det humane genom
DESCRIPTION
Det humane genom. Menneskekroppen har 100 billioner celler, hver med 46 kromosomer. Samlet lengde av DNA: 2 meter/celle. …er ganske stort. Andre genomer som kan lære oss mye om det humane genom. Antall kromosomer i forskjellige organismer. - PowerPoint PPT PresentationTRANSCRIPT
Det humane genom
Menneskekroppen har 100 billioner celler, hver med 46 kromosomer. Samlet lengde av DNA: 2 meter/celle
…er ganske stort
Andre genomer som kan lære oss mye om det humane genom
Antall kromosomer i forskjellige organismer
K-value paradox: Complexity K-value paradox: Complexity does not correlate with does not correlate with chromosome number.chromosome number.
46 250
Ophioglossum reticulatumHomo sapiens Lysandra atlantica
1260
Størrelse av genomer
C-value paradox: Complexity C-value paradox: Complexity does not correlate with does not correlate with genome size.genome size.
3.4 109 bpHomo sapiens Amoeba dubia
6.7 1011 bp
Det humane genom
The human genome The human genome is disappointing:is disappointing:
• It is smallIt is small• It is emptyIt is empty• It is unoriginalIt is unoriginal• It is repetitiveIt is repetitive
En oversikt over det humane genom
Hvor mange gener i genomet?
Genomstørrelser – hvor mange gener?
N-value paradox: Complexity N-value paradox: Complexity does not correlate with gene does not correlate with gene number.number.
~31,000 genes~31,000 genes ~26,000 genes~26,000 genes ~50,000 genes~50,000 genes
Sammensetning av genomet
Intergenicregions(junk)
Introns (junk)Exons
1.5%1.5%
The genome is empty.The genome is empty.
Den molekylære funksjonen til 26383 humane gener
Funksjonelle kategorier i eukaryote proteomer
Flere proteiner fra samme gen (alternativ spleising)
Menneske: 60 % av genene koder for mer enn ett protein
Orm: 22 % av genene koder for mer enn ett protein
Forskjeller i geninhold
Fibroblastvekstfaktor – menneske 30, bananflue og orm 2 hverTransformerende vekstfaktor β – menneske 42, bananflue 9, orm 6Gener som koder for proteiner med immunglobulindomener – menneske 765, bananflue 140, orm 64”Sinkfinger”-proteiner – menneske dobbelt så mange som bananflue og 5 ganger flere enn orm
CpG-frekvens og CpG-øyer
The typical density of CpG doublets in mammalian DNA is ~1/100 bp, as seen for a -globin gene. In a CpG-rich island, the density is increased to >10 doublets/100 bp. The island in the APRT gene starts ~100 bp upstream of the promoter and extends ~400 bp into the gene. Each vertical line represents a CpG doublet.
CpG-øyer
Vedlikeholdsmetylering
Ved maintenance-metylering induserer metyleringsmønsteret i en parental DNA-tråd det tilsvarende metyleringsmønster i den komplementære tråden. Slik kan et stabilt metyleringsmønster opprettholdes i en cellelinje
CpG – underrepresentert i genomet
The CpG doublet occurs in vertebrate DNA at only ~20% of the frequency that would be expected from the proportion of G·C base pairs. (this is because CpG doublets are methylated on C, and spontaneous deamination of methyl-C converts it to T, introducing a mutation that removes the doublet.) In certain regions, however, the density of CpG doublets reaches the predicted value; in fact, it is increased by 10× relative to the rest of the genome. The CpG doublets in these regions are unmethylated
Cytosin, metylcytosin og tymin
Tme
Repetitive DNA
Iinterspersedinterspersed in tandemin tandem
AluAlus are like that!s are like that!
Repeterte sekvenser skaper problemer
Klasser av intersperserte repetisjoner i det humane genom
Elementer i det humane genom som kan transposeres på en RNA-formidlet måte
SINEs og utledning av fylogenetiske forhold
En SINE er enten der eller ikke
SINEs innsettes på tilfeldig måte i ikke-kodende områder. Samme plassering i to arter tyder på at innsettingen foregitt i en felles stamfar
Innsetting av en SINE er irreversibel, fravær er derfor et ancestralt trekk
Alu elementsLength = ~300 bp
Repetitive: > 1,000,000 times in the human genome
Constitute >10% of the human genome
Found mostly in intergenic regions and introns
Propagate in the genome through retroposition (RNA intermediates).
Evolution of Alu elements
Alu elements can be divided into subfamilies
The subfamilies are The subfamilies are distinguished by distinguished by ~16 diagnostic ~16 diagnostic positions.positions.
Sekvenssammenstilling av Alu-familier
14 Alu-familier hos mennesket, hvorav 1 ikke hos andre primater. 2000 Alu-insersjoner spesifikke for mennesket.
J, S, Y
Evolusjon av Alu-elementer
Transposisjonering av et typisk humant Alu-element
Alu-elementer hos primater
SplicingSplicing
Eukaryotic genes (exons & introns)
TranslationTranslation
SplicingAlternative
Mature splice variant II
Mature splice variant I
Alternative splicing: One gene, several proteins!
Types of alternative
splicing
Cassette exon or
internal-exon skipping
A
1 2
1 2A-OH
1 2YYYYYYYYYNCAGGTRAGT ACAG G
Donor site Acceptor siteBranch point
Lariat
Pyrimidine tract
Signals of splicing
Because mRNAs and Alus are frequently reverse transcribed and incorporated into the genome, pyrimidine tracts are ubiquitous
The complementary strand of The complementary strand of polyA is polyT = pyrimidine polyA is polyT = pyrimidine tract.tract.
The minus strand of Alu elements contains “near” splice sites
The minus strand of Alu contains ~3 sites that resemble the acceptor recognition site:
Consensus acceptor site:YYYYYYNCAG/RAlu-J: (127-114) :TTTTTTGtAG/A
The minus strand of Alu contains ~9 sites that resemble the consensus donor site:
Consensus donor site: CAG/GTRAGTAlu-J: (25-17) : CAG/GTGtGA
Our findings
Out of 1,182 alternatively spliced cassette exons, 62 have a significant hit to an Alu sequence.
Out of 4,151 constitutively spliced exons, none has a significant hit to an Alu sequence.
all Alu-containing exons are alternatively spliced.
Retention Ratio
Retention ratio = number of mRNA molecules containing the alternatively spliced exon divided by total number of mRNA molecules.Retention ratio for Alu-containing exons was ~10%. Retention ratio for alternatively spliced exons that do not contain Alu was ~45%.
Proposed model for Alu exonization
Exon Exon
Hvordan studere genomet?
http://www.genome.ucsc.edu/cgi-bin/hgGateway?org=human
http://www.ensembl.org/
Men NCBI har også en genombrowser: MapView!