Eukaryotic genes architecture is characterized by incorporation of non-coding sequences interrupting the coding sequences. Through splicing, excision of those non-coding sequences, known as introns, is taking place co-transcriptionally, i.e. synchronically with the synthesis of precursor messenger m-RNA from the template DNA, in a precisely-regulated manner. Alternative splicing is a phenomena where not all splice sets are used in each transcript processed. Thus, this process enhances the proteome and transcriptome complexity through generating different transcripts, with different functionality or stability, from a single gene. Aberrant splicing have been associated with a lot of disease including cancer as well as Parkinsonism. Chemical compounds or drugs that target splicing regulation have also been developed and characterized. Indole derivatives have proven before their potency in targeting serine-arginine rich splicing regulators of alternative splicing. In this study, alternative splicing in Arabidopsis have been targeted through three different Indole derivatives, 6-Methylindole, 2, 5-Dimethylindole and 5-Bromoindole-2-Carboxylic Acid. Full transcriptomic analysis of the RNA-seq data generated from treated samples, at both 24 and 72 hrs time points, was conducted to reveal the alternative splicing modulation and gene expression patterns changes under those splicing modulators treatment. Interestingly, observation of splicing pattern alteration under the influence of Indole derivatives used in this study indicate that most treatments, 4 out of 6, and specifically after certain onset of time 72 hrs, showed significant enhancement of AS, mostly through intron retention splicing events. Photorespiration related genes were altered frequently, on AS and/or expression level, under different Indole derivatives treatments and time points. More interestingly, RNA binding proteins and splicing factors were differentially spliced, a finding that is consistent with the prevalence of auto-regulatory nature of those genes. Furthermore, various potential functional outcomes may originate from differential splicing exhibited under Indole treatments. In hydrolase-like protein (AT5G17670), an alternative 5’ splice site skipped a pre-mature termination codon. In SR34a SR splicing factor, exon skipping event at the 5’ untranslated region might help the transcript escape regulatory miRNAs. Overall, this study shall introduce a transcriptomic snapshot of Genome-wide gene expression and alternative splicing after targeting serine-arginine splicing factors by Indole derivatives.


Biotechnology Program

Degree Name

MS in Biotechnology

Graduation Date


Submission Date

May 2016

First Advisor

Moustafa, Ahmed

Committee Member 1

Assem, Shireen, Walid, Magdy,Ahmed Fouad, Mahfouz, Abdelatif



Document Type

Master's Thesis


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Institutional Review Board (IRB) Approval

Not necessary for this item