We have designed two new experimental approaches to overcome limitations of previously established methods. Their usefulness, however, turned out to be limited and we were unable to provide a reliable improvement to existing methodologies. Secondly, we provided an extensive atlas of the transcriptional landscape of MCF-7 cells during the DDR. We employed three different high-throughput RNA sequencing approaches to provide a comprehensive analysis of the transcriptome. Our efforts led to identification of differentially expressed transcripts regardless of their polyadenylation or stability, or towards their presence in existing genome annotations. We have provided a foundation for future functional studies of lncRNAs potentially involved in DDR and investigated four lncRNAs upregulated in this condition in more detail. Thirdly, we have provided a new important insight into regulatory mechanism of DDX3 – a protein, which has been previously reported to associate with lncRNAs and is implicated in both DDR and tumorigenesis. We have described the nature of DDX3-lncRNAs interactions on a transcriptome-wide scale and furthered our understanding of DDX3 mediated regulation of translation. We have determined the global effects of DDX3 depletion on the abundance of mRNAs and their translation efficiency. In combination with the analysis of DDX3-mRNA binding specificity those results show that the protein is required for translation initiation on subset of mRNAs harboring structured 5’ UTRs.