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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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...

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Related Experiment Video

Updated: May 12, 2026

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Non-coding transcription at cis-regulatory elements: computational and experimental approaches.

Marta Simonatto1, Iros Barozzi, Gioacchino Natoli

  • 1Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy.

Methods (San Diego, Calif.)
|April 2, 2013
PubMed
Summary

Mammalian genomes produce many non-coding RNAs (ncRNAs) from regulatory DNA. This review explores identifying and functionally analyzing these ncRNAs to understand gene regulation.

Keywords:
ChromatinEnhancersGenomicsNon-coding RNAsTranscription

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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: May 12, 2026

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Published on: April 21, 2023

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
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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
  • Epigenetics

Background:

  • Mammalian genomes are pervasively transcribed, producing abundant non-coding RNAs (ncRNAs).
  • A significant portion of ncRNAs originate from cis-regulatory elements like promoters and enhancers.
  • The functional roles of these ncRNAs in gene regulation remain largely undetermined.

Purpose of the Study:

  • To review methods for identifying and characterizing ncRNAs transcribed from cis-regulatory elements.
  • To discuss experimental and computational strategies for dissecting the function of nc transcription.
  • To highlight the importance of understanding ncRNA roles in gene regulation.

Main Methods:

  • Identification and characterization of cis-regulatory elements and associated ncRNAs.
  • Analysis of chromatin signatures linked to specific ncRNA classes.
  • Review of experimental strategies for studying ncRNA function, considering low abundance and transcription vs. RNA roles.
  • Discussion of computational approaches for analyzing next-generation sequencing data of regulatory sequences.

Main Results:

  • Emerging classes of ncRNAs associated with specific chromatin signatures have been identified.
  • Challenges in studying enhancer-templated ncRNAs due to low abundance are highlighted.
  • The distinction between transcription per se and RNA products in regulatory functions is a key consideration.

Conclusions:

  • Further research is needed to elucidate the precise roles of ncRNAs from cis-regulatory elements in gene regulation.
  • Development of advanced experimental and computational tools is crucial for functional dissection.
  • Understanding these ncRNAs contributes to a comprehensive view of genome regulation.