Det humane genom Menneskekroppen har 100 billioner celler

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 does not correlate with chromosome number. Homo sapiens 46 Lysandra atlantica 250 Ophioglossum reticulatum 1260

Størrelse av genomer

C-value paradox: Complexity does not correlate with genome size.

Det humane genom

The human genome is disappointing: • It is small • It is empty • It is unoriginal • It is repetitive

En oversikt over det humane genom

Hvor mange gener i genomet?

Genomstørrelser – hvor mange gener?

N-value paradox: Complexity does not correlate with gene number. ~31, 000 genes ~26, 000 genes ~50, 000 genes

Sammensetning av genomet

1. 5% Exons Introns (junk) Intergenic regions (junk) 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 hver Transformerende vekstfaktor β – menneske 42, bananflue 9, orm 6 Gener 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

Cp. G-frekvens og Cp. G-øyer The typical density of Cp. G doublets in mammalian DNA is ~1/100 bp, as seen for a -globin gene. In a Cp. Grich 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 Cp. G doublet.

Cp. G-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

Cp. G – underrepresentert i genomet The Cp. G 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 Cp. G 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 Cp. G doublets reaches the predicted value; in fact, it is increased by 10× relative to the rest of the genome. The Cp. G doublets in these regions are unmethylated

Cytosin, metylcytosin og tymin me T

Repetitive DNA Alus are like that! interspersed I in tandem

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 ikkekodende 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 elements Length = ~300 bp Repetitive: > 1, 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 distinguished by ~16 diagnostic positions.

Sekvenssammenstilling av Alu -familier 14 Alu-familier hos mennesket, hvorav 1 ikke hos andre primater. 2000 Aluinsersjoner spesifikke for mennesket. J, S, Y

Evolusjon av Alu-elementer

Transposisjonering av et typisk humant Alu-element

Alu-elementer hos primater

Eukaryotic genes (exons & introns) Splicing Translation

Alternative splicing: One gene, several proteins! Alternative Splicing Mature splice variant II

Types of alternative splicing

Cassette exon or internal-exon skipping

Signals of splicing Donor site 1 Branch point CAG GTRAGT A Acceptor site 2 YYYYYNCAG G Pyrimidine tract 1 -OH 2 A Lariat A 1 2

Because m. RNAs and Alus are frequently reverse transcribed and incorporated into the genome, pyrimidine tracts are ubiquitous The complementary strand of poly. A is poly. T = pyrimidine 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/R Alu-J: (127 -114) : TTTTTTGt. AG/A The minus strand of Alu contains ~9 sites that resemble the consensus donor site: CAG/GTRAGT Alu-J: (25 -17) : CAG/GTGt. GA

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 m. RNA molecules containing the alternatively spliced exon divided by total number of m. RNA 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

Hvordan studere genomet? http: //www. genome. ucsc. edu/cgi-bin/hg. Gateway? org=human http: //www. ensembl. org/ Men NCBI har også en genombrowser: Map. View!