Computational RNA Biology

Chromatin and Splicing

There is currently increasing evidence for a relation between the state of chromatin and pre-mRNA splicing. Chromatin structure and histone modifications have been shown to affect both constitutive and alternative splicing, either by recruitment of splicing factors or by modulating Pol II elongation. Along with these basal level controls, identification of specific histone markers could also explain the different splicing patterns between in specific conditions and cell types. Using high-throughput sequencing data, we study the role of various chromatin regulators in the regulation of alternative splicing.

Small RNAs and Splicing

Recent reports suggest that new classes of small RNAs can be produced from longer RNAs. We study the biogenesis and activity of these new RNA classes and their potential effect in the regulation of pre-mRNA splicing, and how these mechanisms can play a role in cancer.

Cancer and Splicing

Many of the hallmarks of cancer, such as evasion of cell-death and tissue invasiveness, are profoundly influenced by alterations in splicing. AS alterations in cancer are generally related to the production of protein variants with opposing functions, e.g. pro- and anti- apoptotic; or simply to the activation of proto-oncogenes or the inactivation of tumor-suppressor genes.  We aim to describe the landscape of splicing alterations in cancer  through a pan-cancer data analysis using TCGA data.

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