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Related Concept Videos

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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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Regulation of Expression Occurs at Multiple Steps02:24

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Transcription01:17

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Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
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MTD: a mammalian transcriptomic database to explore gene expression and regulation.

Xin Sheng, Jiayan Wu, Qianqian Sun

    Briefings in Bioinformatics
    |January 30, 2016
    PubMed
    Summary

    A new Mammalian Transcriptomic Database (MTD) offers comprehensive, comparative transcriptome data across species. This resource aids in understanding gene expression and evolutionary studies.

    Keywords:
    RNA-seqgene expression and regulationmammalian transcriptomic database

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    Area of Science:

    • Genomics
    • Bioinformatics
    • Comparative transcriptomics

    Background:

    • Transcriptome analysis is crucial for understanding molecular mechanisms of phenotypic variation.
    • Existing mammalian transcriptomic databases are limited by tissue- or species-specificity.
    • RNA-sequencing (RNA-seq) enables efficient transcriptome data acquisition.

    Purpose of the Study:

    • To present the Mammalian Transcriptomic Database (MTD), a novel resource for comparative transcriptomic analysis.
    • To integrate diverse mammalian transcriptome data, including humans, mice, rats, and pigs.
    • To provide advanced tools for gene expression analysis and evolutionary studies.

    Main Methods:

    • Development of a novel transcript nomenclature system based on genomic position and features.
    • Integration of transcriptomic data into a genome browser for detailed expression analysis (exons, transcripts, genes).
    • Implementation of comparative analysis tools for intraspecies and interspecies gene expression regulation.

    Main Results:

    • The MTD contains transcriptome data from humans, mice, rats, and pigs.
    • The database supports gene browsing by genomic coordinates or KEGG pathways.
    • Flexible search options for genes/isoforms with user-defined characteristics are available.
    • Visualizations and table-based descriptions enhance data exploration.

    Conclusions:

    • The MTD serves as a valuable, freely accessible resource for transcriptomic and evolutionary research.
    • Comparative analysis capabilities within the MTD facilitate deeper understanding of gene expression dynamics.
    • The database supports a wide range of users, from basic researchers to bioinformaticians.