bims-micpro 2025-10-26 papers

Genome Biol. 2025 Oct 23. 26(1): 366

Identification of microprotein-coding intronic polyadenylation isoforms and function in genotoxic anticancer drug response.

BACKGROUND: Many transcript isoforms generated by intronic polyadenylation (IPA) encode isoforms of canonical proteins. Microproteins are an emerging class of small proteins translated from small open reading frames (sORFs) in noncoding RNAs and mRNAs, but their production by IPA isoforms is unknown.
RESULTS: Here, by crossing 3'-seq, Ribo-Seq, and mass-spectrometry data, we identify 297 genes with a microprotein-coding IPA isoform terminating in a 5'UTR intron (coined miP-5'UTR-IPA isoform). By 3'-seq and long-read RNA-seq analyses in lung cancer cells treated with cisplatin, a DNA-cross-linking anticancer drug, we find that cisplatin globally favors the expression of (miP-5'UTR-)IPA isoforms relative to full-length mRNAs, mainly by decreasing the latter through an inhibition of transcription processivity in a FANCD2 and senataxin-dependent manner. The cisplatin-regulated miP-5'UTR-IPA isoform in the PRKAR1B gene is translated, as it is associated with light polysome fractions and contains Ribo-Seq-supported sORFs in its alternative last exon, and the microprotein (PRKAR1B-IPA-miP2) encoded by its sORF#2 is detected by Western blot and immunofluorescence. CRISPR editing of either the IPA site or the sORF#2 initiation site leads to decreased cell growth inhibition by cisplatin and camptothecin, another genotoxic drug. Mechanistically, PRKAR1B-IPA-miP2 promotes p53 protein induction by cisplatin. Finally, 70 miP-5'UTR-IPA isoforms are detected in normal cells, and 143 are upregulated by cisplatin.
CONCLUSIONS: Here, we show that IPA isoforms are a novel source of microproteins, and we reveal the novel paradigm of miP-5'UTR-IPA genes that produce both a canonical full-length mRNA and a microprotein-coding IPA isoform.

Keywords: Alternative last exon; DNA-damaging agent; Intronic polyadenylation; Micropeptide; Small ORF

DOI: https://doi.org/10.1186/s13059-025-03829-7

J Proteome Res. 2025 Oct 22.

Identification and Validation of SmORF-Encoded Peptides by Genomics and Proteomics in Five Cyanobacteria.

Zhao Peng, Qianru Xiao, Cuihong Wan.

Small open reading frames (smORFs) and smORF-encoded peptides (SEPs) are now perceived as essential components alongside canonical genes and proteins. In cyanobacteria, SEPs were initially associated with photosynthesis and were later found to regulate metabolism and stress responses. However, SEPs have not been comprehensively identified in model cyanobacteria. Here, we used genomic and proteomic methods to identify and validate SEPs in five cyanobacteria. We integrated known SEPs from databases with genome-based predictions to construct a comprehensive data set. Generally, SEPs shared characteristics with canonical proteins in terms of amino acid frequency and codon bias. They also exhibited evolutionary features including paralogs within species and conservation across species, similar to canonical proteins. We found that most SEPs were related to photosynthesis, ribosomal proteins, and prokaryotic defense systems. Through SEP enrichment, we identified 817 SEPs with no previous evidence, and 103 novel SEPs through LC-MS/MS. They were identified as components of type II TA systems in cyanobacteria. The conserved SEP BolA might interact with Grx4 to mediate iron homeostasis. We also found several SEPs with potential functions, including sulfur transfer and protein translocation. In sum, our study excavates SEPs and suggests their biological roles in cyanobacteria.

Keywords: SEP; cyanobacteria; iron homeostasis; proteomics; smORF; toxin−antitoxin system

DOI: https://doi.org/10.1021/acs.jproteome.5c00685

Nucleic Acids Res. 2025 Oct 21. pii: gkaf1022. [Epub ahead of print]

riboCIRC v2.0: an expanded resource for translatable CircRNAs.

Yunhao Xu, Lei Yang, Yuewen Tang, Yan Wang, Hongwei Wang.

riboCIRC (http://www.ribocirc.com) is a translatome data-oriented database dedicated to cataloging translatable circRNAs and their encoded peptides across six model species, including Homo sapiens, Mus musculus, Rattus norvegicus, Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio. Here, we present riboCIRC v2.0, a major update featuring expanded content and enhanced functionality to facilitate and accelerate research into circRNA translation and function characterization. Key improvements include (i) expanded data coverage: now documenting 5212 computationally predicted translatable circRNAs and 7563 predicted finite ORF-encoded peptides, representing a substantial increase from the initial release (2247 and 2234 entries, respectively); (ii) enhanced evidence integration: incorporation of new evidence layers supporting translation of circRNAs, including RNA editing sites and RBP interactions, supplementing existing evidence from ribosome profiling, mass spectrometry, IRES elements, and m6A modifications; (iii) comprehensive peptide annotation: systematic in silico characterization of finite ORF-encoded peptides, detailing their physicochemical properties, predicted structures, and potential functions; and (iv) optimized user interface: improved navigation and dedicated modules for streamlined data exploration, retrieval, and visualization. Collectively, these enhancements establish riboCIRC v2.0 as a more powerful resource for investigating the functional roles of translatable circRNAs and their products across diverse biological systems.

DOI: https://doi.org/10.1093/nar/gkaf1022

Acta Naturae. 2025 Jul-Sep;17(3):17(3): 44-48

Cabbage Peptide miPEP156a Enhances the Level of Accumulation of Its mRNA in Transgenic Moss Physcomitrium patens.

T N Erokhina, E V Ryabukhina, I S Lyapina, D Y Ryazantsev, S K Zavriev, S Y Morozov.

MicroRNAs are endogenous, small non-coding RNAs that regulate gene expression at the post-transcriptional level by cleaving target mRNAs. Mature microRNAs are products of the processing of their primary transcripts (pri-miRNAs). Now, it has been discovered that the products of the translation of some plant pri-miRNAs are peptide molecules (miPEP). These peptides have the capacity to physically interact with their open reading frames (ORFs) in the transcribed pri-miRNAs and, thus, positively regulate the accumulation of these RNAs and the corresponding mature microRNAs. Most conserved microRNAs play an important role in plants development and their response to stress. In this work, we obtained transgenic Physcomitrium patens moss plants containing Brassica oleracea miPEP156a ORF in the genome under the control of a strong 35S cauliflower mosaic virus promoter and analyzed the effect of the exogenous peptide on the transcription of this ORF in the protonemata of two transgenic moss lines. It turned out that the chemically synthesized peptide miPEP156a increases the accumulation of its own mRNA during moss culture growth, as was previously shown in studies by foreign researchers and in our own work for a number of peptides in monocotyledonous and dicotyledonous plants. These findings confirm that pri-miRNA regions that are located outside the coding region of the peptide are not required for transcriptional activation. Moreover, we have also succeeded in showing that the presence of a specific promoter of the microRNA gene does not affect the phenomenon of transcription activation; this phenomenon per se is not species-specific and is observed in transgenic plants, regardless of the origin of the miPEP.

Keywords: PCR analysis; miPEP; microRNA; peptides; pri-miRNA; transgenic plants

DOI: https://doi.org/10.32607/actanaturae.27668