1 JetGene – online database and toolkit for an analysis of regulatory regions or nucleotide - PowerPoint Presentation

1. 1JetGene – online database and toolkit for an analysis of regulatory regions or nucleotide contexts at differently translated plants transcriptsNataliya Sadovskaya 1,*, Orkhan Mustafaev 2, Alexander Tyurin 1 and Irina Goldenkova-Pavlova 11 Timiryazev Institute of Plant Physiology, Russian Academy of Science; 2 Genetic Resources Institute, Azerbaijan National Academy of Sciences. * Corresponding author: nataliya.sadovskaya@gmail.com

2. Translation is a fundamental process in all living cellsSource: (ck12.org, s.d.)2

3. (K.V. Kabardaeva et al, Russian Journal of Plant Physiology, 2019, 66, 835–849)Regulatory codes and nucleotide contexts3

4. How to identify regulatory codes?JetGene https://jetgene.bioset.orgHigh expressed transcripts(HT)Low expressedtranscripts (LT)???Regulatory codes HTJetGenethe context around the AUG start codon;motives at the 5’-/3’-UTR;codon usage. . .Analysis: cDNA, CDS, 5’-UTR, 3’-UTR and interval of transcriptBeta version JetGene allows to compare two datasets of cDNA! 4

5. https://jetgene.bioset.org5

6. “System of nested datasets” algorithm(1)cDNAlength(3)Motifs Graphics(2)5’-UTRlength6

7. How to obtain 5’-UTR and 3’-UTR? e!Ensembl : CDS and cDNA 5’-UTRCDNASubtraction CDS from cDNA!3’-UTRCDS7

8. General structure of JetGenecDNACDSUTRJetGenecDNAA)B)Chromosome+ Strand5’-UTRCDS3’-UTR8

9. The available options for each of the data types (cDNA, CDS, 5’-/3’-UTR).SizeCpG-IslandGC-ContentNucleotide by PositionNucleotide A/C/G/TGene NamesTranscript NamesChromosomeStrand MotifsAminoAcid PositionCodon PositionCodon UsageCDS datacDNA data5’-UTR data3’-UTR data>fasta-formatAATGTTTCGC…Toolkit of JetGenehttps://jetgene.bioset.org GO-Annotation9

10. Beta version JetGene https://beta.bioset.org 5’-UTR AUG CDS 3’-UTRAnalysisVerification by experimentDetection of potential regulatory codesJetGene??LTtranscripts?HTtranscriptsUnverifiedcodesUnverified regu-latory codes HTVerified regulatory codes HTUnder Construction! 10

11. Why JetGene? Benefits of JetGene:1. For experimentalists. Wide set of options which are necessary for experiment designs.2. Transcripts from a huge number of organisms into JetGene. Time!3. Simple transfers between CDNA/CDS/UTR and from one module to another. Avoiding mistakes and reducing time of the analysis.4. An opportunity to analyze any part of transcript (CDNA, CDS, UTR and interval of transcripts). An opportunity to extract selected sequences in fasta-format. 5. The simplicity of using JetGene, friendly interface, graphical interpretation of the results. 6. Beta version JetGene allows to compare two cDNA datasets 11

12. JetGene usage example12

13. Selected parameters:5’-UTR > 200 bp (minimum size of CpG-island);GC-content > 50% (one of the characteristics of CpG-islands); nucleotides surrounding of the start codon at positions +4 and –3 according to Kozak sequence;the absence of alternative start and stop codons. Authors searched for six-nucleotide motifs, which are contained not less than in 50% of sequences from the result dataset. These motifs were incorporated into the design of the synthetic sequence.13

14. Examples!14

15. https://jetgene.bioset.org15

16. Selected rules (moduls) and the order of the selectionhttps://jetgene.bioset.org16

17. https://jetgene.bioset.org17

18. Available after a free registration!18

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20. Beta version JetGene https://beta.bioset.orgUnder Construction! 20

21. Nataliya S. Sadovskaya*Orkhan N. MustafaevAlexander A. TyurinIrina V. Goldenkova-Pavlova* nataliya.sadovskaya@gmail.comorkhan@bioset.orgSkype: sdv.natashaSupported by the Russian Science Foundation (project no. 18-14-00026; IVG-P)Thank you for your attention! 21