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What is Gene Expression?01:36

What is Gene Expression?

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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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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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Regulation of Expression at Multiple Steps01:23

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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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Chromatin Structure Regulates pre-mRNA Processing02:41

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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
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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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Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code.

L Deng1, J Kumar1, R Rose2

  • 1Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA.

Mass Spectrometry Reviews
|September 2, 2022
PubMed
Summary
This summary is machine-generated.

RNA posttranscriptional modifications (rPTMs) are crucial for cellular processes and human health. This review details analytical methods for identifying and characterizing these diverse RNA modifications, emphasizing complementary approaches for comprehensive epitranscriptomic analysis.

Keywords:
NGSRNA posttranscriptional modificationsRNA-seqepitranscriptomicshigh-throughput sequencingmononucleotide variantsnanopore sequencingnatural RNAreverse transcriptasesingle-molecule analysisstrand cleavagetandem MS sequencing

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Non-protein-coding RNAs (ncRNAs) play vital regulatory roles, with malfunctions linked to human diseases.
  • Over 170 variants of canonical ribonucleotides contribute to RNA's structural diversity.
  • Understanding RNA posttranscriptional modifications (rPTMs) is essential for a complete view of RNA's cellular significance.

Purpose of the Study:

  • To survey analytical approaches for identifying, characterizing, and detecting RNA posttranscriptional modifications (rPTMs).
  • To provide a comprehensive overview of methods for analyzing rPTMs, including their distribution and function.
  • To guide researchers in selecting optimal strategies for epitranscriptomic analysis.

Main Methods:

  • Analysis of individual modified ribonucleotides after hydrolysis.
  • Sequencing-based methods for identifying rPTM positions within RNA strands.
  • Mass spectrometry and next-generation sequencing technologies for rPTM detection and characterization.

Main Results:

  • Outlines the advantages of analyzing individual modified units versus their location in parent RNA strands.
  • Details the strengths and weaknesses of next-generation sequencing and mass spectrometry for rPTM analysis.
  • Highlights the necessity of complementary techniques for comprehensive epitranscriptomic studies.

Conclusions:

  • Deciphering the epitranscriptomic code requires mapping rPTM locations and quantifying expression levels.
  • No single platform can fully address the demands of epitranscriptomic analysis.
  • Combining diverse analytical approaches is crucial for obtaining complete information on rPTMs and their roles.