bims-micpro 2025-09-21 papers

Brief Bioinform. 2025 Aug 31. pii: bbaf458. [Epub ahead of print]26(5):

CircCode3: integrating deep learning to mine and evaluate translatable circular RNAs from ribosome profiling sequencing and mass spectrometry data.

Zonghui Zhu, Xiaojuan Liang, Rui Ma, Shuwei Yin, Meng Xu, Guanglin Li.

Translatable circular RNAs (circRNAs), distinguished by their capacity to encode proteins or peptides, rely on cap-independent mechanisms such as m6A-mediated or internal ribosome entry site (IRES)-driven translation initiation. Currently, identification translatable circRNAs and their open reading frame accurately are challenging. In this study, we developed an integrated analysis pipeline, CircCode3, to mine translatable circRNAs from high throughput sequencing data, building upon existing tools and significantly enhancing their functionalities. CircCode3 also introduces new capabilities, including the identification and assessment of open reading frames (ORFs) spanning back-splice junction sites. To evaluate IRES potential, we incorporated IRESfinder into the pipeline. Furthermore, we developed two deep learning tools: DeepCircm6A for predicting m6A modification sites in circRNAs, and DLMSC for assessing the reliability of stop codons. These enhancements make CircCode3 a comprehensive solution for analyzing ribosome profiling sequencing and mass spectrometry data, identifying and evaluating ORFs, and visualizing results. The CircCode3 tool is publicly available and can be downloaded from https://github.com/Lilab-SNNU/CircCode3.

Keywords: circular RNAs; mass spectrometry; ribosome profiling sequencing; translatable circRNAs

DOI: https://doi.org/10.1093/bib/bbaf458

Plant J. 2025 Sep;123(5): e70476

RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana.

Mitsuru Saraumi, Takahiro Tanaka, Daiki Koyama, Yoshitaka Nishi, Yoshihiro Takahashi, Hiroyasu Motose, Taku Takahashi.

Thermospermine is involved in negative regulation of xylem differentiation by enhancing the translation of mRNAs of the SAC51 gene family in Arabidopsis (Arabidopsis thaliana). These mRNAs contain conserved upstream open reading frames (uORFs) that interfere with the translation of the main ORF. To investigate the mechanism by which thermospermine acts in this process, we isolated mutants insensitive to thermospermine, named 'its'. We show that the four genes responsible for these mutants, its1 to its4, encode: (i) a homolog of SPOUT RNA methyltransferase, (ii) an rRNA pseudouridine synthase CBF5/NAP57, (iii) a putative spliceosome disassembly factor STIPL1/NTR1, and (iv) a plant-specific RNA-binding protein PHIP1. These four mutants were found to have much higher levels of thermospermine than the wild-type. While all these mutants except its1 appear almost normal, they enhance the dwarf phenotype of a mutant of ACL5, which encodes thermospermine synthase, resulting in tiny plants resembling a double knockout of ACL5 and SACL3, a member of the SAC51 family. Reporter assays revealed that GUS activity from the CaMV 35S promoter-SAC51 5'-GUS fusion construct was significantly reduced in its1 and its4 or not affected in its2 and its3, while it was slightly increased in its1, its3, and its4, or not changed in its2 by thermospermine. These findings underscore the critical role of RNA processing and modification in the thermospermine-dependent translational regulation of uORF-containing transcripts.

Keywords: RNA methyltransferase; SPOUT domain; pseudouridine synthase; spliceosome disassembly; thermospermine; translation; uORF; xylem

DOI: https://doi.org/10.1111/tpj.70476

Oncogene. 2025 Sep 15.

The novel protein SEMA3C-319aa triggers glutathione metabolism-dependent ferroptosis in gastric cancer.

Siyu Xiao, Yin Peng, Lehua Peng, Xiaoya Xie, Jiequan Qin, Huizhen Ma, Xinyi Kang, Chuhan Bing, Bingyan Huang, Ke Liang, Yidan Zhao, Xueying Rong, Xianling Feng, Xinmin Fan, Hassan Ashktorab, Zhong Zhang, Zhe Jin, Xiaojing Zhang.

The lack of effective, targeted therapies for gastric cancer (GC) continues to limit patient survival. Circular RNAs (circRNAs), known to act as epigenetic regulators, may also encode functional proteins. In this study, RNA-seq combined with ribosome profiling (Ribo-seq) of human GC cells identified a non-canonically translated circRNA, circSEMA3C, which encodes a novel 319-amino-acid (aa) protein, SEMA3C-319aa. Functionally, both circSEMA3C and SEMA3C-319aa suppressed GC cell viability and tumor growth in vitro and in vivo. Using proteomics and metabolomics, we found that SEMA3C-319aa targets ferroptosis-associated metabolites and metabolic pathways in GC. Notably, SEMA3C-319aa upregulated the production of polyunsaturated fatty acid chains and inhibited glutathione metabolism-particularly the GSH cycle-thereby suppressing GPX4 activity. Mechanistically, SEMA3C-319aa binds to LDHA and, via its non-canonical nuclear localization signal (NLS), sequence shuttles LDHA into the nucleus, where it enhances transcription of the E3 ligase PARK2, promoting GPX4 degradation. Furthermore, combination treatment with SEMA3C-319aa and the GPX4 inhibitor RSL3 was more effective than monotherapy in vivo. Taken together, our findings reveal a novel NLS-dependent nuclear translocation mechanism mediated by SEMA3C-319aa and identify a new ferroptosis pathway in GC. SEMA3C-319aa may offer a promising adjuvant therapeutic strategy for GC.

DOI: https://doi.org/10.1038/s41388-025-03542-6

J Mol Evol. 2025 Sep 19.

Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA.

Yaohui Chen, Jung-Hyun Kim, Hee-Sheung Lee, Sergey Koren, Vladimir Larionov, Adam M Phillippy, David Schlessinger, Ramaiah Nagaraja.

An open reading frame in the intergenic spacer of human ribosomal (r)DNA codes for a 190 amino acid, 22 kDa protein that we have named ORF3. It comprises a 5'AluSx repeat sequence encoding 96 amino acids followed by a stretch of 94 amino acids containing a unique repeated stretch of 5 hydrophobic residues. Full copies of ORF3 have been isolated as transformation-associated recombination clones from mouse:human hybrid cell lines containing human chromosomes 21 or 22. In initial instances where the chromosome complement of rDNA repeats is fully resolved in whole genomes, in CHM13 cells, complete copies of ORF3 are mainly concentrated in a tandem cluster on chromosome 21, while other chromosomes contain 1 or 2 full copies, with the sequence in other rDNA repeats interrupted by a frameshift mutation. A diploid cell complement (HG002) again has both complete open reading frames (ORFs) and other copies with the frameshift or deletions. In searches among non-human primate sequences to assess the evolutionary history of ORF3, a > 93% conserved copy of the full sequence of the ORF, as well as copies with in-frame deletions, was found in bonobo, but only fragments homologous to the ORF were seen in chimpanzee, orangutan, and gorilla rDNA examined thus far. ORF3 was expressed as a V5-tagged chimeric protein in human kidney epithelial HEK293 cells, and both ORF3-V5 and endogenous ORF3 were detected with a newly generated antibody. The protein is found in both cytoplasm and nucleus. However, upon treatment of cells with RNase A, the protein is excluded from the nucleus, suggesting that it is in complexes with RNA. Although any function is currently unknown, the ORF3 protein is upregulated, speculatively associated with changes in chromatin, in viral-transformed HEK293 cells and in human diploid fibroblast cells rendered senescent by treatment with etoposide, ionizing radiation, or an oxidant (H2O2).

Keywords: Cancer cells; Ribosomal RNA; Senescence

DOI: https://doi.org/10.1007/s00239-025-10269-1