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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
The Eukaryotic Promoter Region02:40

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...
The Eukaryotic Promoter Region02:40

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...
Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a DNA...

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HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
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Published on: March 31, 2019

Identifying regulatory elements in eukaryotic genomes.

Leelavati Narlikar1, Ivan Ovcharenko

  • 1Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Briefings in Functional Genomics & Proteomics
|June 6, 2009
PubMed
Summary
This summary is machine-generated.

Identifying gene regulatory elements is crucial for understanding organism development. This review covers methods to find these elements and their role in human diseases.

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

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Last Updated: Jun 22, 2026

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
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Published on: March 31, 2019

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Gene expression must be precisely controlled in space and time for proper organism development.
  • Transcriptional regulation, mediated by transcription factors binding DNA, governs gene expression patterns.
  • Combinatorial binding of transcription factors creates regulatory codes that dictate gene expression.

Purpose of the Study:

  • To review experimental and computational methods for identifying gene regulatory elements in complex eukaryotes.
  • To highlight approaches that use diverse data (gene expression, chromatin structure, TF binding) to understand regulatory element function.
  • To discuss the implications of mutations in regulatory elements for human health and disease.

Main Methods:

  • Survey of experimental techniques for regulatory element identification.
  • Review of computational approaches leveraging genomic and epigenomic data.
  • Analysis of transcription factor binding specificities and cooperative interactions.

Main Results:

  • A comprehensive overview of current strategies for discovering proximal and distal gene regulatory elements.
  • Integration of multiple data types enhances the deciphering of regulatory element function.
  • Identification of key regulatory elements and their roles in gene misregulation.

Conclusions:

  • Accurate identification of gene regulatory elements is vital for understanding biological processes.
  • Dysregulation of these elements due to mutations is linked to various human disorders.
  • Further research into regulatory elements will advance diagnostics and therapeutics for genetic diseases.