Researchers from the University of Eastern Finland, Aalto University, and the University of Oulu have introduced a powerful computational method called KMAP, designed to explore patterns in DNA sequences more intuitively. By projecting short DNA sequences—known as k-mers—into a two-dimensional space, KMAP enables clearer visualization and interpretation of biologically significant DNA motifs. This breakthrough approach helps researchers uncover how regulatory elements behave in different biological contexts.
The new study, recently published by the team, demonstrates KMAP’s capabilities in a variety of applications. One key example is its use in re-analyzing data from Ewing sarcoma, a rare type of cancer. The researchers discovered that the transcriptional repressor ETV6 binds to and blocks enhancer regions that are normally targeted by the transcription factor FLI1, thus contributing to disease progression. However, when ETV6 is degraded, these enhancers become accessible again, allowing FLI1 and other transcription factors—BACH1, OTX2, KCNH2, and possibly an unidentified one—to bind and regulate gene expression.
Continue reading… “KMAP: A New Tool for Visualizing DNA Motifs and Unlocking Gene Regulation in Cancer and Genome Editing”