The recent advances in molecular and computational biology have made possible the study of complicated transcriptional regulatory networks that control a wide range of biological processes and phenotypic traits. In this thesis, several approaches were combined including next generation sequencing, gene expression profiling, chromatin and RNA immunoprecipitation, bioinformatics and genome editing methods in order to characterize the biological significance of the ZBED6 and ZC3H11A genes. A mutation in the binding site of ZBED6, located in an intron of IGF2, disrupts the binding and leads to 3-fold upregulation of IGF2 mRNA in pig muscle tissues. The first part of the thesis presents a detailed functional characterization of ZBED6. Transient silencing of ZBED6 expression in mouse myoblasts led to increased Igf2 expression (~2-fold). ChIP-seq analysis of ZBED6 and histone modifications showed that ZBED6 preferentially binds active promoters and modulates their transcriptional activities (paper I). In the follow-up studies using CRISPR/Cas9 we showed that either the deletion of ZBED6 or its binding site in Igf2 (Igf2ΔGGCT) led to more than 30-fold up-regulation of Igf2 expression in myoblasts. Differentiation of these genetically engineered cells resulted in hypertrophic myotubes. Transcriptome analysis revealed ~30% overlap between the differentially expressed genes in Zbed6-/- and Igf2ΔGGCT myotubes, with significant enrichment of muscle-specific genes. ZBED6-overexpression in myoblasts led to cell cycle arrest, reduced cell viability, reduced mitochondrial activities and impaired the differentiation of myoblasts (paper II). Further studies on cancer cells showed that ZBED6 influences the growth of colorectal cancer cells with dramatic changes in the transcription of hundreds of cancer-related genes (paper III). The phenotypic characterization of Zbed6-/- and Igf2pA/mG mouse models showed that the ZBED6-Igf2 axis has a major effect on regulating muscle growth and the growth of internal organs. Transcriptome analysis demonstrated a massive up-regulation of Igf2 expression (~30-fold) in adult tissues, but not in fetal tissues, of transgenic mice (paper IV). In the second part of the thesis we investigated the cellular function of Zc3h11a, the gene harboring ZBED6 in one of its first introns. The function of the ZC3H11A protein is so far poorly characterized. We show that ZC3H11A is a novel stress-induced protein that is required for efficient mRNA export from the nucleus. The inactivation of ZC3H11A inhibited the growth of multiple viruses including HIV, influenza, HSV and adenoviruses (paper V).

ZC3H11A (ZC3) protein has been reported to be part of the TREX (TRanscription-EXport) nuclear export system for mammalian cells. According to our previous publication, ZC3 not only plays an unelucidated role in the TREX complex, but also supports the growth of several human nucleus replicating virus, such as influenza virus, adenovirus (HAdV), herpes simplex virus and HIV. We thought to further elucidate the role of ZC3 in immunological stress based on previous observations that ZC3 was upregulated in stress condition. Our previous experiment tested the effect of knocking out ZC3 in HeLa cell then stimulating the cells with IL-1β to induce immunological stress. It showed that IL-1β stimulated ZC3 knockout Hela cells produce more than double fold IL6 compared to IL-1β stimulated HeLa Cas 9 wild type. Since IL-6 is downstream of NFkB signalling pathway, we aimed to explore a possible role of ZC3 protein in mammalian cell’s NFkB pathway. Our primary results showed that NFkB pathway might be more upregulated in ZC3 KO cells than in wild type HeLa Cas9 cells. This up-regulation was found to be correlated to defective IkBα inhibitory mRNA biogenesis in knockout cells. Our results indicate that ZC3 might play a role in IkBα inhibitory mRNA biogenesis, process, and/or export. Further work is needed to describe the exact role of ZC3 in IKBα mRNA biogenesis.