Download New roles for RNA

New roles for RNA
New fields for bioinformatics?
Morten Lindow
Centre for Bioinformatic
University of Copenhagen
RNA modul
• Torsdag
– Forelæsning
• ncRNA, RNAi, miRNA
– Opgave gennemgang, Bioperl, næste
hjemmeopgave
• Tirsdag
– Morgen: Øvelse – lave færdig, snakke
snakke.
– Eftermiddag: Opsamling
• Foredrag: mit projekt
Øvelser
• Formål:
– Få basal øvelse i at håndtere sekvenser i perl
– Værdsætte BioPerl
– Prøve at finde miRNA i Arabidopsis
Plan for this lecture
• Abundance of ncRNA
• Types of ncRNA
• RNAi – discovery and mechanisms
– miRNA
• RNAi as a technology
• RNAi – the genome’s immune system
• ncRNA and chromatin
What is the difference?
Source of variation
• What is the homology of protein coding genes
between human and mice?
– 99 % !!!!!!
• There are ~3 000 000 nucleotide differences
between two humans.
– 10 000 in protein coding genes (0.03%)
• Most are silent (third base)
• So where do the phenotypic differences between
two individuals or two species come from?
Source of differences?
• Whole system properties:
– Variations in gene expression (time/space).
• Control architecture is the primary source of
complex traits variation
– Background for
• Intercellular communication & integration
• Interorgan communication & integration
• Interindividual communication & integration
Systems biology
Control Architecture
Genome
Regulation by
proteins
Transcriptome
Proteome
Regulation by
RNA
Types of RNA
RNA
mRNA
rRNA
Ribosomal RNA
Participate in
protein synthesis
tRNA
Transfer RNA
Interface between
mRNA &
amino acids
ncRNA
Non-coding RNA. Transcribed RNA with a structural,
functional or catalytic role
snRNA
snoRNA
Small nuclear RNA Small nucleolar RNA
-Incl. RNA that
Found in nucleolus,
form part of the
involved in modification
spliceosome
of rRNA
miRNA
Micro RNA
Small RNA involved
regulation of expression
Other
Including large RNA
with roles in
chromotin structure and
imprinting
siRNA
stRNA
Small temporal RNA.
RNA with a role in
developmental timing
Small interfering RNA
Active molecules in
RNA interference
Discovery of RNAi
• Conventional antisense:
– ~50% downregulation
• Fire et al. : Synergy when given together
with sense RNA
Examples of RNAi
GFP expressed in nuclei
Control dsRNA
GFP specific dsRNA
Red =
silencing
of GFP
hairpin against pigment
RNA interference
RNAi mechanism
RNase III like enzyme
Endogenous vs exogenous
Inhibition of translation
Imperfect match
 Block translation
Near-perfect match
 Degrade mRNA
Defense against transposons?
• In C.elegans and Drosophila mutation of
RNAi components  activation of
transposons
•  Is RNAi a genomic immune system?
– The vertebrate adaptive immune system:
• Distinquish self from non-self
• Amplify a response
• Kill the intruder
Genomic immune system
hypothesis 1
• Self/non-self discrimination (generation od
dsRNA)
– Multicopy transposons:
• read through from flanking promotors create
complementary strands to form dsRNA
– Some transposons have terminal inverted
repeats  hairpin
Genomic immune system
hypothesis 2
• Amplification of
signal:
– siRNA may work as
primers on the mRNA
• Amplification by RNA
dependent RNA
polymerase
• (only detected in plants
& yeast)
Control Architecture
Genome
RNAi
Regulation by
proteins
Transcriptome
Proteome
Regulation by
RNA
Regulation of transcription
• What governs when a stretch of DNA is
transcribed?
– Transcription factors
– Accessabilitity of DNA to transcription factors
• Structure of the chromatin
– Proteins
– RNAs........
DNA & chromosome structure
Movie
Transcription and chromatin
structure
• Euchromatin – open structure –
transcriptionally active
• Heterochromatin – closed structure –
silenced
• Structure determined by
– > methylation of cytosines  histone binding
Spread of DNA methylation
Silent chromatin & RNAi
• Centromers contain repeats and are
often heterochromatic (silenced)
•Finding: Deletion of RNAi machinery
causes desilencing centromeric
regions
CREDIT: KATHARINE SUTLIFF/SCIENCE
Control Architecture
Imprinting – methylation
Splicing
Genome
RNAi
Regulation
by proteins
Transcriptome
Proteome
Regulation by
RNA
Ribozymes
Why use RNA in regulation?
• Less cost
– Genomic space. Compare RNA vs protein
– Metabolic space. Cost of aminoacids
• Speed
– RNA produced and active very quickly
• Easier to evolve. Less costly to explore
’expression space’
So why proteins?
• More adaptable
• Better at sensing environment –
responding to signal transduction etc