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Related Concept Videos

RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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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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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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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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Related Experiment Video

Updated: Sep 20, 2025

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
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Quantifying Nascent Transcription in Early Embryogenesis.

Hui Chen1

  • 1Department of Biological Sciences, University of South Carolina, Columbia, SC, USA. huic@sc.edu.

Methods in Molecular Biology (Clifton, N.J.)
|May 26, 2025
PubMed
Summary
This summary is machine-generated.

Detecting early embryonic gene activation is challenging. A new method using 5-ethynyl uridine (5-EU) labeling and EU-RNA sequencing accurately measures zygotic transcription and its onset time in Xenopus embryos.

Keywords:
5-ethynyl uridine (5-EU)Early embryogenesisNascent transcriptionRNA sequencing (RNA-seq)TranscriptomeZygotic genome activation

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Area of Science:

  • Developmental Biology
  • Molecular Biology
  • Genomics

Background:

  • Early embryonic genomes are transcriptionally silent after fertilization.
  • Zygotic genome activation (ZGA) initiates gene expression crucial for development.
  • Distinguishing nascent zygotic transcripts from maternal RNA is a significant challenge.

Purpose of the Study:

  • To develop a sensitive method for measuring zygotic transcription during ZGA.
  • To determine the precise onset time of zygotic gene activation.
  • To overcome limitations of total RNA sequencing in detecting early transcripts.

Main Methods:

  • Metabolic labeling of nascent RNA with 5-ethynyl uridine (5-EU).
  • Purification and sequencing of 5-EU labeled RNAs (EU-RNA-seq).
  • Application to early Xenopus embryos to study ZGA.

Main Results:

  • EU-RNA-seq successfully detects early zygotic transcripts missed by total RNA-seq.
  • The method accurately determines the transcriptional activation onset time for zygotic genes.
  • Novel insights into early embryogenesis gene regulation were obtained.

Conclusions:

  • 5-EU labeling followed by EU-RNA-seq is a sensitive and accurate method for studying ZGA.
  • This technique is broadly applicable to various embryonic model systems.
  • The method advances our understanding of gene regulation during early development.