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Class 5: RNA Structure Prediction

Class 5: RNA Structure Prediction. RNA types. Messenger RNA (mRNA) Encodes protein sequences Transfer RNA (tRNA) Adaptor between mRNA molecules and amino-acids (protein building blocks) Ribosomal RNA (rRNA) Part of the ribosome, a machine for translating mRNA to proteins

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Class 5: RNA Structure Prediction

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  1. Class 5:RNA Structure Prediction .

  2. RNA types • Messenger RNA (mRNA) • Encodes protein sequences • Transfer RNA (tRNA) • Adaptor between mRNA molecules and amino-acids (protein building blocks) • Ribosomal RNA (rRNA) • Part of the ribosome, a machine for translating mRNA to proteins • mi-RNA (micro-) • Sn-RNA (small nuclear) • RNA-I (interfering) • Srp-RNA (Signal Recognition Particle)

  3. Functions of RNAs Information Transfer: mRNA Codon -> Amino Acid adapter: tRNA Other base pairing functions: ??? Enzymatic Reactions: Structural: Metabolic: ??? Regulatory: RNAi

  4. RNA World Hypothesis • Before the “invention” of DNA and protein, early organisms relied on RNA for both genetic and enzymatic processes • DNA was a selective advantage because it greatly enhanced the fidelity of genetic replication • Proteins were a selective advantage because they make much more efficient enzymes • Remnants of the RNA world remain today in catalytic RNAs in ribosomes, polymereases and slicing molecules

  5. Why is RNA structure important? • Messenger RNA is a linear, unstructured sequence, encoding an amino-acid sequence • Most non-coding RNA’s adopt 3D structures and catalyse bio-chemical reactions. • Predicting structure of a new RNA => information about its function

  6. Terminology of RNA structure • RNA: a polymer of four different nucleotide subunits: • adenine (A) , cytosine (C), guanine (G)and uracil (U) • Unlike DNA, RNA is a single stranded molecule folding intra-molecularly to form secondary structures. • RNA secondary structure = set of base pairings in the three dimensional structure of the molecule • G-C has 3 hydrogen bonds • A-U has 2 hydrogen bonds • Base pairs are almost always stacked onto other pairs, creating stems.

  7. Base Pairing in RNA guanine cytosine adenine uracil

  8. Non-canonical pairs and pseudoknots • In addition to A-U and G-C pairs, non-canonical pairs also occur. Most common one is G-U pair. • G-U is thermodynamically favourable as Watson-Crick pairs (A-U, G-C) . • Base pairs almost always occur in nested fashion. Exception: pseudoknots.

  9. Elements of RNA secondary structure

  10. RNA Secondary Structure(more…)

  11. AGCTACGGAGCGATCTCCGAGCTTTCGAGAAAGCCTCTATTAGC

  12. RNA Tertiary Structure • Do not obey “parantheses rule”

  13. tRNA structure

  14. Structure vs Sequence • Homologous RNA’s that have common secondary structure without sharing significant sequence similarity are important. • It is advantageous to search conserved secondary structure in addition to conserved sequence in databases.

  15. Two Problems • RNA secondary structure for a single sequence. The dynamic programming algorithms – Nussinov and Zuker, SCFG algorithms. • Analysis of multiple alignments of families of RNA’s. Covariance Models – used for both multiple alignment and database searches.

  16. Problem I: Structure Prediction • Input:An RNA sequence X • Output: Most likely secondary structure of X • Algorithms: Nussinov, CYK, MFOLD, …

  17. Problem II: RNA family modeling • Input:A family for RNA sequence X1, …, XN sharing a common secondary structure • Aligned / Not aligned • Output: A probabilistic generative model representing the RNA family • Model: Covariance model

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