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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
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Gene finding in metatranscriptomic sequences.

Wazim Mohammed Ismail, Yuzhen Ye, Haixu Tang

    BMC Bioinformatics
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    Summary
    This summary is machine-generated.

    TransGeneScan accurately identifies genes in microbial communities using metatranscriptomic data. This new tool refines gene prediction and enhances understanding of microbial community functions.

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    Area of Science:

    • Microbiology
    • Bioinformatics
    • Genomics

    Background:

    • Metatranscriptomic sequencing offers sensitive functional insights into microbial communities, complementing metagenomic data.
    • It aids in refining metagenome annotations and studying gene activity and regulation.

    Purpose of the Study:

    • To introduce TransGeneScan, a novel software tool for gene prediction from assembled metatranscriptomic sequences.
    • To improve the accuracy of gene identification in complex microbial communities.

    Main Methods:

    • TransGeneScan utilizes a Hidden Markov Model incorporating metatranscriptomic features like strand-specificity and antisense transcripts.
    • The software predicts both sense transcripts (operons) and antisense transcripts.

    Main Results:

    • TransGeneScan demonstrated superior performance compared to metagenomic gene finders (MetaGeneMark, FragGeneScan) for assembled transcripts.
    • It achieved accuracy comparable to or exceeding microbial genome gene finders (Glimmer, GeneMark).

    Conclusions:

    • TransGeneScan enhances the precision of gene identification in microbial communities.
    • Combined with metatranscriptomic sequencing, it provides a comprehensive view of microbial gene functions.