than in females (see e.g. Berlin et al., J Molec Evol 62(2) 226-233), probably due to more cell divisions in the male germline. This results in low mutation rates on the X, and high mutation rates on the Y chromosome.

In mammals, the rate of transitions (pyrimidine-to-pyrimidine or purine-to-purine) is about twice higher than the rate of transversions (pyrimidine-to-purine or vice versa).

2. Genome evolution CpG mutation rate

Methylation of Cytosine (mC) involves adding a methyl group (CH3) on to the C5 carbon.

Accidental de-amination of the C4 carbon turns a mC into a normal Thymine.

This results in a mismatch, but the wrong base cannot be identified, since both are in the alphabet.

Result: substitution rate on CpG dinucleotides is about 15x higher than for ordinary Cs or Gs.

(The same process on the reverse-strand mC causes a high mutation rate on the G).

Over time, this causes CpGs to be about 4x underrepresented compared to the expectation based on C and G frequencies.

For sequences that are not methylated (in the germline), this mechanism does not apply, resulting in high (i.e. normal) levels of CpG in so-called CpG islands. These are often promoters of ubiquitously expressed genes.

2. Genome evolution Transcription-coupled repairWhen RNA polymerase II encounters a mutated nucleotide, it stops. This triggers the TCR pathway which repairs the mutation.

Failure of TCR leads to Cockayne syndrome, extreme form of accelerated aging.

TCR is strand-asymmetric (mutations in the untranscribed strand are not corrected by TCR), and leads to asymmetric mutation rates in transcribed regions.

2. Genome evolution - IndelsWhen the ancestral sequence is not known, insertions and deletions cannot be distinguished, and are often referred to as indels.

Indels form an important source of sequence change more on this later.

Most small indels are in fact deletions (by a factor 3 in human).

Indels can have any size, up to several Mb. The majority are 1 nt indels.

CGACATTAA--ATAGGCATAGCAGGACCAGATACCAGATCAAAGGCTTCAGGCGCACGACGTTAACGATTGGC---GCAGTATCAGATACCCGATCAAAG----CAGACGCAIndelIndelIndel2. Genome evolution Indel mechanismshttp://www.sci.sdsu.edu/~smaloy/

During replication, the template and copy can become separated.

If this happens in a tandem-repetitive region, there is a possibility of incorrect re-pairing (slippage)

This can lead to both short insertions and deletions.

Long stretches of short-period tandem repeats (microsatellites) are particularly prone to slippage. This is the reason behind the fast evolution of microsatellite length.

The gene encoding for huntingtin contains a repeat region of CAG triplets. Expansion of the number of CAG units beyond 36 causes Huntingtons disease.

2. Genome evolution indel mechanisms

http://www.sci.sdsu.edu/~smaloy/Recombination between direct repeats in a single chromosome leads to a (potentially Mb size) deletion.

Recombination requires (near) sequence identity over fairly large region (100s nt?), so these deletions are mostly not very small.

Unequal recombination (involving similar or identical regions at different chromosomal locations) can also lead to insertions (segmental duplications).

In the picture, unequal recombination between sister chromatids at replication is shown. The same process may also happen between parental (homologous) chromosomes.2. Genome evolution RecombinationMechanism of recombination:

1. Double-stranded break (DSB) formation

2. Broken ends get digested

3. Single strands invade region with high sequence similarity

4. Repair and re-synthesis Holliday junction

5. Holliday junction resolution:Crossing over (black arrows), or NO crossing over (grey arrows)

Gabriel Marais, Trends Genet, 19(6)2003 2. Genome evolution - types of recombination

Double-stranded breaks appear:

Accidentally (somatic & germ cells)Repair recombination

Deliberately (germ cells at meiosis)Sexual (or meiotic) recombination

Different (but overlapping) pathways

Preference for: sister chromatid in repair recombinationparental chromosome in sexual recombination

Recombination is obligatory during meiosis. Rate of recombination is >1 per generation per chromosome.

2. Genome evolution Gene conversion

Gene conversion = copying of one stretchof DNA into another

Single-stranded DNA can invade sister chromatidIdentical DNA, so no mutations

If single strand invades parental chromosome:Without crossing over: gene conversionWith crossing over: gene conversion + recombination

When the nicked strand invades a non-homologous but sequence-similar region (as in unequal recombination), gene conversion causes sideways copying of genetic material. Causes similarities to increase / persist.

The effect of gene conversion (without recombination) on the genome sequence is equivalent to two recombination events happening close to each other (order 1kb).

2. Genome evolution Biased Gene ConversionMutation bias for GC as a side effect of gene conversion

Two repair mechanisms:Base Excision Repair (BER)Targets hetero-mismatches, AG, TG, AC, TCEfficient; replaces just one baseFavours GCNucleotide Excision Repair (NER)Targets AA, CC, TT, GG mismatchesDigests ~1kb, resynthesizesFavours unbroken strand, no nucleotide bias

Second source of biased gene conversionAT sites seem to be target for DSBs in sexual recombinationDSB strand gets digested, copied back from other alleleResult: bias towards GC

2. Genome evolution - Recombination hotspotsRate of recombination is measured in centiMorgans (cM). Two genetic loci are 1 cM apart if 1 recombination per 100 generations occurs between them.

Recombination rate not uniform:Background rate ~0.04 cM/MbAverage rate ~1 cM/Mb0.5% of genome >15 cM/Mb

Recombination hotspot = gene conversion hotspot

Cause of hotspots not known:CCTCCCT motif?Bias for high GC

One mutation can change hotspot activityDNA2 locus in MHC region,CT suppresses hotspot

Perhaps differences in recombination rates have, over time, caused the current isochore structure through biased gene conversion.Myers, Bottolo, Freeman, McVean, Donnelly, Science 310 Oct 2005 2. Genome evolution double stranded break repairAccidental breaks are also repaired through the non-homologous end joining (NHEJ) pathway. Does not require homologous sequence.

Evolutionary very old pathway: yeast and some bacterial species have NHEJ.

Repairs most breaks correctly, but is also able to induce translocations (chromosome rearrangements).

Gill and Fast BMC Molecular Biology 2007 8:24 doi:10.1186/1471-2199-8-242. Genome evolution chromosomal rearrangements

Mouse chromosomes (1-19 and X) coloured according to homology with human chromosomes (1-22 and X). In the about 2 x 80 million years that separate humans and mice, many chromosomal rearrangements have occurred.Terima Kasih :v :v :v