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Related Concept Videos

Transcription Elongation Factors02:35

Transcription Elongation Factors

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Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
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Transcription Initiation01:47

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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
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Bacterial Transcription01:53

Bacterial Transcription

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RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
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Transcription Attenuation in Prokaryotes02:42

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Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
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Improving Translational Accuracy02:07

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Measuring the Kinetics of mRNA Transcription in Single Living Cells
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Measuring the Kinetics of mRNA Transcription in Single Living Cells

Published on: August 25, 2011

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A code for transcription elongation speed.

Eyal Cohen1, Zohar Zafrir2, Tamir Tuller2,3

  • 1a Balavatnick School of Computer Science , Tel Aviv University , Tel Aviv , Israel.

RNA Biology
|November 23, 2017
PubMed
Summary
This summary is machine-generated.

Short DNA sequences influence RNA polymerase speed, impacting gene expression. This finding reveals that transcription rate is encoded in the transcript and optimized by evolution, affecting organismal fitness.

Keywords:
RNA polymeraseTranscription elongationcodon-usage biastranscript evolution

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Gene expression involves transcription and translation.
  • Previous research focused on translation elongation, with limited studies on transcription elongation rates influenced by sequence features.

Purpose of the Study:

  • To investigate the effect of short transcript sub-sequences on RNA polymerase (RNAP) speed.
  • To explore the relationship between RNAP speed, mRNA levels, and gene expression.

Main Methods:

  • Analysis of nucleotide 5-mers to determine typical RNAP speeds.
  • Correlation analysis between relative RNAP speed and mRNA levels.
  • Comparison of estimated transcription and translation elongation rates.
  • Validation using high-resolution experimental measurements of RNAP densities.

Main Results:

  • Nucleotide 5-mers exhibit typical RNAP speeds, consistent across gene regions and gene groups.
  • Relative RNAP speed correlates with mRNA levels of endogenous and heterologous genes.
  • Estimated transcription and translation elongation rates show correlation in endogenous genes.
  • Results are consistent across different experimental measurements of RNAP densities.

Conclusions:

  • Transcription elongation rate is partly encoded within the transcript sequence.
  • Codon usage and evolutionary optimization significantly affect transcription elongation and gene expression.
  • These findings have implications for understanding gene expression regulation and organismal fitness.