Alternative polyadenylation and dynamic 3' UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs

Aruana F F Hansel-Frose; Jens Allmer; Marcel Friedrichs; Hellen Geremias Dos Santos; Bruno Dallagiovanna; Lucía Spangenberg

doi:10.3389/fmolb.2024.1336336

Alternative polyadenylation and dynamic 3' UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs

Front Mol Biosci. 2024 Feb 6:11:1336336. doi: 10.3389/fmolb.2024.1336336. eCollection 2024.

Authors

Aruana F F Hansel-Frose¹, Jens Allmer², Marcel Friedrichs³, Hellen Geremias Dos Santos⁴, Bruno Dallagiovanna¹, Lucía Spangenberg^{5

6}

Affiliations

¹ Laboratory of Basic Stem Cell Biology, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ/PR), Curitiba, Brazil.
² Department of Medical Informatics and Bioinformatics, University of Applied Sciences Ruhr West, Mülheim, Germany.
³ Bioinformatics and Medical Informatics Department, University of Bielefeld, Bielefeld, Germany.
⁴ Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ/PR), Curitiba, Brazil.
⁵ Bioinformatics Unit, Pasteur Institute of Montevideo, Montevideo, Uruguay.
⁶ Departamento Basico de Medicina, Hospital de Clinicas, Universidad de la República (Udelar), Montevideo, Uruguay.

Abstract

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.

Keywords: cardiomyocytes; cardiomyogenesis; gene regulatory network; human embryonic stem cells; miRNA; polysome profiling.

Grants and funding

The authors declare that financial support was received for the research, authorship, and/or publication of this article. This study was financed in part by the Coordination for the Improvement of Higher Education Personnel (CAPES)—Brazil, financial code 001.