Skrivnostni svet nekodirajočih delov evkariontskih genomov

Kordiš DušanOdsek za biokemijo in molekularno biologijo, IJS, Ljubljana

Nekodirajoča DNA zavzema pretežni del genomov pri eukariontih

Human Genome At Glance

Genomska arhitektura

Chromosome organization

Human Chromosome Y:Organization of Genes and DNA Elements

Heterochromatin *

*Centromere

Euchromatin

Evolucija kromosomov

2

• Coding sequence gene not continuous

Eukaryote gene structure

Fig 18-8

9

Intergenicregions(junk)

Introns (junk)Exons

1.5%1.5%

The genome is empty.The genome is empty.

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Junk DNAJunk DNAJunk can sometimes be useful:Junk can sometimes be useful:

•• spare parts (spare parts (modulesmodules))

•• motif donors (motif donors (exon exon shufflingshuffling))

•• molds (molds (gene conversiongene conversion))

7

C-value paradox: ComplexityC-value paradox: Complexitydoes not correlate withdoes not correlate withgenome size.genome size.

3.4 10 9 bpHomo sapiens Amoeba dubia

6.7 1011 bp

The forces affecting genome size evolution

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K-value paradox: ComplexityK-value paradox: Complexitydoes not correlate withdoes not correlate withchromosome number.chromosome number.

46 250

Ophioglossum reticulatumHomo sapiens Lysandra atlantica

1260

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N-value paradox: ComplexityN-value paradox: Complexitydoes not correlate with genedoes not correlate with genenumber.number.

~31,000 genes~31,000 genes ~26,000 genes~26,000 genes ~50,000 genes~50,000 genes

Velikosti genomov in število genov pri

prokariontih in eukariontih

Funkcionalna evolucija nekodirajoče DNA

Human vs. Chimpanzee

• A difference every 100 bases.• A new transposon every 50000 bases• Two chromosome in one species fused

compared to the other.

Human vs. Mouse

• In general 40% of bases have changed.• In functional regions only 15% of bases have

changed.• Looking for conserved regions between human

and mouse helps identify functional parts ofhuman genome.

Deletion of a conserved noncoding sequence selectively reduces expression of cytokine genes over a long distance

Percent identity plots comparing human and other sequences at three loci (CNS:red, exons:blue, introns:yellow)

Cis-regulatorna evolucija

gradual, stepwise accumulation of sites that impart quantitatively greater Hox influence over gene regulation

Important regulatory inventions leading to the crown group bilaterians

Cis-regulatory logic during development

Introni: izvor, evolucija in vloga v genomu

• What are introns?

Stretches of DNA that are transcribed intoRNA, then spliced out during RNA processing.

Contain functional elements such as splicingsignals, regulatory promoters, and other genes.

Evolve very rapidly in size and content.

Constitute 26%, 11%, and 24% of thenematode, fly, and human genomes.

What forces drive the evolution of intron size?

I ntrons are transcribed

Precursor RNA (dotted)hybridized with DNA (red)

Mature mRNA (dotted)hybridized with DNA (red)

I nton Size - 10 to 100,000 nt

I ntrons vary in size and number

Gene numbers do not increase as much as expected with complexity:

- worm and fly gene numbers (12-14,000) are only about twice those of yeast (6,000) and P. aeruginosa (5,500)- mammalian (human, mouse) gene numbers (~30,000) are only about twice those of invertebrates.

The complexity problem

This suggests that:- animals have a relatively stable core proteome, whose components are multitasked in differentiation and development- variations in phenotype occurs mainly by variation in the control architecture (unlike prokaryotes)

Phenotypic variation in mammals is primarily associated with noncodingregions:- only ~10,000 out of ~3,000,000 polymorphisms between individual humans (0.3%) occur in protein coding sequences- only 1% of genes are different between humans and mice.

98% of transcriptional output in humans is noncoding RNA

Transpozicijski elementi

B. McClintock: odkritje transpozicijskih elementov/dinamični genom

Four classes of parasitic DNA elements arefound interspersed throughout the human genome

Retrotransposons

Transposons

1.

2.

3.

4.

Kakšen % genoma zavzemajo TE

Spremembe sesalskih genomov po retrotranspoziciji L1 elementov

Do LINEs Mediate Genomic Plasticity ?

12.5%13.1%SINEs

8.3%8.3%LTRs

45.3%20.4%LINEs

Breakpoints(245 Mb)

Whole Genome(3300 Mb)

Kakšen vpliv ima načina razmnoževanja

na preživetje TE

nespolno

spolno

Povezava ekologije in velikosti genoma: dinamika genoma na populacijskem nivoju

Kako lahko Alu elementi poškodujejo človeški genom ?

Homologna rekombinacija med Alu elementi

Fig 18-11

Mechanisms of genome expansion in the grass genomes

Mechanisms leading to genome contraction

Genome organization and gene distribution in cereal genomes

Model for evolution of gene-containing regions in cereal genomes

Genome defense and regulation by small RNAs

RNA interferenca

MicroRNA (miRNA)

Epigenetsko utišanje transpozicijskih elementov

Model of the origin and potential functions of

microRNAs

Model delovanja RNAi

How RNAi initiates chromatin silencing

Chromatin remodeling, transcriptional activity and heterochromatin

Epigenetsko reprogramiranje med gametogenezo

chromatin remodeling and demethylation during

(a) normal fertilization and

(b) during cloning by nuclear transfer.

epigenetics as process inducing differentiated cellular states

Chromatin as a template of genetic inheritance

Central role for RNAi in genome maintenance: RNAi responds not only to exogenous nucleic acids but also to endogenous DNA parasites

Uporaba RNA interference v funkcionalni genomiki in medicini

Potencialna uporaba RNAi pri sesalcih

RNA interferenca in zdravljenje raka

(a) A viral vector delivers a gene encoding a small interfering RNA (siRNA) to silence the mutant allele of a cancer-causing gene. The vector encodes a short RNA hairpin, which is processed in the cytoplasm by the ribonuclease Dicer into the siRNA.

(b) The siRNA acts as a sequence-specific guide for the RNA-induced silencing complex (RISC) to target cleavage of the mRNA from a specific gene, in this case, the mutant allele of an oncogene.

The genetic flow and mRNA processing, indicating possible strategies for gene regulation

HIV infection and replication have been targeted by RNA interference (RNAi) (red).

preventing HIV entry and subsequent replication: RNAi has also been used to suppress CD4 expression in host cells (blue).

Inhibicija HIV replikacije z RNAi

Future possibilities for therapy treatments using RNAi vectors