bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2025–06–15
two papers selected by
Thomas Farid Martínez, University of California, Irvine



  1. Plant Cell Environ. 2025 Jun 11.
      Deep sequencing of ribosome footprints, also known as ribosome profiling (Ribo-seq), enables the quantification of mRNA translation and a comprehensive view of the translatome landscape. Here, we report an optimised Ribo-seq protocol and analysis pipeline for the model green alga, Chlamydomonas reinhardtiii (Chlamydomonas). Compared to the previously published data sets, the ribosome-protected fragments generated by our protocol showed improved mapping rates to the main open reading frames, reduced bias mapping to the gene coding regions and high 3-nt footprint periodicity. Using this optimised protocol, we employed Ribo-seq alongside RNA-seq to compute translation efficiency and identify genes with differential translation during the diurnal cycle. Interestingly, we found that the translation efficiency of many core cell cycle genes was significantly enhanced in cells at the early synthesis/mitosis (S/M) stage. This result suggests that translational regulation plays a role in cell cycle regulation in C. reinhardtii. Furthermore, the high periodicity of ribosome footprints allowed us to identify potential C. reinhardtii upstream open reading frames (uORFs). Further analysis revealed that some of these uORFs are differentially regulated and may play a role in diurnal regulation. In summary, we used an optimised Ribo-seq protocol to generate a high-quality Ribo-seq data set that constitutes a valuable resource for Chlamydomonas genomics. The ribosome profile data is linked to the Chlamydomonas reference genome and accessible to the scientific community.
    Keywords:  3‐nucleotide periodicity; Chlamydomonas reinhardtii; cell cycle; ribosome footprint; translatome; upstream ORF
    DOI:  https://doi.org/10.1111/pce.15681
  2. Science. 2025 Jun 12. 388(6752): 1218-1224
      Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively parallel ribosome profiling (MPRP) to determine open reading frames (ORFs) across tens of thousands of designed oligonucleotides. MPRP identified 4208 unannotated ORFs in 679 human-associated viral genomes. We found viral peptides originating from detected noncanonical ORFs presented on class-I human leukocyte antigen in infected cells and hundreds of upstream ORFs that likely modulate translation initiation of viral proteins. The discovery of viral ORFs across a wide range of viral families-including highly pathogenic viruses-expands the repertoire of vaccine targets and reveals potential cis-regulatory sequences.
    DOI:  https://doi.org/10.1126/science.ado6670