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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.
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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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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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ARTDeco: automatic readthrough transcription detection.

Samuel J Roth1, Sven Heinz2, Christopher Benner3

  • 1Bioinformatics and Systems Biology Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA.

BMC Bioinformatics
|May 28, 2020
PubMed
Summary
This summary is machine-generated.

A new tool, ARTDeco, detects readthrough transcription and its consequences, improving gene expression analysis. This method is crucial for understanding diseases involving transcription termination defects and interpreting gene regulation accurately.

Keywords:
Gene expressionNext-generation sequencing analysisReadthrough transcriptionTranscription terminationTranscriptomics

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcription termination is crucial for regulating gene expression.
  • Disruptions in transcription termination can lead to aberrant gene expression, novel transcripts, and altered genome structure.
  • Understanding these disruptions is vital for studying various diseases.

Purpose of the Study:

  • To develop a computational tool for detecting and analyzing readthrough transcription.
  • To characterize readthrough transcription phenotypes in different biological contexts, including viral infections.
  • To assess the impact of readthrough transcription on gene expression and downstream analyses like eQTL interpretation.

Main Methods:

  • Development of Automatic Readthrough Transcription Detection (ARTDeco), a novel bioinformatics tool.
  • Utilizing RNA-seq and other next-generation sequencing data.
  • Validation of ARTDeco using influenza A virus (IAV) infection models and systems with known transcription termination defects.

Main Results:

  • ARTDeco robustly quantifies readthrough transcription severity and identifies readthrough, read-in, and downstream of gene (DoG) transcripts.
  • The tool demonstrated high specificity and sensitivity in detecting readthrough transcription.
  • Analysis of IAV-infected monocytes revealed that read-in gene-associated eQTLs likely regulate upstream genes, highlighting the importance of considering readthrough transcription for eQTL interpretation.

Conclusions:

  • ARTDeco is an effective tool for researchers studying readthrough transcription.
  • The tool aids in the analysis of gene expression and downstream interpretation in systems with transcription termination defects.
  • Incorporating readthrough transcription analysis enhances the understanding of gene regulation and disease mechanisms.