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!