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Related Concept Videos

RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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...
Transcription01:17

Transcription

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.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
Transcription01:10

Transcription

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.
Transcription Can Produce Different Kinds...
Transcription Initiation01:47

Transcription Initiation

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.
The promoters and enhancers and their accessory proteins allow tight regulation of...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...

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Updated: Jul 3, 2026

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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An Explainable Deep Learning Framework Integrating DNA Sequence and Transcription Initiation Signals for Gene

Jianbo Qiao1, Wenjia Gao1, Ding Wang2,3

  • 1The School of Software, Shandong University, Jinan 250101, China.

ACS Synthetic Biology
|July 1, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces an interpretable deep learning model to predict gene expression levels by integrating DNA sequence, mRNA half-life, and transcription initiation signals. The framework offers insights into gene regulation mechanisms across various human cell lines.

Keywords:
DNA sequence analysisbioinformaticsdeep learningexplainabilitygene expression predictiongenome

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Published on: September 25, 2021

Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Gene expression regulation is crucial for cellular function and phenotype.
  • Predicting gene expression accurately is a challenge in human genetics.
  • Existing deep learning models often neglect transcription initiation signals and lack interpretability.

Purpose of the Study:

  • To develop an interpretable deep learning framework for predicting gene expression levels.
  • To integrate DNA sequence, mRNA half-life, and transcription initiation signals.
  • To enhance understanding of gene regulatory mechanisms.

Main Methods:

  • Developed an interpretable deep learning framework using convolutional neural networks and Gated Recurrent Units.
  • Integrated DNA sequence, mRNA half-life, and transcription initiation signals as input features.
  • Validated the model on GM12878, HepG2, and K562 human cell line datasets.

Main Results:

  • The framework efficiently predicts gene expression levels.
  • The model demonstrates robustness across different human cell lines.
  • Interpretability analysis provides valuable insights into gene expression mechanisms.

Conclusions:

  • The developed deep learning framework is a robust tool for predicting gene expression.
  • The model enhances the understanding of gene regulatory mechanisms.
  • This approach offers practical utility for gene expression studies.