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Related Concept Videos

Transcription Factors02:16

Transcription Factors

82.9K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Transcription Elongation Factors02:35

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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 Elongation Factors02:35

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Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
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Prokaryotic Transcriptional Activators and Repressors01:58

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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
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General Transcription Factors01:30

General Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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Enhancer RNA profiling predicts transcription factor activity.

Joseph G Azofeifa1,2, Mary A Allen2, Josephina R Hendrix1,3

  • 1Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA.

Genome Research
|February 17, 2018
PubMed
Summary
This summary is machine-generated.

Enhancer RNAs (eRNAs) originate from transcription factor (TF) binding sites, serving as a novel metric for TF activity. This research reveals new connections between stimuli and the TFs they regulate.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Genomics

Background:

  • Transcription factors (TFs) regulate gene expression by binding to enhancers.
  • Active enhancers are associated with enhancer RNAs (eRNAs), though their function is not fully understood.

Purpose of the Study:

  • To establish enhancer RNAs (eRNAs) as a reliable indicator of transcription factor (TF) activity.
  • To identify novel stimulus-TF relationships using eRNA data.

Main Methods:

  • Inferred eRNA origins from publicly available nascent transcription data.
  • Quantified the colocalization of TF binding motifs and eRNA initiation sites.
  • Developed a statistic to infer TF activity based on eRNA origins.

Main Results:

  • Demonstrated that eRNAs initiate from TF binding sites.
  • Showed eRNAs are a powerful readout of TF activity.
  • Uncovered numerous previously unknown links between stimuli and affected TFs.

Conclusions:

  • eRNA origination serves as a direct measure of TF binding and activity.
  • This approach provides a new tool for mapping regulatory networks and stimulus-response pathways.