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The Eukaryotic Promoter Region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

Transcription Initiation

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...

RNA Polymerase II Accessory Proteins

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...

Reporter Genes

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.

Transcription Factors

Transcription Factors

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...

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

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DeeProPre: A promoter predictor based on deep learning.

Zhi-Wen Ma¹, Jian-Ping Zhao¹, Jing Tian¹

¹College of Mathematics and System Sciences, Xinjiang University, Urumqi, China.

Computational Biology and Chemistry

|September 18, 2022

Summary

This study introduces DeeProPre, a deep learning model using BiLSTM and CNN for accurate eukaryotic promoter recognition. The model enhances understanding of gene transcription mechanisms and promoter functions.

Keywords:

Attention mechanism BiLSTM Bioinformatics Deep learning Eukaryotic promoter

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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Promoters are DNA sequences crucial for gene transcription initiation by RNA polymerase.
Promoter structure influences RNA polymerase binding affinity and gene expression levels.
Accurate identification of core promoters is vital for biomedical research, but current methods require improvement.

Purpose of the Study:

To develop a highly accurate deep learning model for eukaryotic promoter region identification.
To provide a tool for advancing the understanding of promoter functions and gene transcription.

Main Methods:

A deep learning model, DeeProPre, was developed using Bidirectional Long Short-Term Memory (BiLSTM) and Convolutional Neural Network (CNN).
The model employed a supervised embedding layer for sequence mapping, followed by 1D convolutional layers, BiLSTM, and an attention mechanism for feature extraction.
A Sigmoid-activated fully connected layer was used for classification.

Main Results:

The DeeProPre model demonstrated high accuracy in identifying eukaryotic promoter regions.
The model's architecture effectively extracts relevant sequence features for promoter recognition.

Conclusions:

DeeProPre offers a significant advancement in promoter recognition accuracy.
This tool can aid further research into promoter physiological functions and gene transcription mechanisms.