CS273A

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Lecture 11

• HW1 Feedback (ours)
• (Upcoming Project discuss Wed)
• Non-Coding RNAs
• Halfway Feedback (yours)

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non coding RNAs
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Central Dogma of Biology
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RNA is an Active Player
reverse transcription
long ncRNA
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What is ncRNA?

• Non-coding RNA (ncRNA) is an RNA that functions
  without being translated to a protein.
• Known roles for ncRNAs
• RNA catalyzes excision/ligation in introns.
• RNA catalyzes the maturation of tRNA.
• RNA catalyzes peptide bond formation.
• RNA is a required subunit in telomerase.
• RNA plays roles in immunity and development
  (RNAi).
• RNA plays a role in dosage compensation.
• RNA plays a role in carbon storage.
• RNA is a major subunit in the SRP, which is
  important in protein trafficking.
• RNA guides RNA modification.
• In the beginning it is thought there was an RNA
  World, where RNA was both the information carrier
  and active molecule.

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RNA Folds into (Secondary and) 3D Structures
AAUUGCGGGAAAGGGGUCAA CAGCCGUUCAGUACCAAGUC UCAGGGGA
AACUUUGAGAUG GCCUUGCAAAGGGUAUGGUA AUAAGCUGACGGACAU
GGUC CUAACCACGCAGCCAAGUCC UAAGUCAACAGAUCUUCUGU UGA
UAUGGAUGCAGUUCA
We would like to predict them from sequence.
Cate, et al. (Cech Doudna). (1996) Science
2731678.
Waring Davies. (1984) Gene 28 277.
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RNA structure rules

• Canonical basepairs
• Watson-Crick basepairs
• G - C
• A - U
• Wobble basepair
• G U
• Stacks continuous nested basepairs.
  (energetically favorable)
• Non-basepaired loops
• Hairpin loop.
• Bulge.
• Internal loop.
• Multiloop.
• Pseudo-knots

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RNA structure Basics

• Key RNA is single-stranded. Think of a string
  over 4 letters, AC,G, and U.
• The complementary bases form pairs.
• Base-pairing defines a secondary structure. The
  base-pairing is usually non-crossing.

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Ab initio structure prediction lots of Dynamic
Programming

• Maximizing the number of base pairs (Nussinov et
  al, 1978)

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Pseudoknots drastically increase computational
complexity
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Nearest Neighbor Model for RNA Secondary
Structure Free Energy at 37 OC
Mathews, Disney, Childs, Schroeder, Zuker,
Turner. 2004. PNAS 101 7287.
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Zukers algorithm MFOLD computing loop dependent
energies
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Energy Landscape of Real Inferred Structures
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Unfortunately

• Random DNA (with high GC content) often folds
  into low-energy structures.
• What other signals determine non-coding genes?

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Evolution to the Rescue
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Stochastic context-free grammar (SCFG)
S ? aSu L ? aL S ? uSa L ? cL S ? gSc L ? a S
? cSg L ? c S ? L
S
S
L
L
L
L
a a c
g u u
c c c c
u c u
a g a
c
c

• Each derivation tree corresponds to a structure.

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Stochastic context-free grammar (cont)
S ? aSu S ? cSg S ? gSc S ? uSa S ? a S ? c S ?
g S ? u S ? SS 1. A CFG
S ? aSu ? acSgu ? accSggu ? accuSaggu
? accuSSaggu ? accugScSaggu ?
accuggSccSaggu ? accuggaccSaggu ?
accuggacccSgaggu ? accuggacccuSagaggu ?
accuggacccuuagaggu 2. A derivation of
accuggacccuuagaggu
3. Corresponding structure
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MicroRNA
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Genomic context
known miRNAs in human
intergenic
intronic
polycistronic
monocistronic
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tRNA
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tRNA Activity
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Human specific accelerated evolution
rapid change
Human
Chimp
conserved
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Human Accelerated Regions

• Human-specific substitutions in conserved
  sequences

rapid change
Human

• HAR1
• Novel ncRNA
• Co-expressed in Cajal-Retzius cells with reelin.
• Similar expression inhuman, chimp, rhesus.
• 18 unique human substitutionsleading to novel
  conformation.
• All weak (AT) to strong (GC).

Chimp
conserved
Human Derived
Chimp Ancestral
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Pollard, K. et al., Nature, 2006
Beniaminov, A. et al., RNA, 2008
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Other Non Coding Transcripts
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mRNA
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EST
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lincRNAs (long intergenic non coding RNAs)
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X chromosome inactivation in mammals
X
X
X
Y
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Xist X inactive-specific transcript
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Microarrays, Next Gen(eration) Sequencing etc.
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End Results
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Transcripts, transcripts everywhere
Human Genome
Leaky tx? Functional?
Transcribed (Tx)
Tx from both strands
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Or are they?
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Halfway Feedback