Ionizing radiation induces a plethora of changes in the cell influencing the course of various chemical processes on the level of individual transcripts and proteins by a mechanism which is still poorly understood. It is known that the presence of certain sequence motifs in the mRNA is required for interactions with cytoplasmic proteins or functional RNA particles affecting mRNA half-life, however their exact role in induction of cellular response to stress conditions still remains unknown.

In this project mechanisms that modulate transcript levels in cells exposed to ionizing radiation will be studied. The main goal will be the identification of nucleotide structure features of genes and their transcripts, which control mRNA stability in cells exposed to ionizing radiation. The study will be based on our results of microarray experiments concerning transcript levels and gene sequences present in public databases. Large number of sequences that will be analyzed need a new set of bioinformatic tools which will be created. These tools and scientific publications concerning transcript stabilization mechanisms will be the main outcomes of the project.

• Classification of human genes based on the response to ionizing radiation
• Identification of transcript structural features correlated with their radiation response
• Development of bioinformatic applications
• Experimental validation of transcript stabilization determinants based on identified sequence features
• Summary of the project: publications, PhD thesis

Project manager

Roman Jaksik

Contractors

Roman Jaksik

PhD thesis

R. Jaksik: Analysis of gene expression regulatory processes in cells exposed to ioninzing radiation. (in Polish)

Software

NucleoSeq - update do the version 2.0 which includes enhanced sequence comparison options, new sequence retrieval mechanism, ability to automatically download promoter sequences and a new simplified interface

scGC-RMA - new microarray data normalization method based on modified GC-RMA algorithm and LOESS regression which aims at reducing signal intensity differences between probes varying in GC content

MicroarrayHPC - This is a set of applications designed to test various hypothesis on extremely large number of samples from various microarray experiments. Apart from methods that automatically download microarray data from ArrayExpress database for a selected platform or tools which gather some basic sample data it is designed to harness the possibilities of high performance computers in order to conduct a very efficient analysis using some of the pre-prepared scripts or any other script in Python or R provided by the user.

MicroProbeTools - This set of applications includes utilities used to analyze microarray probe sequences and to convert probe data between various formats