Interplay between m6A modification and overall transcripts quantity: Impacts on mRNA composition in plant stress granules

Kubiak, D. J.; Szczesniak, M. W.; Ostrowska, K.; Bielewicz, D.; Bhat, S. S.; Niedojadlo, K.; Szweykowska-Kulinska, Z.; Jarmolowski, A.; Fray, R. G.; Niedojadlo, J.

doi:10.1101/2023.12.14.569339

bioRxiv · 10.1101/2023.12.14.569339

Interplay between m6A modification and overall transcripts quantity: Impacts on mRNA composition in plant stress granules

Kubiak, D. J.·Szczesniak, M. W.·Ostrowska, K.·Bielewicz, D.·Bhat, S. S.·Niedojadlo, K.·Szweykowska-Kulinska, Z.·Jarmolowski, A.·Fray, R. G.·Niedojadlo, J.

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Abstract

Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. They contain a rich pool of RNA, including non-translated mRNA. The mechanisms governing transcripts accumulation in SGs is only partially understood. Despite the recognized role of m6A in plant transcriptome regulation, its impact on SGs composition and assembly remains elusive. We examined the formation of SGs, the presence of m6A, and the transcription-level-dependent localization of selected mRNAs within these granules during hypoxia in the roots of Lupinus angustifolius and Arabidopsis thaliana. In lupine, SGs exhibit a distinctive bi-zonal structure, comprising of a ring and a central area with differences in ultrastructure and composition. Following the transcriptome analysis, mRNAs were selected for examination of their localization in SGs and m6A levels. Transcripts from genes responsive to hypoxia (ADH1 and HUP7) exhibited significant lower levels of m6A compared to housekeeping genes but only ADH1 was not present in SGs. HUP7 mRNA with low quantity of m6A, is present both in the SGs and cytoplasm probably due to extremely high expression level. It was also shown that the amount of m6A in SGs was higher than in the cytoplasm only in the first hours of hypoxia and then decreased. In mutants of A. thaliana with reduced level of m6A, formation and quantity of SGs were studied. In this line, ECT2 was not observed and poly(A) RNA levels were slightly reduced in SGs. Additionally the number of SGs was lower than that of the wild type. In summary, our findings demonstrate the limited impact of m6A modification on SGs assembly. However the interplay between m6A modification and the overall transcript quantity in the cytoplasm plays a regulatory role in mRNA partitioning into SGs.

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Kubiak, D. J., Szczesniak, M. W., Ostrowska, K., Bielewicz, D., Bhat, S. S., Niedojadlo, K., Szweykowska-Kulinska, Z., Jarmolowski, A., Fray, R. G., Niedojadlo, J.. 2023-12-14. Interplay between m6A modification and overall transcripts quantity: Impacts on mRNA composition in plant stress granules. https://doi.org/10.1101/2023.12.14.569339

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