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Major splice variants and multiple polyadenylation site utilization in mRNAs encoding human translation initiation factors eIF4E1 and eIF4E3 regulate the translational regulators?

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Abstract

Alternative polyadenylation is an important and pervasive mechanism that generates heterogeneous 3′-termini of mRNA and is considered an important regulator of gene expression. We performed bioinformatics analyses of ESTs and the 3′-UTRs of the main transcript splice variants of the translational initiation factor eIF4E1 and its family members, eIF4E2 and eIF4E3. This systematic analysis led to the prediction of new polyadenylation signals. All identified polyadenylation sites were subsequently verified by 3′RACE of transcripts isolated from human lymphoblastic cell lines. This led to the observation that multiple simultaneous polyadenylation site utilization occurs in single cell population. Importantly, we described the use of new polyadenylation site in the eIF4E1 mRNA, which lacked any known polyadenylation signal. The proportion of eIF4E1 transcripts derived from the first two polyadenylation sites in eIF4E1 mRNA achieved 15% in a wide range of cell lines. This result demonstrates the ubiquitous presence of ARE-lacking transcripts, which escape HuR/Auf1-mediated control, the main mechanism of eIF4E1 gene expression regulation. We found many EST clones documenting the significant production of transcript variants 2–4 of eIF4E2 gene that encode proteins with C-termini that were distinct from the mainly studied prototypical isoform A. Similarly, eIF4E3 mRNAs are produced as two main variants with the same very long 3′-UTR with potential for heavy post-transcriptional regulation. We identified sparsely documented transcript variant 1 of eIF4E3 gene in human placenta. eIF4E3 truncated transcript variants were found mainly in brain. We propose to elucidate the minor splice variants of eIF4E2 and eIF4E3 in great detail because they might produce proteins with modified features that fulfill different cellular roles from their major counterparts.

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Abbreviations

ARE:

A/U-rich element

CS:

Cleavage site

AP:

Alternative polyadenylation

PAS:

Polyadenylation site

PaS:

Polyadenylation signal

EST:

Expressed sequence tag

GS:

Gene specific primer

ALL:

Acute lymphoblastic leukemia

3′RACE:

3′-Rapid amplification of cDNA ends

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Acknowledgements

The authors wish to thank Jan Trka for providing them with cell lines.

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Authors and Affiliations

  1. Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague, Czech Republic

    Silvia Mrvová, Klára Frydrýšková, Martin Pospíšek, Václav Vopálenský & Tomáš Mašek

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  1. Silvia Mrvová
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  2. Klára Frydrýšková
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  3. Martin Pospíšek
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  4. Václav Vopálenský
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  5. Tomáš Mašek
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Correspondence to Tomáš Mašek.

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This work was supported by the Ministry of Health of the Czech Republic, project NT13713-4 and the Czech Science Foundation, project No. GBP305/12/G034.

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The authors declare that they have no conflict of interest.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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Communicated by S. Hohmann.

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Mrvová, S., Frydrýšková, K., Pospíšek, M. et al. Major splice variants and multiple polyadenylation site utilization in mRNAs encoding human translation initiation factors eIF4E1 and eIF4E3 regulate the translational regulators?. Mol Genet Genomics 293, 167–186 (2018). https://doi.org/10.1007/s00438-017-1375-4

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