Long non coding RNA in the pea aphid; iden3fica3on and compara3ve expression in sexual and asexual embryos
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1 Long non coding RNA in the pea aphid; iden3fica3on and compara3ve expression in sexual and asexual embryos Fabrice Legeai, Thomas Derrien, Valen3n Wucher, Audrey David, Gael Le Trionnaire and Denis Tagu
2 Role of the long non coding RNAs HOTAIR (HOX an3sense intergenic RNA) regulates the transcrip3on of HOXD transcrip3on factor by modifying the methyla3on of the chroma3n. lincrna Cox2 : regulates immunity genes rox1 and rox2 play a key role in the dosage compensa3on in dropsophila as they are involve in the transcrip3onal upregula3on of genes on the single X chromosome in males to match the expression from the two X chromosomes COOLAIR an3sense RNAs are upregulated in response to cold temperatures and inac3ves arabidopsis flowering genes Wang K C, Chang, H Y Mol Cell 2011
3 Reads.fq lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging < 200bp, single exon Sense to mrna predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict lncrna.fa
4 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging Align reads to genome < 200bp, single exon Sense to mrna predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict lncrna.fa Merging between condi3ons and replicates
5 Reads.fa lncrna Predic3on workflow Genome Transcriptome reconsctruc3on Mapping Predic3on Merging predic3ons Everything that is overlapping a protein coding gene in same strand is not removed from the set. < 200bp, single exon Sense to mrna predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict Only RNA larger than 200 bp are taken into account. Due to the tophat/cufflinks overpredic3on of genes, only genes with more than one exon are considered lncrna.fa
6 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging < 200bp, single exon Sense to mrna predic3on Coding Poten3al Calcula3on Probability that a RNA is coding for a protein Intersec3on of 3 methods Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict z TxCPSPre dict lncrna.fa
7 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging < 200bp, single exon Sense to mrna predic3on Coding Poten3al Calcula3on Probability that a RNA is coding for a protein Intersec3on of 3 methods Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict z TxCPSPre dict lncrna.fa
8 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging < 200bp, single exon Sense to mrna predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict Coding Poten3al Calcula3on TXCDSPredict : Scoring and ranking of the RNA with criteria: ORF size Presence of an ATG Presence of a stop codo,n Number of upstream nucleo3des Kozak sequence Stop in the last exon lncrna.fa
9 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging < 200bp, single exon Sense to mrna predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict Coding Poten3al Calcula3on : SVM based on 6 parameters 3 criteria based on the quality of the largest ORF (size, coverage, ATG) 3 criteria based on a result of a comparison to a protein databases (NR, Swissprot, ) (number of hits, mean of the e value, frameshids) lncrna.fa
10 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging < 200bp, single exon Sense to mrna predic3on Coding Poten3al Calcula3on : logis3c regression 1. ORF size 2. Coverage (ORF size/transcript size) 3. Fickee score (combina3on of the nucleo3de composi3on and codon usage) 4. Hexamer score : composi3on of adjacent amino acids Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict lncrna.fa
11 Reads.fa lncrna Predic3on workflow Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging Coding Poten3al Calcula3on < 200bp, single exon Sense to mrna predic3on genome Predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict Build of a learning set And training lncrna.fa
12 lncrna mrna Interac3ons Derrien et al. Genome Research 2012
13 Applica3on : the reproduc3ve polyphenism Jaquiéry et al. Plos 3cs 2013
14 Applica3on : the reproduc3ve polyphenism T0 2 condi3ons 3 replicates 24 samples >627 millions of RNA Seq reads (100 bp PE)
15 Applica3on : the reproduc3ve polyphenism Reads.fa Genome predic3ons Transcriptome reconsctruc3on Mapping Predic3on Merging transcrits < 200bp, single exon Sense to mrna predic3on Protein Coding Poten3al Filter Coding Poten3al Calculator ab ini&o scoring Coding Poten3al Assesment Tool TxCDSPredict lncrna 47 new mrna lncrna.fa
16 Applica3on : the reproduc3ve polyphenism Differen3ally expressed lncrna (cuffdiff, p value FDR < 0.05) interac3ons lncrna T1 T2 T3 Sexual Asexual Intergenic : «Same strand» : 1887 Divergent : 1014 Convergent : 767 Genic : Intronic : 674 Exonic : 1731 overlapping: 15 «Nested» : 743
17 Integra3on mrna (4996) lncrna (370) mirna (15)
18 Availability
19 Availability
20 Ackowledgments Gaël Le Trionnaire, Aurore Gallot Valen3n Wucher Julie Jaquiéry Audrey David, Thomas Derrien Denis Tagu
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