Genomic identification of Structural RNAs using phylo-SCFGs

Jakob Skou Pedersen

Bioinformatics Center, University of Copenhagen

Structural RNA identification problem

independently transcribed ncRNAs

ncRNA protein-coding gene

Structural RNA: any transcribed region with functional structure.

ncRNAs co-transcribed with protein-coding genes

Such as:

Highly diverse settRNA Xist (~20 kb long)miRNA

UTR RNase P

Little single sequence signal:Lack of common nucleotide biasesLack of common sequence motifs

Evolutionary signal

Structure functionally important

Primary sequence subs tolerated

Signal Unprecedented comparative data

Introduction to phylogenetic models

Captures:

Nucleotide biases

Patterns of substitution

Evolutionary sequence correlations

Correlated changes (multi nucleotide models)

: Continuous time Markov chain acting on

branches of phylogenetic tree

Alignment column

Substitution rates of Markov chain

Felsenstein 81:

Transition prob.:

Single-nucleotide model

• 4x4 rate matrix

• Marginal average of di

nucleotide matrix

• Fast substitution rate

-nucleotide model

16x16 rate matrix

Learned from data

Favors pairing di-nucs

Slow substitution rate

EvoFold Phylogenetic models

-nucleotide model

16x16 rate matrix

Learned from data

Favors pairing di-nucs

Slow substitution rate

Single-nucleotide model

• 4x4 rate matrix

• Marginal average of di

nucleotide matrix

• Fast substitution rate

EvoFold SCFGsStructural model: Non-structural model:

Structure derivation

Structure

Single nucleotide phylogenetic model

Di-nucleotide phylogenetic model

fold

Single nucleotide phylogenetic model

Di-nucleotide phylogenetic model

fold

Single nucleotide phylogenetic model

Di-nucleotide phylogenetic model

fold

Algorithms and training

Algorithms: Traditional SCFG algorithms (CYK and insideoutside) combined with Felsenstein 81.

Training of EvoFold:: Rfam structures mapped onto genomic alignments

Complexities:For an n long alignment with msequences:

Space:

vertebrates & drosophilidsInput: conserved segments

sub-fold

……(((((((..))).(((….))))))).………………(((((….)))))..sub-fold

Output: sub-folds

Sensitivity: 43%Performance

Experimentally studied vertebrate cases

HAR1Expression in developing neocortex

A

Editing in Mouse Brain

I/M siteGABRA3 A-to-I RNA editing substrate

High confidence subset from Drosophila screen

Selection criteria:Min. two compensatory substitutions#compensatory subs > 2 x #contradictory subs

Predictions (394 total) Genomic background

UTR structures

Gene involved in biogenesis and assembly of the ribosome

(by homology to RPL24)

High fraction of UTR predictions on transcribed strand (5’UTR: 80% & 3

Significant enrichment of genes regulatory roles.

Acknowledgments

GABRA3 study: Johan Ohlson, Marie Ohman (Stockholm University), and David Haussler (UCSC)

HAR1 study: Katherine S. Pollard (UCSC), Sofie R. Salama (UCSC), Nelle Lambert (ULB), Marie-Alexandra Lambot (ULB), Sandra Coppens (ULB), Sol Katzman (UCSC), Bryan King (UCSC), Courtney Onodera (USCS), Adam Siepel (Cornell), Andrew D. Kern (UCSC), Colette Dehay (Lyon), Haller Igel (UCSC), Manuel Ares, Jr (UCSC), Pierre Vanderhaeghen (ULB)

EvoFold: Gill Bejerano (Stanford), Adam Siepel (Cornell), Kate Rosenbloom (UCSC), Kerstin Lindblad-Toh (Broad), Eric S. Lander (Broad), Jim Kent (UCSC), Webb Miller (Penn State), and David Haussler (UCSC)

Fly screen: Manolis Kellis (MIT), David Haussler (UCSC), Drosophila Sequencing and Analysis Consortium

Structure predictions

UU

GCC

UAU

UGU

GUC

GCC

A -> I (G)U

UCA

U•

GG

U A C

•

New case of A-to-I RNA editing

A

Genomic

cDNA

I/M

Mouse Brain

Slide with structures, perhaps browser screenshot.

Highlight collaborationsRNA editing

regulation

Slide with structures, perhaps browser screenshot.

Highlight collaborationsRNA editing

regulation

Intronic hairpin in RDL flanked by Ato-I edited exons

SpenSpen function: Transcription co-factor and involved in neuronal cell fate, survival, and axon guidance. It has three RNA recognition motifs.

Staufen hairpin similar to known localization element in Orb

Stau

Orb

Hairpin in highly expressed intergenic region

Structure can be extended

EvoFold str.RNAfold str.

Alignment & full structure