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Related Concept Videos

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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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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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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Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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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.
The chromatin structure, especially...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Regulation of Expression Occurs at Multiple Steps02:24

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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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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing 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 the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
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Related Experiment Video

Updated: Oct 11, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability

Yu-Jian Kang1, Jing-Yi Li1, Lan Ke1

  • 1Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China.

Briefings in Bioinformatics
|December 1, 2021
PubMed
Summary

We developed Ribosome Calculator (RiboCalc) to model RNA coding ability in humans. This tool accurately predicts coding abundance and reveals context-dependent coding transcripts, challenging traditional views.

Keywords:
Expression RegulationLong noncoding RNAsNoncoding RNAs

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Gene transcription and protein translation are fundamental processes in the central dogma.
  • Quantitatively assessing factors influencing transcript coding ability in mammals remains challenging.

Purpose of the Study:

  • To develop a quantitative model, Ribosome Calculator (RiboCalc), for assessing RNA coding potential in the human genome.
  • To identify sequence and transcriptional features that determine coding abundance.

Main Methods:

  • Development of the RiboCalc model using sequence and transcription features.
  • High-throughput prediction of experimentally confirmed coding abundance.
  • Large-scale analysis of transcript coding ability across different cell types.

Main Results:

  • RiboCalc accurately predicts coding abundance using sequence and transcription features.
  • The model provides interpretable parameters with biological insights.
  • Identified numerous transcripts with cell-specific coding abilities (context-dependent coding transcripts).

Conclusions:

  • RNA coding ability is not binary but exists on a continuous spectrum.
  • Coding ability is context-dependent, varying across different cell types.
  • RiboCalc offers a novel approach to modeling and understanding RNA coding potential.