Abundant capped RNAs are derived from mRNA cleavage at 3'UTR G-Quadruplexes

Haberman, N.; Digby, H.; Faraway, R.; Cheung, R.; Jobbins, A. M.; Parr, C.; Yasuzawa, K.; Kasukawa, T.; Yip, C. W.; Kato, M.; Takahashi, H.; Carninci, P.; Ule, J.; Sibley, C. R.; Martinez-sanchez, A.; Lenhard, B.; Vernia, S.

doi:10.1101/2023.04.27.538568

bioRxiv · 10.1101/2023.04.27.538568

Abundant capped RNAs are derived from mRNA cleavage at 3'UTR G-Quadruplexes

Haberman, N.·Digby, H.·Faraway, R.·Cheung, R.·Jobbins, A. M.·Parr, C.·Yasuzawa, K.·Kasukawa, T.·Yip, C. W.·Kato, M.·Takahashi, H.·Carninci, P.·Ule, J.·Sibley, C. R.·Martinez-sanchez, A.·Lenhard, B.·Vernia, S.

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Abstract

The 3 untranslated region (3UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. Cap analysis gene expression (CAGE), a method for the detection of capped 5 ends of mRNAs, additionally reveals a large number of apparently 5 capped RNAs derived from 3UTRs. Here we provide the first direct evidence that these 3UTR-derived RNAs are indeed capped and often more abundant than the corresponding full-length mRNAs. By using a combination of AGO2 enhanced individual nucleotide resolution UV crosslinking and immunoprecipitation (eiCLIP) and CAGE following siRNA knockdowns, we find that these 3UTR-derived RNAs likely originate from AGO2-mediated cleavage, and most often occur at locations with potential to form RNA-G-quadruplexes and are enriched by RNA-binding protein UPF1. High-resolution imaging and long-read sequencing analysis validates several 3UTR-derived RNAs, demonstrates their abundance and shows that they tend not to co-localise with the parental mRNAs. We also find that production of 3UTR-derived RNA could explain the previously reported role of a 3UTR G-quadruplex in regulating the production of APP protein. Taken together, we provide new insights into the origin and abundance of 3UTR-derived RNAs, show the utility of CAGE-seq for their quantitative detection, and provide a rich dataset for exploring new biology of a poorly understood new class of RNAs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/538568v3_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@3f2ca7org.highwire.dtl.DTLVardef@18ca1b6org.highwire.dtl.DTLVardef@1ccdd8dorg.highwire.dtl.DTLVardef@e58938_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Haberman, N., Digby, H., Faraway, R., Cheung, R., Jobbins, A. M., Parr, C., Yasuzawa, K., Kasukawa, T., Yip, C. W., Kato, M., Takahashi, H., Carninci, P., Ule, J., Sibley, C. R., Martinez-sanchez, A., Lenhard, B., Vernia, S.. 2023-04-27. Abundant capped RNAs are derived from mRNA cleavage at 3'UTR G-Quadruplexes. https://doi.org/10.1101/2023.04.27.538568

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