RESUMEN
Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34' is included in the neuronal form of TAF1 mRNA, which encodes the largest subunit of the basal transcription factor TFIID. In this study, we investigate the tissue distribution of TAF1-34' mRNA and protein and the mechanism responsible for its neuronal-specific splicing. Using isoform-specific RNA probes and antibodies, we observe that canonical TAF1 and TAF1-34' have different distributions in the brain, which distinguish proliferating from post-mitotic neurons. Knockdown and ectopic expression experiments demonstrate that the neuronal-specific splicing factor SRRM4/nSR100 promotes the inclusion of microexon 34' into TAF1 mRNA, through the recognition of UGC sequences in the poly-pyrimidine tract upstream of the regulated microexon. These results show that SRRM4 regulates temporal and spatial expression of alternative TAF1 mRNAs to generate a neuronal-specific TFIID complex.
Asunto(s)
Exones , Regulación de la Expresión Génica , Histona Acetiltransferasas/genética , Proteínas del Tejido Nervioso/metabolismo , Neuronas/metabolismo , Empalme del ARN , ARN Mensajero/genética , Factores Asociados con la Proteína de Unión a TATA/genética , Factor de Transcripción TFIID/genética , Animales , Encéfalo/metabolismo , Diferenciación Celular , Inmunohistoquímica , Ratones , Neurogénesis/genética , Neuronas/citologíaRESUMEN
Published transcriptomic data from surgically removed metastatic clear cell renal cell carcinoma samples were analyzed from the genomic fabric paradigm (GFP) perspective to identify the best targets for gene therapy. GFP considers the transcriptome as a multi-dimensional mathematical object constrained by a dynamic set of expression controls and correlations among genes. Every gene in the chest wall metastasis, two distinct cancer nodules, and the surrounding normal tissue of the right kidney was characterized by three independent measures: average expression level, relative expression variation, and expression correlation with each other gene. The analyses determined the cancer-induced regulation, control, and remodeling of the chemokine and vascular endothelial growth factor (VEGF) signaling, apoptosis, basal transcription factors, cell cycle, oxidative phosphorylation, renal cell carcinoma, and RNA polymerase pathways. Interestingly, the three cancer regions exhibited different transcriptomic organization, suggesting that the gene therapy should not be personalized only for every patient but also for each major cancer nodule. The gene hierarchy was established on the basis of gene commanding height, and the gene master regulators DAPK3,TASOR, FAM27C and ALG13 were identified in each profiled region. We delineated the molecular mechanisms by which TASOR overexpression and ALG13 silencing would selectively affect the cancer cells with little consequences for the normal cells.
RESUMEN
Basal transcription factor TFIID connects transcription activation to the assembly of the RNA polymerase II preinitiation complex at the core promoter of genes. The mechanistic understanding of TFIID function and dynamics has been limited by the lack of high-resolution structures of the holo-TFIID complex. Recent cryo-electron microscopy studies of yeast and human TFIID complexes provide insight into the molecular organization and structural dynamics of this highly conserved transcription factor. Here, we discuss how these TFIID structures provide new paradigms for: (i) the dynamic recruitment of TFIID; (ii) the binding of TATA-binding protein (TBP) to promoter DNA; (iii) the multivalency of TFIID interactions with (co)activators, nucleosomes, or promoter DNA; and (iv) the opportunities for regulation of TBP turnover and promoter dynamics.