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Project. RNA editing. RNA editing (Base modification). A. Primary transcript ( Predicted sequence ). C. U. C. 5’- A. G. U - 3’. A. RNA-Editing. After editing ( Observed sequence ). A. C. U. U. 5’- A. G. U - 3’. A.

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Project

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  1. Project RNA editing

  2. RNA editing(Base modification) A Primary transcript (Predicted sequence) C U C 5’- A G U - 3’ A RNA-Editing After editing (Observed sequence) A C U U 5’- A G U - 3’ A Difficulty: Distinguish genuine RNA-editing from sequencing errors

  3. Increasing transcript complexity by editing bases • It has been suggested that RNA editing is very common in humans. • In plants, it was first suspected that RNA editing was limited to transcripts within the organels. • However, in a recent study it was reported that RNA-editing of nuclear transcripts is also common in Arabidopsis. • However, is this true ? • It is possible to find out by searching for RNA-editing that is conserved in multiple accessions of Arabidopsis (There are now 19 accessions available) • The question is RNA editing of nuclear transcripts also common in rice? • If it is than we have many nice additional questions. (Such as). • Is RNA-editing regulated in a tissue or condition specific matter • Does the editing effect the protein diversity • Does RNA editing sites have particular sequence or secondary structure features ?

  4. What is data you will be using • You will be getting the following data: • 2 papers which you have to read before you do anything • Repeating the same study is boring hence we use other datasets • Datasets (rice 2 groups) • Chromosome sequences of rice • The annotation gff3 of rice • Several RNA-seq datasets of different tissues and also two biological conditions.

  5. What is data you will be using (II) • Arabidopsis accessions (1 group) • 19 accessions • Chromosome files • Annotations (Gff) • RNA seq data sets (seedlings) • For two accessions we also have RNA-seq data from the • Root • Flower bud

  6. What is the plan ? • Read the literature • Discuss the research plan (most important). • Determine what kind of tools you will need for each of the steps in the research plan. • If you know what kind of tool you need we will help you in deciding which specific software package you can use • Determine what kind of scripts you might have to make your self. • Split the tasks

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