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Biochemistry, Genetics and Molecular Biology · Research topic

Open research questions in RNA and protein synthesis mechanisms

151 unresolved questions extracted from the limitations and future-work sections of 430 RNA and protein synthesis mechanisms papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • further study of the structural response of viruses to a dehydrating environment, - application of single-particle imaging using XFELs to other viral capsids

    High-throughput in situ single particle X-ray imaging of dehydrating viral capsids · 2026 · DOI

  • The inability to study viral capsids in situ under dehydrating conditions. The lack of direct experimental evidence for the predicted low-energy buckling transitions in icosahedral capsids.

    High-throughput in situ single particle X-ray imaging of dehydrating viral capsids · 2026 · DOI

  • further characterization of the evolutionary relationships of highly divergent RNA viruses, - analysis of the human gut RNA virome in the context of complex diseases, - development of more accurate structural prediction methods for deeply divergent sequences

    Deep learning coupled with scalable domain-specific structural validation expands RNA virus discovery from metatranscriptomes · 2026 · DOI

  • Existing methods have limitations in detecting highly divergent viral signals. Prior work has focused on motif-centric tools that miss short fragments and deeply divergent viruses. The systematic exclusion of short sequences in current metagenomic pipelines is a fundamental limitation.

    Deep learning coupled with scalable domain-specific structural validation expands RNA virus discovery from metatranscriptomes · 2026 · DOI

  • The need for a comprehensive study of the translation of IRES-containing mRNAs, - The possibility of artifacts due to promoter activity of the putative IRES element and other upstream sequences, - The possibility of splicing of transcripts in the nucleus to form alternative mRNAs

    Reassessment of IRES Element Activity in Komagataella phaffii Using a Standardized Bicistronic System: Cryptic Promoter Activity Mimics Cap-Independent Translation · 2026 · DOI

  • The search for cellular IRES elements, - The characterization of heterologous viral IRES elements, - The development of a comprehensive study of the translation of IRES-containing mRNAs

    Reassessment of IRES Element Activity in Komagataella phaffii Using a Standardized Bicistronic System: Cryptic Promoter Activity Mimics Cap-Independent Translation · 2026 · DOI

  • Comprehensive analyses of codon usage bias in the chloroplast genomes of Gnetales species are lacking. The factors that influence codon usage bias in Gnetales species are not well understood.

    Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species · 2024 · DOI

  • AutoRNA demonstrates that variational autoencoders can learn meaningful coarse-grained structural representations of RNA from limited data.

    AutoRNA: RNA tertiary structure prediction using variational autoencoder. · 2026 · DOI

  • Although equilibration is a critical component of umbrella sampling workflows, the impact of equilibration length on thermodynamic predictions remains poorly understood.

    Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities · 2026 · DOI

  • The coding sequence of an mRNA directs its own decay, yet how codons, codon context, and amino acids collectively regulate mRNA stability remains poorly understood.

    Beyond codon optimality: codon pairs regulate mRNA stability dependent on translation · 2026 · DOI

  • Abstract The minute-scale lifetime of mRNA strongly influences bacterial gene expression, whereas a robust and programmable approach to directly control the mRNA stability and topology remains elusive.

    Programmable in vivo mRNA circularization for enhanced gene expression in bacteria · 2026 · DOI

  • How the assembling proteins distinguish viral RNA from host RNA is not fully understood, but RNA structure is thought to play a key role.

    Measuring the selective packaging of RNA molecules by viral coat proteins in cells · 2025 · DOI

  • Particularly, the role of conformational dynamics in ribozyme catalysis remains elusive.

    A hammerhead ribozyme selects mechanically stable conformations for catalysis against viral RNA · 2025 · DOI

  • -glycosylated and terminated with sialic acids, although the glycosylation sites and potential functions remain unclear.

    In Situ Visualization of RNA-Specific Sialylation on Living Cell Membranes to Explore N -Glycosylation Sites · 2024 · DOI

  • However, comprehensive analyses of CUB within the chloroplast genomes of Gnetales species remain unexplored.

    Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species · 2024 · DOI

  • RNA polymerase ribozymes (PR) - including a variant that uses trinucleotide triphosphates (triplets) as substrates - have been created by in vitro evolution and are the closest functional analogues of the replicase, but the structural basis for their function is poorly understood.

    Cryo-EM structure and functional landscape of an RNA polymerase ribozyme · 2024 · DOI

  • In bacteria, RNA-binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half-lives has not been extensively studied.

    Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives · 2024 · DOI

  • On general grounds, the model predicts how the fraction of ribosomes in the proteome depends on total mRNA concentration and inspects an underexplored regime in which the trade-off between transcript levels and ribosome abundances sets the cellular growth rate.

    How total mRNA influences cell growth · 2024 · DOI

  • The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection.

    Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection · 2024 · DOI

  • Our structural bioinformatics studies not only provided insight into the differences between the hydrophobic helices and hydrophilic helices in the glutamate transporters, but they are also expected to stimulate further study of other water-soluble transmembrane proteins.

    Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F · 2024 · DOI

  • Further exploration of the implications of the new model. Investigation of the role of RNA and the ribosome in the cell. Development of new therapies based on the concept of restoring balance in the recycling system.

    The Ribosome, RNA, and the Architecture of the Living Cell A Revision of Conventional Molecular Biology · 2026 · DOI

  • Uncertain structure and low evolutionary constraint of microproteins. The need for improved detection and annotation methods. The complexity of the human proteome.

    Expanding the human proteome with microproteins and peptideins · 2026 · DOI

  • The number of ncORFs that represent true protein-coding genes is a subject of controversy. Few microproteins have been annotated as canonical proteins by reference annotation catalogues.

    Expanding the human proteome with microproteins and peptideins · 2026 · DOI

  • The need for a lightweight adapter to transform DNA language models into effective RNA analyzers. The need for a principled path toward unifying genomic language modeling.

    CodonMoE: DNA Language Models for Codon-Dependent mRNA Prediction · 2026 · DOI

  • The detection of the ppGpp effect on TL folding relies on distributions of ePEC conformations that include TL-folded states and not direct detection of ppGpp action on the NAC. Computational sorting of particles to distinct conformational states during cryo-EM data processing is inherently limited by the signal-to-noise ratio of the underlying individual particle images.

    ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition · 2026 · DOI

Most-cited papers in RNA and protein synthesis mechanisms

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151 open questions have been extracted from the limitations and future-work passages of 430 RNA and protein synthesis mechanisms papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

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