TISU: A dual transcription and translation initiation element of very short 5’UTRs
Our search for new core promoter elements revealed another transcription-translation link. We identified a prevalent downstream transcription regulatory element that, remarkably, also serves as a translation initiation element in mRNAs with an extremely short 5’UTR. We termed this element Translation Initiator of Short 5’UTR (TISU) (1-5). This observation led us to expand our interests to the translation field. We showed that TISU directs a unique mode of translation initiation that is cap-dependent but scanning-free (2,6). We further demonstrated that a key step in the recognition of AUG close to the cap, as in TISU, involves cap-complex eviction and the requirement of eIF4G1 and eIF1 (6-8). In this way, a clash between the closely spaced cap complex and the ribosome is prevented. Physiologically, this novel mechanism allows continuous translation of TISU genes under energy stress, when global translation is inhibited (6). Site-specific UV crosslinking revealed that TISU binds ribosomal proteins at the E and the A sites in a sequence-specific manner (9). Interestingly global analysis revealed that very short 5’UTR mRNAs constitute a higher proportion of the mammalian translatome than previously anticipated (9). Our recent genetic studies provide strong support for the idea that TISU-ribosome-specific interactions underlie its unique features and strength (10).
Transcription start-site selection and mRNA translation
We uncovered additional transcription-translation links involving alternative promoter usage and generation of transcript isoforms with different 5’ends. We found that alternative promoters and transcription start site selection are markedly elevated in response to metabolic stress (11) and following transformation by the TCL1 oncogene (12) and are coordinated with translation. Moreover, both studies revealed that the identity of the first nucleotide of the mRNA, which is selected during transcription, affects translation efficiency under energy stress via differential binding of eIF4E to cap-proximal nucleotides. We currently use mapping and the 5’ and 3’ ends and machine learning to identify regulatory features of translation and mRNA stability for mRNA therapeutics.
Mediators of the crosstalk between transcription and mRNA stability
Transcription and mRNA decay are major determinants of mRNA levels. We uncovered two molecular pathways that maintain balanced mRNA levels through links between transcription and mRNA stability. First, we found that transcription strength impacts mRNA decay by modulating poly(A) tail length via m6A and CCR4-Not complex (the 3’-end mRNA degradation machinery). In addition, global and persistent fluctuations in transcription rates inversely affect the expression of CCR4-Not and global mRNA stability (13).
References
1. Elfakess, R. and Dikstein, R. (2008) A translation initiation element specific to mRNAs with very short 5'UTR that also regulates transcription. PloS one, 3, e3094.
2. Elfakess, R., Sinvani, H., Haimov, O., Svitkin, Y., Sonenberg, N. and Dikstein, R. (2011) Unique translation initiation of mRNAs-containing TISU element. Nucleic acids research, 39, 7598-7609.
3. Dikstein, R. (2011) The unexpected traits associated with core promoter elements. Transcription, 2, 201-206.
4. Dikstein, R. (2012) Transcription and translation in a package deal: the TISU paradigm. Gene, 491, 1-4.
5. Slobodin, B. and Dikstein, R. (2020) So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO reports, 21, e50799.
6. Sinvani, H., Haimov, O., Svitkin, Y., Sonenberg, N., Tamarkin-Ben-Harush, A., Viollet, B. and Dikstein, R. (2015) Translational tolerance of mitochondrial genes to metabolic energy stress involves TISU and eIF1-eIF4GI cooperation in start codon selection. Cell metabolism, 21, 479-492.
7. Haimov, O., Sehrawat, U., Tamarkin-Ben Harush, A., Bahat, A., Uzonyi, A., Will, A., Hiraishi, H., Asano, K. and Dikstein, R. (2018) Dynamic interactions of eIF4G1 with eIF4E and eIF1 underlie scanning dependent and independent translation. Mol Cell Biol.
8. Haimov, O., Sinvani, H. and Dikstein, R. (2015) Cap-dependent, scanning-free translation initiation mechanisms. Biochim Biophys Acta, 1849, 1313-1318.
9. Haimov, O., Sinvani, H., Martin, F., Ulitsky, I., Emmanuel, R., Tamarkin-Ben-Harush, A., Vardy, A. and Dikstein, R. (2017) Efficient and Accurate Translation Initiation Directed by TISU Involves RPS3 and RPS10e Binding and Differential Eukaryotic Initiation Factor 1A Regulation. Mol Cell Biol, 37, e00150-00117.
10. Havkin-Solomon, T., Fraticelli, D., Bahat, A., Hayat, D., Reuven, N., Shaul, Y. and Dikstein, R. (2023) Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling. Nucleic acids research, 51, 4415-4428.
11. Tamarkin-Ben-Harush, A., Vasseur, J.J., Debart, F., Ulitsky, I. and Dikstein, R. (2017) Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress. eLife, 6.
12. Ogran, A., Havkin-Solomon, T., Becker-Herman, S., David, K., Shachar, I. and Dikstein, R. (2022) Polysome-CAGE of TCL1-driven chronic lymphocytic leukemiarevealed multiple N-terminally alteredepigeneticregulators and a translationstress signature. eLife, 11.
13. Slobodin, B., Bahat, A., Sehrawat, U., Becker-Herman, S., Zuckerman, B., Weiss, A.N., Han, R., Elkon, R., Agami, R., Ulitsky, I. et al. (2020) Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol Cell, 78, 434-444.