RNA editing

hordeprobableΒιοτεχνολογία

4 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

80 εμφανίσεις

Project

RNA editing

RNA editing

(Base modification)

U

A

C

G

A

C

5’
-

A

U
-

3’

RNA
-
Editing

U

A

U

G

A

C

5’
-

A

U
-

3’

Primary transcript

(
Predicted sequence
)

After editing

(
Observed sequence
)

Difficulty: Distinguish genuine RNA
-
editing from sequencing errors

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 ?




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.


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



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