ATRA modulates the expression of alternative Transglutaminase 2 in brain tumors through interactions between regulatory factors and intronic regions

Transglutaminase 2 is multifunction enzyme encoded from a very long gene (among 40 kb) responsible to several stimuli (TNFα, TGFβ, INFγ, NF-kB, cytokines, interleukins, hormones) that rapidly induce transcription process. Consequently to strong induction, this as other genes belonging to network TGFβ/NF-kB presents pausing sites which regulate RNApol II speed during elongation. The major checkpoint is located at the beginning of the gene where the insulators RAD21 and CTCF are engaged in the chromatin remodelling in corrispondence to H3K4me3 mark and a region containing regulatory lncRNA. Notably TGM2 synthetize several altered isoforms mostly lacking 3’terminal portion that have lost cellular functions, such as signals localization and hydrolysis of GTP which affects also interaction with PLCδ1. These variants are produces by alternative transcripts using different polyadenylation or splicing sites and are associated to inflammatory processes, neurodegenerative diseases and cancer. In particular, the canonical full-length TG2 is linked to Epithelial-Mesenchymal Transition, cell survival, while the truncated TGH (the most expressed among the variants) promotes differentiation and cell death. From this point of view study TGM2 gene expression could useful to investigate the responsiveness and/or resistance to drugs. Indeed, molecules such as retinoids, as well as other anticancer compounds, change the ratio among the variants possibly modifying cellular signals to drive cancer cells to apoptosis or to therapeutic ineffectiveness. In this work we analyse the expression of the alternative transcripts of TG2 in brain tumor cell lines after modulation with all-trans retinoic acid, an agent employed in combined therapies. With the aim to investigate whether there are factors interacting with intronic sequences putatively involved in the generation of TGM2 variants we examined ChIP-seq data from ENCODE on cells untreated or treated with ATRA, highlighting those which could play regulatory roles. Behaviour of ATRA thinly modulates the levels of isoforms modifying interactions between factors and intronic DNA sequence likely interfering with RNApol II at checkpoints along the gene. These interactions influence the use of alternative polyadenylation and splicing sites, hence the production of altered isoform