Shaping the genome Flashcards
The C-value paradox
- Related eukaryotes have genomes of different sizes
Polychaos dubium genome size is 670-Gb
– ~1000X bigger than other protozoan genomes!!!
- ~220X the human genome - Eukaryote genome size does not scale precisely with gene number
e.g. Yeast genome – 12-Mb/6K genes, whereas the human genome has 4x more genes but genome size is 264x larger (3,200-Mb)
Suggests variable gene density in eukaryotes – other elements contained within their genomes
Human genome and repetitive element
Repetitive elements make up about half of the genome!
Interspersed –repeat units are randomly distributed around the genome 45%
Tandem – repeat units are adjacent to each other in an array (~3%)
Classes of tandem repeats
-Satellite (2-100bp)– 1,000 to 1 million tandem repeats
Tandem repeats mainly in heterochromatin, centromeres and telomeres
-Megasatellites (>100bp) – 100 to 10,000 tandem repeats, ie. tRNA, rRNA
-Minisatellites (15-100bp) – 10 to 1000 tandem repeats
Sub-telomeric and also dispersed along chromosomes – some are highly variable between individuals
-Microsatellites (2-6bp) – 5 to 200 tandem repeats
Tandem repeats mainly dispersed along chr – highly variable between individuals
Slipage mechanism
-during replication, the daughter strand can loop out, causing a DNA strand to be replicated again
-the loop DNA stabilised by repetitive sequences
– can pair with adjacent repeats
Interspersed repeats include?
Includes
•Retroelements
•DNA transposons
Transposable elements (TEs) : segments of DNA that can move from one position of the genome to another
item needed for Mechanisms of transposition
•Transposition – process by which the movement of TEs (transposable element) occurs
Replicative transposition (copy and paste) Leads to an increase in repetitive DNA
Class I retrotransposons – Eukaryotes
Simple transposons - Prokaryotes
Conservative transposition (cut and paste) No net increase in repetitive element number
IS elements – Prokaryotes
P-elements - Eukaryotes
Prokaryotic TEs (transposon element)
Found in bacterial chromosomes and large integrative plasmids (F/R)
1. Insertion-sequence (IS) elements
§Encode ONLY genes required for mobilization and insertion
§cut and paste mechanism
2. Simple transposons
§Genes for mobilization AND other unrelated functions
§Some utilize copy and paste mechanism (involves resolvase)
§Provide a selective advantage to the organism
§TIRs – transposase encoded separately
3. Composite transposons
§Two separate IS elements lead to a single unit containing advantageous genes
§Provide a selective advantage to the organism
§cut and paste mechanism
Eukaryotic Class II TEs (DNA transposons)
•First cloned from Drosophila – P elements
•Have perfect terminal inverted repeats (TIR) and encode a transposase
Autonomous element
•Some elements have internal deletions or mutations affecting activity of the transposase – non-autonomous
Transposition of non-autonomous elements of maize
3 phenotype: colored (WT), mutant colorless, mosaic
- code in chromosome 9, unable to map the factor involve => show that it is transposons element
- hypothesis that element inserted in some are unable to move, name disassociation
- another element called activator, could move and cause other to move (act in trans)
- transposes cut part of the gene, if this is not repaired, it is loss leading to disassociation
why did some mutant reverse to WT in maize
- cross between mutant parent, some of the F1 have WT or mosaic pt
- Cause by additional tranposes element (Ac)
- these cause the phenotype to be unstable and could revert at random
Hybrid dysgenesis: the importance of controlling TEs
cross between F M and W T M
-all offsrping have limited fertility or none
test cross: all ofspring normal
-> the tranpose element is maternal
Eukaryotic Class I TEs (LTR retrotransposons)
•First isolated from yeast and Drosophila
•Categorized based on their similarity to retroviruses
Suggests transposition occurs via an RNA intermediate
Retrovirus lifecycle
the mRNA is inserted into host
- the reverse transcriptase convert the mRNA into DNA
- the revert transcriptase then create the double DNA strand
- intergration and translation by the host
Transposition of retrotransposons
•RNA intermediate is copied by pol
•dsDNA inserts randomly into the genome – “copy and paste”
-in human 9% but non fuctional
For exp
When TY1 is transcribe, a retro transcriptase is created, cretting a new DNA strand and have integration activity which insert it
-it create 5 bp direct repeat due to the cutting of integrase and repair by pol
Non-LTR retroelements
- Lack long terminal repeats, but may have reverse transcriptase
- LINE – long interspersed nuclear elements (1-6.5kb in length)
- SINE – short interspersed nuclear elements (100 300bp in length)
- SINEs are non-autonomous elements that require pol from L1
Genome size and transpone activity
- in different species, that have common ancestor. they have similar gene and organization but genome size and chromosome size changes. hypothesis that the change in genome are due to LTR retrotransposon.
Cytogenetics
- The study of the chromosome number and structure of an organism
- Genomes have a characteristic number of chromosomes
- Visualised by various techniques
- G-banding
- FISH
- Chromosome painting
Polyploids
•Polyploids are individuals or organisms that havemore than two chromosome sets
Diploid 2n AA BB CC 6
Triploid 3n AAA BBB CCC 9
Tetraploid 4n AAAA BBBB CCCC 12
Aneuploids
•Aneuploids have genomes where the chromosome number either greater or smaller than wildtype
Dipolid 2n
Monosonic 2n-1
trisomic 2n+1
Non-disjunction effect
•Polyploidy and aneuploidy occur spontaneously
•Non-disjunction
•Chromosomes fail to move to opposite poles
•During Mitosis or meiosis
•changes in the Entire set of chromosomes
– polyploidy
•Individual chromosome number
– aneuploidy (2n+1, 2n-1)
Non-disjunction during meiosis
•Meiotic non-disjunction is more common than mitotic non-disjunction
•Non-disjunction at meiosis I is more common
-Homologous chromosomes fail to separate at meiosis I - both go to the same pole ( 2 2n+ 1 and 2 2n-1, the 2n+1 are non-sister chromatid)
Sister chromatids fail to separate at meiosis II – both go to the same pole (2n+1 of sister chromatid, null and 2 normal)
Why might non-disjunction be more frequent in meiosis I than II?
•Bivalent – both dyad chromosomes
•Crossover process form a structure called a chiasmata
•Chiasmata are formed at meiosis I
•Helps correct segregation to opposite poles after crossing over
inability to crossover lead to non disjuction
polypoid in relationship to their parent
Autopolyploid
-One ancestral species
-Resembles parent species
-Autotetraploid - may display reduced fertility
-Autotriploid – sterile3n – trivalents, bivalents, univalents
-Instant new species –reproductive isolation
Allopolyploid
-Two ancestral species
-Resembles a blend of parent species
-Allotetraploid – fully fertile
-Instant new species – reproductive isolation
Chromosome pairing in autotetraploids
•There are various combinations of chromosome pairing possible in a autotetraploid A tetraploid can : -two bivalent -one quadrivalent -one univalent and a trivalent
Chromosome pairing in allotetraploids
•Chromosomes pair as pairs of bivalents allowing normal segregation – diploid gametes
Chromosome pairing in triploids
- Synapsis in a triploid results in one chromosome remaining unpaired at meiosis
- Univalent will segregate randomly and gametes will receive either 1 or 2 of every chromosome type
- Aneuploid gametes not viable
- Polyploid organisms with an odd number of chromosome sets are usually sterile
Consequences of altered ploidy: banana
- Triploid bananas arose naturally
- Banana are sterile and hence maintained as cuttings
- Banana are parthenocarpic –produce fruit in the absence of successful fertilisation
Consequences of altered ploidy watermelon
- Triploid watermelons created by 4n crossed to 2n
* Requires wildtype pollen to promote fruit development -parthenocarpy
