Transcript GeneticsLecture3

Genetics II (eukaryotes)
IT Carlow Bioinformatics
September 2006
Homo sapiens
• That’s us.
• 3.1 Gbases, 25,000 genes
• Genetic code same as E.coli
– Hence “universal”
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DNA replication (DNApol)
Transcription RNApol
Ribosomes, translation
So “essentially” the same?
Other Eukaryotes
• Mouse, Rat, Cow, Chimp etc.
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Chimp human 5mya L.C.Ancestor
Mouse rat 30mya LC Ancestor
Mouse human 100mya LC Ancestor
Chicken human 300mya LC Ancestor
• C.elegans 19,000 genes, 300 cells, 97Mbase
• Drosophila 14,000genes, 180Mbase
• S. cerevisiae 6,000genes, 12Mbase
Eukaryotes have nucleus
• DNA bundled in discrete units – chromosomes
– Ends need capping, telomerase issues
• Bundling = additional access complications
– histones, supercoiling
• Nucleus forces decoupling transscr translat
• Two way traffic in/out nucleus – NFB - Transcriptional regulators
Operons?
• In general not.
• But yeast often has common promoters on
divergent (opp strand) genes
• Singer Lloyd Humniecki Wolfe 2005
– Find tissue specific clusters – spleen expressed
– Chance or “design”
– Compare human and mouse cluster breaks
Operons in Mammals?
Telomeres
• Eukaryotic chromosomes are linear
• chromosomes seem to have fixed location.
• Telomeres have characteristic # of repeats
– Human TTAGGG, Oxytricha TTTTGGGG
• Chrs get shorter each generation
– Priming for Okazaki fragments
– Telomerase adds repeats
– Telomerase fails: cancer, senescence
How similar is the machinery?
• DNA polymerase size % ID
• RNA polymerase
• Ribosomes
– rRNA bigger 5S, 5.8S, 18S and 28S
– Bases: 120bp,160bp,1900bp,4700bp
– Protein count 50 rplX & 33 rpsX
tRNA
• Essential mediators of translation
• 74-90 base in size clover-leaf stucture
• Anti-codon loop
– Curved so “wobble” is possible at third posn –
– One anti-codon can serve 2 or 3 codons
• XXG can pair with C … Or U
• XXI (inosine) can pair with A, C or U
Introns
• About 5% of yeast genes
• Most mammalian genes
• Alternative splicing
– Explain why we are more complex than worms
– Challenges dogma 1 gene = 1 protein
– Accounts for 80,000 diff proteins
Intron splice site
Alternative splicing 1
• Splice / don’t splice
• If stop codon in frame in intron then
truncated protein.
• Can be used as a genetic switch to control
production of two alternative proteins
Alternative splicing 2
• Competing 5' or 3' Splice Site
• Here two different 3’ splice sites
• Proximal, distal
Alternative splicing 3
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Exon skipping
Could be more than one exon skipped
Lots of potential for variant transcripts
Slightly different enzymes
Missing protein domains
Alternative splicing 4
• Mutually exclusive exons
• Here exons 1, 2, & 4 or 1, 3, & 4
• Two different forms of protein
Alternative splicing 5
• That’s just 1 classification
– Can you think of another?
• Binf consequences
– Gene prediction difficult in eukaryotes
– No one answer in any one case
– EST as binf tool for prediction
Junk?
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Human genome 3Gb but only 25K genes
Even when introns accounted for
3% genome coding for “genes”
1% is actual codons
The rest?
Pseudogenes
• Defined as gene inactivated because of mutation
– Most obviously by nonsense/stop codon mutation
– Genetic code arranged so many mutations tolerable
– Once inactivated more mutations accumulate
• Processed pseudogene
– Reverse transcriptase copy of mRNA
– Lacks introns, 5’ upstream control regions
• 1/3rd of human genome gene and gene related
– pseudogenes,
– gene fragments, truncated genes
– introns/UTRs
Repetitive elements
• 2/3rd of genome “intergenic”
– 1400Mb interspersed repeats (transposable
elements) 44% of genome
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640Mb LINES, LINE-1
420Mb SINES, Alu million copies
250Mb LTR, ERV 200,000 copies
90Mb DNA transposons, PiggyBac 2000 copies
– 600Mb Microsatellites etc.
• 90Mb CACACA and other repeats (forensics)
A bit of history
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Darwin Origin of Species
1860s Mendel sends ms to Darwin (ignores)
1909 Gene “invented”
1910 Genes sit on chromosomes, in order
1941 One gene = one enzyme
1944 Genes definitely DNA
1953 Double helix
1977 Splicing
1993 MicroRNA identified
What is a gene?
• Nature 25 May 2006 News Feature p399-401
• Plants (Hothead), now mice may hold RNA copy
of gene to “correct” DNA!
• ENCODE project Encyclopedia of DNA elements
– Close look at 1% of human genome
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Alternative splicing (1977) can be fitted in.
5% of genome transcribed as read-through!
Exons can combine with exons many genes away!
63% of mouse genome transcribed!
8/500 non-coding RNAs essential for signalling
and growth
Bioinformatic consequences
• Pseudogenes a bioinf problem
– Transcribed? See ESTs
• Alternative splicing a gene prediction prob
– Exon prediction “easy”
– Gene prediction harder
• Careers in RNA bioinformatics.