Transcript Evolucijska genomika 2

Skrivnostni svet nekodirajočih
delov evkariontskih genomov
Kordiš Dušan
Odsek 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
Euchromatin
*Centromere
Evolucija kromosomov
Eukaryote gene structure
• Coding sequence gene not continuous
2
Fig 18-8
The forces affecting
genome size evolution
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.
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 into
RNA, then spliced out during RNA processing.
 Contain functional elements such as splicing
signals, regulatory promoters, and other genes.
 Evolve very rapidly in size and content.
 Constitute 26%, 11%, and 24% of the
nematode, fly, and human genomes.
What forces drive the evolution of intron size?
Inton Size - 10 to 100,000 nt
Introns are transcribed
Precursor RNA (dotted)
hybridized with DNA (red)
Mature mRNA (dotted)
hybridized with DNA (red)
Introns vary in size and number
The complexity problem
 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.
 Phenotypic variation in mammals is primarily associated with noncoding
regions:
- 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.
 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)
 98% of transcriptional output in humans is noncoding RNA
Transpozicijski elementi
B. McClintock: odkritje transpozicijskih elementov/dinamični genom
Four classes of parasitic DNA elements are
found interspersed throughout the human genome
Retrotransposons
1.
2.
3.
Transposons
4.
Kakšen % genoma
zavzemajo TE
Spremembe sesalskih
genomov po
retrotranspoziciji L1
elementov
Do LINEs Mediate Genomic Plasticity ?
Whole Genome
Breakpoints
(3300 Mb)
(245 Mb)
LINEs
20.4%
45.3%
SINEs
13.1%
12.5%
LTRs
8.3%
8.3%
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.
Chromatin as a template
of genetic inheritance
epigenetics as process
inducing differentiated
cellular states
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