2,754 results found
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

    David H Burkhardt, Silvi Rouskin ... Carol A Gross
    Operonic mRNAs in bacteria are comprised of ORF (open reading frame)-wide units of secondary structure, which are intrinsically distinct between adjacent ORFs and encode a rough blueprint for ORF-specific translation efficiency.
    1. Chromosomes and Gene Expression

    An mRNA-binding channel in the ES6S region of the translation 48S-PIC promotes RNA unwinding and scanning

    Irene Díaz-López, René Toribio ... Iván Ventoso
    The ES6S region of the small subunit ribosome makes a place for the threading and secondary structure unwinding of mRNA, which regulates genome-wide translation.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Yeast eIF4A enhances recruitment of mRNAs regardless of their structural complexity

    Paul Yourik, Colin Echeverría Aitken ... Jon R Lorsch
    Eukaryotic translation initiation factor 4A is stimulated by the ribosomal pre-initiation complex and promotes the recruitment of mRNAs regardless of their degree of structure.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Yeast Ded1 promotes 48S translation pre-initiation complex assembly in an mRNA-specific and eIF4F-dependent manner

    Neha Gupta, Jon R Lorsch, Alan G Hinnebusch
    Yeast RNA helicase Ded1 stimulates ribosome recruitment of structure-laden native mRNAs in a reconstituted system by interactions between domains in Ded1 and initiation factor eIF4G that stabilizes a Ded1-eIF4F complex.
    1. Chromosomes and Gene Expression

    Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling

    Jun Yao, Douglas C Wu ... Alan M Lambowitz
    Human plasma contains protein-protected mRNA fragments, myriad repeat RNAs, and novel intron RNAs, including a family of structured full-length excised introns, some corresponding to mirtron pre-miRNAs and agotrons.
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea

    Sinan Uğur Umu, Anthony M Poole ... Paul P Gardner
    Stochastic mRNA and non-coding RNA hybridisation has a major impact on protein expression.
    1. Biochemistry and Chemical Biology

    Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping

    Siqi Tian, Wipapat Kladwang, Rhiju Das
    A new biochemical method tests whether or not the pre-existing RNA structural correlations couple small molecule binding to gene expression in a paradigmatic riboswitch.
    1. Cell Biology

    In vivo reconstitution finds multivalent RNA–RNA interactions as drivers of mesh-like condensates

    Weirui Ma, Gang Zhen ... Christine Mayr
    Binding of a multivalent RNA-binding protein to mRNAs that are able to form pervasive RNA–RNA interactions induces formation of mesh-like condensates, whereas binding of mostly structured mRNAs induces sphere-like condensates.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structural insights into the molecular mechanism of the m6A writer complex

    Paweł Śledź, Martin Jinek
    The structure of the catalytic core of the N6-methyladenosine RNA methyltransferase complex METTL3-METTL14 reveals that METTL3 is the catalytic subunit, while METTL14 plays non-catalytic roles in substrate recognition and in maintaining complex integrity.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

    Jayashree Kumar, Lela Lackey ... Alain Laederach
    A novel model is presented that reconciles in-cell structure probing data with splicing regulatory elements to predict exon 10 inclusion of the Tau gene with high accuracy for 53 splice altering mutations.

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