bims-micpro 2024-03-17 papers

Issue of 2024‒03‒17
three papers selected by
Thomas Farid Martínez, University of California, Irvine

Dokl Biochem Biophys. 2024 Mar 12.

PRPF19 mRNA Encodes a Small Open Reading Frame That Is Important for Viability of Human Cells.

N M Shepelev, A O Kurochkina, O A Dontsova, M P Rubtsova.

High-throughput ribosome profiling demonstrates the translation of thousands of small open reading frames located in the 5' untranslated regions of messenger RNAs (upstream ORFs). Upstream ORF can both perform a regulatory function by influencing the translation of the downstream main ORF and encode a small functional protein or microprotein. In this work, we showed that the 5' untranslated region of the PRPF19 mRNA encodes an upstream ORF that is translated in human cells. Inactivation of this upstream ORF reduces the viability of human cells.

Keywords: micropeptide; microprotein; ribosome profiling; uORF; upstream ORF

DOI: https://doi.org/10.1134/S1607672923700722

Biochem Biophys Res Commun. 2024 Mar 08. pii: S0006-291X(24)00300-0. [Epub ahead of print]706 149764

Light-dependent expression and accumulation of miR408-encoded peptide, miPEP408, is regulated by HY5 in Arabidopsis.

Ravi Shankar Kumar, Tapasya Datta, Hiteshwari Sinha, Prabodh Kumar Trivedi.

Recent studies propose that primary transcripts of miRNAs (pri-miRNAs) contain small Open Reading Frames (ORFs) capable of encoding miRNA-encoded peptides (miPEPs). These miPEPs can function as transcriptional regulators for their corresponding pri-miRNAs, ultimately enhancing mature miRNA accumulation. Notably, pri-miR408 encodes the functional peptide miPEP408, regulating expression of miR408 and its target genes, providing plant tolerance to stresses. While miPEPs are crucial regulators, the factors governing them are have not been studied in detail. Here, we explored the light-dependent regulation of miPEP408 in Arabidopsis. Expression analysis during dark-light transitions revealed light-induced transcription and accumulation of the miPEP408. As the promoter of miR408 contains cis-acting elements responsible for binding to the bZIP-type transcription factor ELONGATED HYPOCOTYL5 (HY5), known for light-mediated regulation in plants, we studied its involvement in the regulation of miR408. Analysis of HY5 mutant (hy5-215), complemented line (HY5OX/hy5), and CONSTITUTIVE PHOTOMORPHOGENIC 1 mutant (cop1-4) plants supported HY5's positive regulation of miPEP408. Grafting and GUS assays further suggested the role of HY5 as a shoot-root mobile signal inducing light-dependent miPEP408 expression. This study underscores the regulatory impact of light on small peptides, exemplified by miPEP408, mediated by the key transcription factor HY5.

Keywords: COP1; Gene expression; HY5; Light; miPEP; miRNA

DOI: https://doi.org/10.1016/j.bbrc.2024.149764

Proc Natl Acad Sci U S A. 2024 Mar 19. 121(12): e2312322121

RN7SL1 may be translated under oncogenic conditions.

Tomoaki Hara, Sikun Meng, Yoshiko Tsuji, Yasuko Arao, Yoshiko Saito, Hiromichi Sato, Daisuke Motooka, Shizuka Uchida, Hideshi Ishii.

RN7SL1 (RNA component of signal recognition particle 7SL1), a component of the signal recognition particle, is a non-coding RNA possessing a small ORF (smORF). However, whether it is translated into peptides is unknown. Here, we generated the RN7SL1-Green Fluorescent Protein (GFP) gene, in which the smORF of RN7SL1 was replaced by GFP, introduced it into 293T cells, and observed cells emitting GFP fluorescence. Furthermore, RNA-seq of GFP-positive cells revealed that they were in an oncogenic state, suggesting that RN7SL1 smORF may be translated under special conditions.

Keywords: RN7SL1; ncRNA; smORF

DOI: https://doi.org/10.1073/pnas.2312322121