Can comparative methods reveal lncRNA function? • If an RNA is under purifying selection: • It must be expressed across species (conservation of expression) • Selection on sequence should preserve (Conservation of sequence) • Structural constraints • RNA-RNA interaction sites • RNA-protein interaction sites • Can we distinguish classes of lncRNAs based on their evolutionary signatures?
Evolutionary profiling RNA-Seq dataset 3 Individuals per species Merkinel al. Science 2012 Human + Chimp Washietl, Kelli & Garber – Genome Research (2014)
1) Acquire ES / iPS RNA-Seq Data ORTHOLOG SYNTOLOG Mouse lncRNA Mouse lncRNA Coding A NO alignment Coding B Alignment Human lncRNA Human lncRNA Coding A Coding B 2) Reconstruct Transcripts blasts to orthologous coding transcript (pseudogenes) blasts to any other expressed transcript(duplications) has 100% repeat content(mappingartifacts) overlap coding transcript 3) Filter for lncRNAs 4) Search for Orthologs/Syntologs 10 1 .6 chimp/bonobo human blk6/nod rat cast
mirRNA host divergent <500 bp snoRNA host intergenic Sequence Identity Exonic Identity coding mirRNA host divergent snoRNA host intergenic Exon-to-exonalignment Sequencealignment
Human Mouse mousespecific mouseconserved Humanspecific Humanconserved random random Primate Rat ratspecific ratconserved primatespecific Humanconserved random random
Application: Single cell RNA-Seq quant PCA Cluster #4: Gcg Clustering Cluster #2: Sst Clusters #1, #5: Ins1/Ins2 Cluster #3: Ppy
Cis regulatory code • Predicting gene expression from of TF binding • Disecting gene regulatory networks • In innate immunity as a model of response to environment • In differentiation with the side goal of using the information to devise differentiation protocols.