New roles for RNA New fields for bioinformatics? Morten Lindow Centre for Bioinformatic University of Copenhagen
New roles for RNA
New fields for bioinformatics?
Morten LindowCentre 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
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
Types of RNA
RNA
mRNAncRNA
Non-coding RNA. Transcribed RNA with a structural, functional or catalytic role
rRNARibosomal RNA
Participate in protein synthesis
tRNATransfer RNA
Interface betweenmRNA &
amino acids
snRNASmall nuclear RNA
-Incl. RNA thatform part of the
spliceosome
snoRNASmall nucleolar RNAFound in nucleolus,
involved in modificationof rRNA
miRNAMicro RNA
Small RNA involvedregulation of expression
OtherIncluding large RNA
with roles in chromotin structure and
imprinting
siRNASmall interfering RNAActive molecules in
RNA interference
stRNASmall temporal RNA.RNA with a role in
developmental timing
Discovery of RNAi
• Conventional antisense:– ~50% downregulation
• Fire et al. : Synergy when given together with sense RNA
Examples of RNAi
hairpin against pigment
GFP expressed in nuclei
Control dsRNA GFP specific dsRNA
Red = silencing of GFP
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)
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........
Transcription and chromatin structure
• Euchromatin – open structure – transcriptionally active
• Heterochromatin – closed structure – silenced
• Structure determined by– > methylation of cytosines histone binding
Silent chromatin & RNAi
CREDIT: KATHARINE SUTLIFF/SCIENCE
• Centromers contain repeats and are often heterochromatic (silenced)
•Finding: Deletion of RNAi machinery causes desilencing centromeric regions
Control Architecture
Genome
Transcriptome
Proteome
Regulation by proteins Regulation by
RNA
Imprinting – methylationSplicing
RNAi
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’