RESUMO
Alternative polyadenylation (APA) increases transcript diversity through the generation of isoforms with varying 3' untranslated region (3' UTR) lengths. As the 3' UTR harbors regulatory element target sites, such as miRNAs or RNA-binding proteins, changes in this region can impact post-transcriptional regulation and translation. Moreover, the APA landscape can change based on the cell type, cell state, or condition. Given that APA events can impact protein expression, investigating translational control is crucial for comprehending the overall cellular regulation process. Revisiting data from polysome profiling followed by RNA sequencing, we investigated the cardiomyogenic differentiation of pluripotent stem cells by identifying the transcripts that show dynamic 3' UTR lengthening or shortening, which are being actively recruited to ribosome complexes. Our findings indicate that dynamic 3' UTR lengthening is not exclusively associated with differential expression during cardiomyogenesis but rather with recruitment to polysomes. We confirm that the differentiated state of cardiomyocytes shows a preference for shorter 3' UTR in comparison to the pluripotent stage although preferences vary during the days of the differentiation process. The most distinct regulatory changes are seen in day 4 of differentiation, which is the mesoderm commitment time point of cardiomyogenesis. After identifying the miRNAs that would target specifically the alternative 3' UTR region of the isoforms, we constructed a gene regulatory network for the cardiomyogenesis process, in which genes related to the cell cycle were identified. Altogether, our work sheds light on the regulation and dynamic 3' UTR changes of polysome-recruited transcripts that take place during the cardiomyogenic differentiation of pluripotent stem cells.
RESUMO
OBJECTIVES: Screening for genes differentially expressed in placental tissues, aiming to identify transcriptional signatures that may be involved in ZIKV congenital pathogenesis. METHODS: Transcriptome data from placental tissues of pregnant women naturally infected with Zika virus during the third trimester were compared to those from women who tested negative for Zika infection. The findings were validated using both a cell culture model and an immunohistochemistry/morphological analysis of naturally infected placental tissues. RESULTS: Transcriptome analysis revealed that Zika virus infection induces downregulation of insulin-like growth factor II (IGF2) gene, an essential factor for fetal development. The Caco-2 cell culture model that constitutively expresses IGF2 was used for the transcriptome validation. Asiatic and African Zika virus strains infection caused downregulated IGF2 gene expression in Caco-2 cells, whereas other flaviviruses, such as dengue serotype 1, West Nile and wild-type yellow fever viruses, had no effect on this gene expression. Immunohistochemical assays on decidual tissues corroborated our transcriptome analysis, showing that IGF2 is reduced in the decidua of Zika virus-infected women. CONCLUSIONS: Our results draw attention to IGF2 modulation in uterine tissues, and this finding is expected to support future studies on strategies to ameliorate the harmful effects of Zika virus infection during pregnancy.